@article{noauthor_notitle_nodate, } @article{mostafiz_efficient_2018, title = {Efficient {Callus} {Induction} and {Regeneration} in {Selected} {Indica} {Rice}}, volume = {8}, issn = {2073-4395}, url = {http://www.mdpi.com/2073-4395/8/5/77}, doi = {10.3390/agronomy8050077}, abstract = {An efficient callus induction and in vitro regeneration were developed using plant growth regulators, carbon sources, and basal media for three selected Malaysian wetland rice varieties (MR220, MR220-CL2, and MR232) and one upland variety (Bario). Effect of plant growth regulator (PGR) was carried out using four different concentrations (1–4 mg/L) of 2,4-D (2, 4-dichlorophenoxyacetic acid), and NAA (1-naphthalene acetic acid) (2.5, 5.0, 7.5, and 10 mg/L) with optimized 2,4-D. Effects of carbon sources (maltose and sorbitol), and basal media (MS, N6, and LS) were also studied with optimized PGR to maximize the induction of regenerable calli. This study found that all four varieties exhibited high frequency of callus induction on MS (Murashige and Skoog) medium that was supplemented with 3 mg/L 2,4-D and 30 g/L maltose. Callus induction frequencies in the cases of MR220, MR220-CL2, MR232, and Bario were found to be 76\%, 94\%, 85\%, and 42\% respectively. Morphological analysis through scanning electron microscopy (SEM) and histological analysis revealed the embryogenicity of the induced callus. In the regeneration study, it was observed that combination of 2 mg/L BAP (6-benzylaminopurine), 2 mg/L Kin (Kinetin) and 0.5 mg/L NAA supplemented MS medium has the potential to promote regeneration of selected indica rice varieties with higher regeneration percentage, i.e., 82\% (MR220-CL2), 68\% (both in MR220 and MR232), and 40\% (Bario). The optimized conditions for callus formation and regeneration can be useful for biotechnological practices for the genetic improvement of Malaysian indica rice.}, language = {en}, number = {5}, urldate = {2021-04-22}, journal = {Agronomy}, author = {Mostafiz, Suraiya Binte and Wagiran, Alina}, month = may, year = {2018}, pages = {77}, file = {agronomy-08-00077 (1).pdf:C\:\\Users\\Syafira\\Zotero\\storage\\SDRV6YH6\\agronomy-08-00077 (1).pdf:application/pdf}, } @article{zhang_common_2020, title = {A common wild rice-derived {BOC1} allele reduces callus browning in indica rice transformation}, volume = {11}, issn = {2041-1723}, url = {http://www.nature.com/articles/s41467-019-14265-0}, doi = {10.1038/s41467-019-14265-0}, abstract = {Abstract Callus browning, a common trait derived from the indica rice cultivar ( Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 ( BOC1 ) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession ( Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1 , which consequently improves the genetic transformation efficiency. The presence of a Tourist -like miniature inverted-repeat transposable element ( Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation.}, language = {en}, number = {1}, urldate = {2021-04-22}, journal = {Nat Commun}, author = {Zhang, Kun and Su, Jingjing and Xu, Min and Zhou, Zhihui and Zhu, Xiaoyang and Ma, Xin and Hou, Jingjing and Tan, Lubin and Zhu, Zuofeng and Cai, Hongwei and Liu, Fengxia and Sun, Hongying and Gu, Ping and Li, Chen and Liang, Yuntao and Zhao, Wensheng and Sun, Chuanqing and Fu, Yongcai}, month = dec, year = {2020}, pages = {443}, file = {boc browning of callus.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\XEXBTEXK\\boc browning of callus.pdf:application/pdf}, } @article{cai_synergistic_2020, title = {Synergistic {Effect} of {NaCl} {Pretreatment} and {PVP} on {Browning} {Suppression} and {Callus} {Induction} from {Petal} {Explants} of {Paeonia} {Lactiflora} {Pall}. ‘{Festival} {Maxima}’}, volume = {9}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/9/3/346}, doi = {10.3390/plants9030346}, abstract = {Browning is prevalent in tissue cultures of Paeonia lactiflora Pall. (herbaceous peony), and severely affects and restricts the growth and differentiation of the explants. In this study, dipping excised explants in a sodium chloride (NaCl) solution as a pretreatment, adding polyvinyl pyrrolidone (PVP) to the culture medium, storing planted explants at 4 ◦C for 24 h, and transferring planted explants to a new medium after 24 h were considered as browning-suppression methods in tissue cultures of herbaceous peony ‘Festival Maxima’. The treated petal explants were cultured in a culture room with a 16-hour photoperiod, 25 ◦C temperature, and 80\% relative humidity in darkness for 4 to 8 weeks. The results demonstrated that dipping excised explants in a 0.5 g·L−1 NaCl solution, adding 0.5 g·L−1 PVP to the medium, storing planted explants at 4 ◦C for 24 h, and transferring planted explants to the same fresh medium after 24 h could effectively inhibit browning. Adding PVP to the medium led to the greatest browning suppression percentage of 95\%. Storing planted explants at 4 ◦C for 24 h reduced the effectiveness of other treatments in suppressing browning. After 8 weeks, dipping excised explants in a NaCl solution resulted in the highest callus induction percentage of 75\%, while storing explants at 4 ◦C for 24 h suppressed callus formation. It was observed in all treatments that decreases in browning was accompanied with higher levels of phenols and lower activities of phenylalanine ammonia-lyase (PAL) and polyphenoloxidase (PPO). Overall, the results suggest that dipping in a NaCl solution was effective in alleviating the browning issues of herbaceous peony tissue cultures, and had positive synergistic effects with PVP on browning suppression and callus induction.}, language = {en}, number = {3}, urldate = {2021-04-23}, journal = {Plants}, author = {Cai, Xuan and Wei, Hao and Liu, Chen and Ren, Xiuxia and Thi, Luc The and Jeong, Byoung Ryong}, month = mar, year = {2020}, pages = {346}, file = {Cai et al. - 2020 - Synergistic Effect of NaCl Pretreatment and PVP on.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\MCM9TZ8Q\\Cai et al. - 2020 - Synergistic Effect of NaCl Pretreatment and PVP on.pdf:application/pdf;ethylene and interaction with other.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\BUPIQZE2\\ethylene and interaction with other.pdf:application/pdf}, } @article{liang_effects_2019, title = {Effects of {Sucrose} and {Browning} {Inhibitors} on {Callus} {Proliferation} and {Anti}-{Browning} of {Chinese} {Kale}}, volume = {252}, issn = {1755-1315}, url = {https://iopscience.iop.org/article/10.1088/1755-1315/252/2/022018}, doi = {10.1088/1755-1315/252/2/022018}, abstract = {The hypocotyl of Chinese kale ‘Cutiaoyusun’ was used as explants, the effects of the different concentrations of sucrose and different browning inhibitors (activated carbon, polyvinylpyrrolidone, and ascorbic acid) on the callus proliferation and anti-browning of Chinese kale were studied in this study. The results showed that the proliferation medium with 20 gꞏL-1 sucrose had the best effects on the proliferation and anti-browning of Chinese kale callus, and its proliferation rate was the highest, reaching 213.5\%, and the browning rate was as low as 27.77\%. In addition, adding 0.2 gꞏL-1 ascorbic acid to the culture medium can significantly promote callus proliferation and reduce browning rate. In this treatment, the callus had the lowest browning rate of 19.45\% and the highest proliferation rate of 266.98\%, and the morphology of the callus was friable. This study lays a foundation for future research in molecular biology and genetic improvement in Chinese kale.}, language = {en}, urldate = {2021-04-23}, journal = {IOP Conf. Ser.: Earth Environ. Sci.}, author = {Liang, Sha and He, Ying and Zheng, Hao and Yuan, Qiao and Zhang, Fen and Sun, Bo}, month = jul, year = {2019}, pages = {022018}, file = {Liang et al. - 2019 - Effects of Sucrose and Browning Inhibitors on Call.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\FJNZJI4T\\Liang et al. - 2019 - Effects of Sucrose and Browning Inhibitors on Call.pdf:application/pdf}, } @article{centre_national_de_recherche_agronomique_cnra_laboratoire_central_de_biotechnologies__lcb_km_17_adiopodoume_01_bp_1740_abidjan_01_cote_divoire_effect_2017, title = {Effect of antioxidants on the callus induction and the development of somatic embryogenesis of cocoa [{Theobroma} cacao ({L}.)]}, volume = {11}, issn = {18352693, 18352707}, url = {http://www.cropj.com/kouassi_11_1_2017_25_31.pdf}, doi = {10.21475/ajcs.2017.11.01.pne174}, abstract = {The browning of plant tissue and organs is a major constraint in tissue culture of cocoa (Theobroma cacao L.). This study aims to evaluate callogenic and embryogenic potentialities of three genotypes cocoa on culture media supplemented with different types and concentrations of antioxidants. Polyvinylpyrrolidone (PVP), ascorbic acid, silver nitrate and cysteine were used as antioxidant agents. The explants staminode and petal were excised from immature buds of the flowers of genotypes cocoa C1, C8 and C14. The results showed that the induction rate of callus derived from the petal and the staminode varied with the genotypes tested. Except 21 mg/l of silver nitrate, the others antioxidants used namely ascorbic acid, PVP and cysteine have enhanced the callus induction of the genotype C8. In comparison with the control, the callus browning of the three genotypes was reduced two to three times when the culture media were supplemented with various concentrations of the silver nitrate. After 72 days of culture, somatic embryos were induced on callus derived from the petal explants with all the studied genotypes. Addition of PVP (300 mg/l) in the induction medium improved the rate of somatic embryos of the genotypes C1 and C14. The improvement of responses to somatic embryogenesis in reducing the rate of browning of cultures will allow a mass production of the high-yield cocoa genotypes.}, language = {en}, number = {1}, urldate = {2021-04-23}, journal = {Aust J Crop Sci}, author = {{Centre National de Recherche Agronomique (CNRA), Laboratoire Central de Biotechnologies (LCB), KM 17 Adiopodoumé, 01 BP 1740 Abidjan 01, Côte d’Ivoire} and Modeste, Kouassi Kan and Eliane, Manlé Tokpapon and {Centre National de Recherche Agronomique (CNRA), Laboratoire Central de Biotechnologies (LCB), KM 17 Adiopodoumé, 01 BP 1740 Abidjan 01, Côte d’Ivoire} and {Université Nangui Abrogoua, UFR Sciences de la Nature, Laboratoire de Biologie et Amélioration des Productions Végétales, 02 BP 801 Abidjan 02, Côte d’Ivoire} and Daouda, Koné and {Université Félix Houphouët-Boigny, UFR Biosciences, Laboratoire de Génétique, 22 BP 582 Abidjan 22, Côte d’Ivoire} and Brahima, Soumahoro André and {Université Nangui Abrogoua, UFR Sciences de la Nature, Laboratoire de Biologie et Amélioration des Productions Végétales, 02 BP 801 Abidjan 02, Côte d’Ivoire} and Tchoa, Koné and {Université Nangui Abrogoua, UFR Sciences de la Nature, Laboratoire de Biologie et Amélioration des Productions Végétales, 02 BP 801 Abidjan 02, Côte d’Ivoire} and Kouablan, Koffi Edmond and {Centre National de Recherche Agronomique (CNRA), Laboratoire Central de Biotechnologies (LCB), KM 17 Adiopodoumé, 01 BP 1740 Abidjan 01, Côte d’Ivoire} and Mongomaké, Koné and {Université Nangui Abrogoua, UFR Sciences de la Nature, Laboratoire de Biologie et Amélioration des Productions Végétales, 02 BP 801 Abidjan 02, Côte d’Ivoire}}, month = jan, year = {2017}, pages = {25--31}, file = {antioksidan rendah pada browning callus.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\ZMATPD6E\\antioksidan rendah pada browning callus.pdf:application/pdf}, } @article{modeste_effect_2017, title = {Effect of antioxidants on the callus induction and the development of somatic embryogenesis of cocoa [{Theobroma} cacao ({L}.)]}, volume = {11}, issn = {18352693, 18352707}, url = {http://www.cropj.com/kouassi_11_1_2017_25_31.pdf}, doi = {10.21475/ajcs.2017.11.01.pne174}, abstract = {The browning of plant tissue and organs is a major constraint in tissue culture of cocoa (Theobroma cacao L.). This study aims to evaluate callogenic and embryogenic potentialities of three genotypes cocoa on culture media supplemented with different types and concentrations of antioxidants. Polyvinylpyrrolidone (PVP), ascorbic acid, silver nitrate and cysteine were used as antioxidant agents. The explants staminode and petal were excised from immature buds of the flowers of genotypes cocoa C1, C8 and C14. The results showed that the induction rate of callus derived from the petal and the staminode varied with the genotypes tested. Except 21 mg/l of silver nitrate, the others antioxidants used namely ascorbic acid, PVP and cysteine have enhanced the callus induction of the genotype C8. In comparison with the control, the callus browning of the three genotypes was reduced two to three times when the culture media were supplemented with various concentrations of the silver nitrate. After 72 days of culture, somatic embryos were induced on callus derived from the petal explants with all the studied genotypes. Addition of PVP (300 mg/l) in the induction medium improved the rate of somatic embryos of the genotypes C1 and C14. The improvement of responses to somatic embryogenesis in reducing the rate of browning of cultures will allow a mass production of the high-yield cocoa genotypes.}, language = {en}, number = {1}, urldate = {2021-04-23}, journal = {Aust J Crop Sci}, author = {Modeste, Kouassi Kan and Eliane, Manlé Tokpapon and Daouda, Kone and Brahima, Soumahoro André and Tchoa, Kone and Kouablan, Koffi Edmond and Mongomake, Koné}, month = jan, year = {2017}, pages = {25--31}, file = {antioksidan rendah pada browning callus.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\8JQKCK59\\antioksidan rendah pada browning callus.pdf:application/pdf}, } @article{kuklin_ethylene_2014, title = {Ethylene {Impact} on {Somatic} {Embryogenesis}: {Biotechnological} {Considerations}}, volume = {9}, issn = {1310-2818, 1314-3530}, shorttitle = {Ethylene {Impact} on {Somatic} {Embryogenesis}}, url = {http://www.tandfonline.com/doi/abs/10.1080/13102818.1995.10818856}, doi = {10.1080/13102818.1995.10818856}, abstract = {The gaseous plant hormone ethylene affects somatic emb1yogenesis in various ways depending on the species or explants used. Inclusion of ethylene action inhibitors, name{\textasciitilde}v silver ions in culture media increased somatic embryogenesis in some species. Large scale (bioreactor) yields of somatic emb1yos were less than these ji·01n flask cultures. Ethylene depletion from the bioreactors due to aeration is considered as a possible reason for the decrease in somatic emb1yogenesis. Ethylene is discussed as a physiological marker related to emb1yogenic potential. {\textasciitilde}Vound ethylene evolved after transformation experiments might have some inhibit01:v role on transformation but results are contradictory. Ethylene plays different roles in long term storage (low and ambient temperatures) of emb1yogenic cultures. Use of transgenic technology in ethylene biosynthesis reduction is discussed as a way to understanding ethylene role in somatic emb(vogenesis.}, language = {en}, number = {4}, urldate = {2021-04-23}, journal = {Biotechnology \& Biotechnological Equipment}, author = {Kuklin, A.}, month = apr, year = {2014}, pages = {12--19}, file = {Kuklin - 1995 - Ethylene Impact on Somatic Embryogenesis Biotechn.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\I6JLHGMX\\Kuklin - 1995 - Ethylene Impact on Somatic Embryogenesis Biotechn.pdf:application/pdf;ethylen.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\DRUGNW4Y\\ethylen.pdf:application/pdf}, } @article{illyas_ahmad_effect_2013, title = {Effect of 2,4-{D} on {Embryogenic} {Callus} {Induction} of {Malaysian} indica {Rice} ({Oryza} sativa {L}.) {Cultivars} {MR123} and {MR127}}, volume = {64}, issn = {2180-3722, 0127-9696}, url = {https://journals.utm.my/index.php/jurnalteknologi/article/view/2048}, doi = {10.11113/jt.v64.2048}, abstract = {The aim of this study is to study the effect of various concentrations of 2,4-D on embryogenic callus induction of indica rice MR123 cultivar and MR127 cultivar using mature seeds. Optimal media for induction of callus of both cultivars was MS basal media supplemented with 30g/L sucrose, 500mg/L glutamine and 500mg/L proline supplemented with 2.5 mg/L 2,4-D. The highest percentage of callus induction was 70\% and 76\% for MR123 and MR127 respectively. Both cultivars produced an embryogenic callus from scutellum after a week in culture with white-yellowish in color. The viability tested using Evans blue show callus obtained was embryogenic. This simple protocol using staining method could be used for screening embryogenic callus before further experiments can be conducted.}, language = {en}, number = {2}, urldate = {2021-04-23}, journal = {Jurnal Teknologi}, author = {Illyas Ahmad, Fauziah and Johan, Nur Shafiqoh and Wagiran, Alina}, month = aug, year = {2013}, file = {Illyas Ahmad et al. - 2013 - Effect of 2,4-D on Embryogenic Callus Induction of.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\LR2FTQMA\\Illyas Ahmad et al. - 2013 - Effect of 2,4-D on Embryogenic Callus Induction of.pdf:application/pdf}, } @article{ikeuchi_plant_2013, title = {Plant {Callus}: {Mechanisms} of {Induction} and {Repression}}, volume = {25}, issn = {1040-4651, 1532-298X}, shorttitle = {Plant {Callus}}, url = {https://academic.oup.com/plcell/article/25/9/3159-3173/6097899}, doi = {10.1105/tpc.113.116053}, language = {en}, number = {9}, urldate = {2021-04-23}, journal = {Plant Cell}, author = {Ikeuchi, Momoko and Sugimoto, Keiko and Iwase, Akira}, month = sep, year = {2013}, pages = {3159--3173}, file = {Ikeuchi et al. - 2013 - Plant Callus Mechanisms of Induction and Repressi.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\53QZD3VJ\\Ikeuchi et al. - 2013 - Plant Callus Mechanisms of Induction and Repressi.pdf:application/pdf;zhang2020 indica japonica hybrid.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\YM9LM8TY\\zhang2020 indica japonica hybrid.pdf:application/pdf}, } @article{a_libin_callus_2012, title = {Callus induction and plant regeneration of {Sarawak} rice ({Oryza} sativa {L}.) variety {Biris}}, volume = {7}, issn = {1991637X}, url = {http://www.academicjournals.org/ajar/abstracts/abstracts/Abstracts%202012/7Aug/Libin%20et%20al.htm}, doi = {10.5897/AJAR12.587}, abstract = {Sarawak Biris rice is a strong aromatic rice variety which can thrive well in rice fields prone to flood, drought and other soil constraints. Tissue culture of Biris rice is important in producing planting materials and conducting genetic improvement work. The present study was conducted to induce callus from Biris rice seed and assess its regeneration ability. Dehusked mature seeds were used as starting materials for callus induction. Sterilized seeds were cultured onto Murashige and Skoog medium containing various concentrations of 2, 4-dichlorophenoxyacetic acid (2, 4-D). The optimum 2, 4-D concentration for callus induction was 2.0 mg/L with a frequency as high as 97\%. The calli produced were of desired features (creamy in colour, globular) and relatively bigger in size as compared to other treatments. The calli produced were further tested with plant growth regulator, naphthaleneacetic acid (NAA) in combination with kinetin (Kn) for plant regeneration ability. All uncontaminated calli were found to regenerate. Up to nine shoots were induced by a callus treated with 0.5 mg/L NAA in combination with 1.0 mg/L Kn. The present study should be noted as the first attempt to induce callus and regenerate plants from seeds of Biris rice.}, language = {en}, number = {30}, urldate = {2021-04-23}, journal = {Afr. J. Agric. Res.}, author = {{A. Libin,}}, month = aug, year = {2012}, file = {A. Libin, - 2012 - Callus induction and plant regeneration of Sarawak.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\P92RGH67\\A. Libin, - 2012 - Callus induction and plant regeneration of Sarawak.pdf:application/pdf}, } @article{mostafiz_efficient_2018-1, title = {Efficient {Callus} {Induction} and {Regeneration} in {Selected} {Indica} {Rice}}, volume = {8}, issn = {2073-4395}, url = {http://www.mdpi.com/2073-4395/8/5/77}, doi = {10.3390/agronomy8050077}, abstract = {An efficient callus induction and in vitro regeneration were developed using plant growth regulators, carbon sources, and basal media for three selected Malaysian wetland rice varieties (MR220, MR220-CL2, and MR232) and one upland variety (Bario). Effect of plant growth regulator (PGR) was carried out using four different concentrations (1–4 mg/L) of 2,4-D (2, 4-dichlorophenoxyacetic acid), and NAA (1-naphthalene acetic acid) (2.5, 5.0, 7.5, and 10 mg/L) with optimized 2,4-D. Effects of carbon sources (maltose and sorbitol), and basal media (MS, N6, and LS) were also studied with optimized PGR to maximize the induction of regenerable calli. This study found that all four varieties exhibited high frequency of callus induction on MS (Murashige and Skoog) medium that was supplemented with 3 mg/L 2,4-D and 30 g/L maltose. Callus induction frequencies in the cases of MR220, MR220-CL2, MR232, and Bario were found to be 76\%, 94\%, 85\%, and 42\% respectively. Morphological analysis through scanning electron microscopy (SEM) and histological analysis revealed the embryogenicity of the induced callus. In the regeneration study, it was observed that combination of 2 mg/L BAP (6-benzylaminopurine), 2 mg/L Kin (Kinetin) and 0.5 mg/L NAA supplemented MS medium has the potential to promote regeneration of selected indica rice varieties with higher regeneration percentage, i.e., 82\% (MR220-CL2), 68\% (both in MR220 and MR232), and 40\% (Bario). The optimized conditions for callus formation and regeneration can be useful for biotechnological practices for the genetic improvement of Malaysian indica rice.}, language = {en}, number = {5}, urldate = {2021-04-23}, journal = {Agronomy}, author = {Mostafiz, Suraiya Binte and Wagiran, Alina}, month = may, year = {2018}, pages = {77}, file = {Binte Mostafiz and Wagiran - 2018 - Efficient Callus Induction and Regeneration in Sel.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\E4Z4R3JF\\Binte Mostafiz and Wagiran - 2018 - Efficient Callus Induction and Regeneration in Sel.pdf:application/pdf;ETILEN LEE 2018.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\BUAK9IP4\\ETILEN LEE 2018.pdf:application/pdf}, } @article{bevitori_morpho-anatomical_2013, title = {Morpho-anatomical characterization of mature embryo-derived callus of rice ({Oryza} sativa {L}.) suitable for transformation}, issn = {0033-183X, 1615-6102}, url = {http://link.springer.com/10.1007/s00709-013-0553-4}, doi = {10.1007/s00709-013-0553-4}, language = {en}, urldate = {2021-04-23}, journal = {Protoplasma}, author = {Bevitori, R. and Popielarska-Konieczna, M. and dos Santos, E. M. and Grossi-de-Sá, M. F. and Petrofeza, S.}, month = oct, year = {2013}, file = {Bevitori et al. - 2013 - Morpho-anatomical characterization of mature embry.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\J7T8X952\\Bevitori et al. - 2013 - Morpho-anatomical characterization of mature embry.pdf:application/pdf}, } @article{wang_genotype-by-environment_2019, title = {Genotype-by-environment interactions inferred from genetic effects on phenotypic variability in the {UK} {Biobank}}, language = {en}, journal = {SCIENCE ADVANCES}, author = {Wang, Huanwei and Zhang, Futao and Zeng, Jian and Wu, Yang and Kemper, Kathryn E and Xue, Angli and Zhang, Min and Powell, Joseph E and Goddard, Michael E and Wray, Naomi R and Visscher, Peter M and McRae, Allan F and Yang, Jian}, year = {2019}, pages = {13}, file = {Wang et al. - 2019 - Genotype-by-environment interactions inferred from.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\CJFSJAJ7\\Wang et al. - 2019 - Genotype-by-environment interactions inferred from.pdf:application/pdf}, } @article{umar_effect_2017, title = {Effect of {Medium} {Compositions} on {The} {Growth} of {Rice} ({Oryza} sativa {L}. cv. {Ciherang}) {Callus}}, abstract = {The efficiency of in-vitro regeneration of rice is spesific, which means a suitable medium for the regeneration of one variety may not be similar to other varieties. In this study, eksplan was derived from sterile radical of Ciherang var. This experiment consist two steps. First, induction of callus, and the second step was callus regeneration. The formulation for calli induction consists of three levels, such as i1 (2.4 D 2 ppm), i2 (2.4 D 3 ppm + BAP 0.25 ppm + Casein Hydrolisate 300 ppm + Proline 600 ppm) and i3 (2.4 D 2 ppm + Kinetin 0.5 ppm + Casein Hydrolisate 500 ppm + Proline 500 ppm) with N6 as a basic medium. Callus generated from those media then used in the next experiments for shoot regeneration which consists of two factors, the first factor was concentration of hormones BAP (r) (1 ppm, 2 ppm) and the second factor was concentration of the hormone Kinetin (k) (1 ppm, 2 ppm) with MS as a basic medium. The results showed that the highest embryogenic callus was obtained from i3 treatment by 62,96\%. The fastest rate of greeny callus and the emergence of shoots were found in i2r2k2 and i2r2k1 treatments. The results indicated that the media supplemented with high concentration of Kinetin (2 ppm) was more effective to induce the greeny of callus, and slightly lower concentration (1 ppm) leads to the formation of shoots.}, language = {en}, journal = {2017}, author = {Umar, Ruliana and Wibisono, Yossi and Ermawati, Netty}, year = {2017}, pages = {4}, file = {Umar et al. - Effect of Medium Compositions on The Growth of Ric.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\WYG7WUWY\\Umar et al. - Effect of Medium Compositions on The Growth of Ric.pdf:application/pdf}, } @article{fanata_daya_2020, title = {{DAYA} {REGENERASI} {KALUS} {DAN} {TUNAS} {IN} {VITRO} {PADI} {VARIETAS} {TARABAS} {PADA} {BERBAGAI} {KONSENTRASI} 2,4-{D}}, volume = {7}, issn = {2548-611X, 2442-2606}, url = {http://ejurnal.bppt.go.id/index.php/JBBI/article/view/4404}, doi = {10.29122/jbbi.v7i2.4404}, abstract = {The Agricultural Research and Development Agency and the West Java Provincial Government are developing new superior varieties with Japonica rice standards, namely the Tarabas variety. However, the equivalence of somatic embryogenesis ability of Tarabas rice with original Japonica variety has not been reported. In this study, the frequency of callus regeneration of Tarabas vs Hwayoung rice varieties was compared. Induction of callus from mature embryos with several concentrations of 2,4-D showed the same extent of callus formation in both rice varieties. Callus induced by 1 ppm of 2,4-D showed the higher rate of shoot formation. On the other hand, percentage of callus formation of Tarabas rice was not affected by the increase of 2,4-D concentrations and was able to show 100\% regeneration rate at the fourth week in the regeneration medium, although the shoot growth was not as fast as those from medium with 1 ppm 2,4-D. Therefore, these results suggest that Tarabas variety has a somatic embryogenesis capacity equivalent to that of japonica rice and has the potential as research objects in the field of biotechnology.}, language = {id}, number = {2}, urldate = {2021-04-24}, journal = {J Bioteknol Biosains Indones}, author = {Fanata, Wahyu Indra Duwi and Qudsiyah, Dalliyah Hadrotul}, month = dec, year = {2020}, pages = {250--258}, file = {Fanata and Qudsiyah - 2020 - DAYA REGENERASI KALUS DAN TUNAS IN VITRO PADI VARI.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\B8XP7BRS\\Fanata and Qudsiyah - 2020 - DAYA REGENERASI KALUS DAN TUNAS IN VITRO PADI VARI.pdf:application/pdf}, } @article{ming_combination_2019, title = {Combination of {Plant} {Growth} {Regulators}, {Maltose}, and {Partial} {Desiccation} {Treatment} {Enhance} {Somatic} {Embryogenesis} in {Selected} {Malaysian} {Rice} {Cultivar}}, volume = {8}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/8/6/144}, doi = {10.3390/plants8060144}, abstract = {The development of efficient tissue culture protocol for somatic embryo would facilitate the genetic modification breeding program. The callus induction and regeneration were studied by using different parameters i.e., auxins, cytokinins, and desiccation treatment. Scanning electron microscopy and histological analysis were performed to identify the embryogenic callus for regeneration. The callus percentage results showed that MS (Murashige and Skoog) basal medium supplemented with 3 mg/L 2, 4-D and 30g/L maltose were the optimal callus induction medium for MR220 (80\%) and MR220-CL2 (95\%). The morphology of the embryogenic callus was confirmed by the SEM (Scanning Electron Microscopy) (presence of extracellular matrix surface network) and later by histological analysis. Finally, MS media supplemented with 0.5 mg/L NAA (Naphthalene Acetic Acid), 2 mg/L kin, and 1 mg/L BAP were selected as the optimum regeneration media treatment while callus desiccated for 48 h was proved to produce more plantlets in MR220 (60\%) and MR220-CL2 (73.33\%) compared to control treatment (without desiccation). The protocol presented here showed the necessity for the inclusion of partial desiccation as an important step in the tissue culture protocol of Malaysian indica rice genotypes in order to enhance their regeneration potential.}, language = {en}, number = {6}, urldate = {2021-04-24}, journal = {Plants}, author = {Ming, NG Ja and Binte Mostafiz, Suraiya and Johon, Nur Syafiqoh and Abdullah Zulkifli, Nur Saliha and Wagiran, Alina}, month = may, year = {2019}, pages = {144}, file = {Ming et al. - 2019 - Combination of Plant Growth Regulators, Maltose, a.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\3W7WLZWG\\Ming et al. - 2019 - Combination of Plant Growth Regulators, Maltose, a.pdf:application/pdf}, } @article{iqbal_ethylene_2017, title = {Ethylene {Role} in {Plant} {Growth}, {Development} and {Senescence}: {Interaction} with {Other} {Phytohormones}}, volume = {08}, issn = {1664-462X}, shorttitle = {Ethylene {Role} in {Plant} {Growth}, {Development} and {Senescence}}, url = {http://journal.frontiersin.org/article/10.3389/fpls.2017.00475/full}, doi = {10.3389/fpls.2017.00475}, abstract = {The complex juvenile/maturity transition during a plant’s life cycle includes growth, reproduction, and senescence of its fundamental organs: leaves, flowers, and fruits. Growth and senescence of leaves, flowers, and fruits involve several genetic networks where the phytohormone ethylene plays a key role, together with other hormones, integrating different signals and allowing the onset of conditions favorable for stage progression, reproductive success and organ longevity. Changes in ethylene level, its perception, and the hormonal crosstalk directly or indirectly regulate the lifespan of plants. The present review focused on ethylene’s role in the development and senescence processes in leaves, flowers and fruits, paying special attention to the complex networks of ethylene crosstalk with other hormones. Moreover, aspects with limited information have been highlighted for future research, extending our understanding on the importance of ethylene during growth and senescence and boosting future research with the aim to improve the qualitative and quantitative traits of crops.}, language = {en}, urldate = {2021-04-24}, journal = {Front. Plant Sci.}, author = {Iqbal, Noushina and Khan, Nafees A. and Ferrante, Antonio and Trivellini, Alice and Francini, Alessandra and Khan, M. I. R.}, month = apr, year = {2017}, file = {Iqbal et al. - 2017 - Ethylene Role in Plant Growth, Development and Sen.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\B668JMMZ\\Iqbal et al. - 2017 - Ethylene Role in Plant Growth, Development and Sen.pdf:application/pdf}, } @article{lee_cytokinin_2013, title = {Cytokinin, auxin, and abscisic acid affects sucrose metabolism conduce to de novo shoot organogenesis in rice ({Oryza} sativa {L}.) callus}, volume = {54}, issn = {1999-3110}, url = {https://as-botanicalstudies.springeropen.com/articles/10.1186/1999-3110-54-5}, doi = {10.1186/1999-3110-54-5}, abstract = {Background: Shoot regeneration frequency in rice callus is still low and highly diverse among rice cultivars. This study aimed to investigate the association of plant hormone signaling and sucrose uptake and metabolism in rice during callus induction and early shoot organogenesis. The immatured seeds of two rice cultivars, Ai-Nan-Tsao 39 (ANT39) and Tainan 11 (TN11) are used in this study. Results: Callus formation is earlier, callus fresh weight is higher, but water content is significant lower in ANT39 than in TN11 while their explants are inoculated on callus induction medium (CIM). Besides, the regeneration frequency is prominently higher in ANT39 ({\textasciitilde}80\%) compared to TN11 callus (0\%). Levels of glucose, sucrose, and starch are all significant higher in ANT39 than in TN11 either at callus induction or early shoot organogenesis stage. Moreover, high expression levels of Cell wall-bound invertase 1, Sucrose transporter 1 (OsSUT1) and OsSUT2 are detected in ANT39 at the fourth-day in CIM but it cannot be detected in TN11 until the tenth-day. It suggested that ANT39 has higher callus growth rate and shoot regeneration ability may cause from higher activity of sucrose uptake and metabolism. As well, the expression levels of ORYZA SATIVA RESPONSE REGULATOR 1 (ORR1), PIN-formed 1 and Late embryogenesis-abundant 1, representing endogenous cytokinin, auxin and ABA signals, respectively, were also up-regulated in highly regenerable callus, ANT39, but only ORR1 was greatly enhanced in TN11 at the tenth-day in CIM. Conclusion: Thus, phytohormone signals may affect sucrose metabolism to trigger callus initiation and further de novo shoot regeneration in rice culture.}, language = {en}, number = {1}, urldate = {2021-04-24}, journal = {Bot Stud}, author = {Lee, Shiang-Ting and Huang, Wen-Lii}, month = dec, year = {2013}, pages = {5}, file = {Lee and Huang - 2013 - Cytokinin, auxin, and abscisic acid affects sucros.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\GVJ3MMGG\\Lee and Huang - 2013 - Cytokinin, auxin, and abscisic acid affects sucros.pdf:application/pdf}, } @incollection{roychoudhury_abiotic_2019, edition = {1}, title = {Abiotic {Stress} {Management} in {Plants}: {Role} of {Ethylene}}, isbn = {978-1-119-46369-6 978-1-119-46366-5}, shorttitle = {Abiotic {Stress} {Management} in {Plants}}, url = {https://onlinelibrary.wiley.com/doi/10.1002/9781119463665.ch10}, language = {en}, urldate = {2021-04-24}, booktitle = {Molecular {Plant} {Abiotic} {Stress}}, publisher = {Wiley}, author = {Sharma, Anket and Kumar, Vinod and Sidhu, Gagan Preet Singh and Kumar, Rakesh and Kohli, Sukhmeen Kaur and Yadav, Poonam and Kapoor, Dhriti and Bali, Aditi Shreeya and Shahzad, Babar and Khanna, Kanika and Kumar, Sandeep and Thukral, Ashwani Kumar and Bhardwaj, Renu}, editor = {Roychoudhury, Aryadeep and Tripathi, Durgesh}, month = aug, year = {2019}, doi = {10.1002/9781119463665.ch10}, pages = {185--208}, file = {Sharma et al. - 2019 - Abiotic Stress Management in Plants Role of Ethyl.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\XBI44E8G\\Sharma et al. - 2019 - Abiotic Stress Management in Plants Role of Ethyl.pdf:application/pdf}, } @article{abiri_enhancing_2017, title = {Enhancing somatic embryogenesis of {Malaysian} rice cultivar {MR219} using adjuvant materials in a high-efficiency protocol}, volume = {14}, issn = {1735-1472, 1735-2630}, url = {http://link.springer.com/10.1007/s13762-016-1221-y}, doi = {10.1007/s13762-016-1221-y}, language = {en}, number = {5}, urldate = {2021-04-25}, journal = {Int. J. Environ. Sci. Technol.}, author = {Abiri, R. and Maziah, M. and Shaharuddin, N. A. and Yusof, Z. N. B. and Atabaki, N. and Hanafi, M. M. and Sahebi, M. and Azizi, P. and Kalhori, N. and Valdiani, A.}, month = may, year = {2017}, pages = {1091--1108}, file = {Abiri et al. - 2017 - Enhancing somatic embryogenesis of Malaysian rice .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\JHVFRBFQ\\Abiri et al. - 2017 - Enhancing somatic embryogenesis of Malaysian rice .pdf:application/pdf;Jha-Kumar2018_Article_BABYBOOMBBMACandidateTranscrip.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\KSXRUWNF\\Jha-Kumar2018_Article_BABYBOOMBBMACandidateTranscrip.pdf:application/pdf}, } @article{kieber_cytokinins_2014, title = {Cytokinins}, volume = {12}, issn = {1543-8120}, url = {http://www.bioone.org/doi/10.1199/tab.0168}, doi = {10.1199/tab.0168}, language = {en}, urldate = {2021-04-25}, journal = {The Arabidopsis Book}, author = {Kieber, Joseph J. and Schaller, G. Eric}, month = jan, year = {2014}, pages = {e0168}, file = {Kieber and Schaller - 2014 - Cytokinins.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\8JV6FDBW\\Kieber and Schaller - 2014 - Cytokinins.pdf:application/pdf}, } @article{pawar_influence_nodate, title = {Influence of different shoot portion and media on vegetative propagation of pomegranate ({Punica} granatum)}, abstract = {An experiment entitled, influence of different shoot portion and media on vegetative propagation of pomegranate was carried out with two factors viz; shoot portion with three levels and media with seven levels making total twenty one treatment combinations. Experiment was laid out in Factorial Completely Randomized Design with three replications. The results of the present investigation on the basis of pooled data revealed that, minimum days to sprouting (11.33) was recorded with treatment s1 (Apical) whereas, significantly highest length of shoot (9.79 cm), maximum number of roots (8.92) and length of root (8.96 cm) was recorded with treatment s2 (Sub-apical). Among different treatments of media, significantly early sprouting (11.14 days), maximum number of roots per cutting (8.40) and highest length of roots per cutting (8.81 cm) and highest shoot length (9.36 cm) at 60 DAP were observed with treatment m4 (Vermiculite: Poultry Manure [1:1]+ Pseudomonas). Use of sub-apical cutting with Vermiculite: Poultry Manure [1:1]+ Pseudomonas media in plug tray for early sprouting, highest shoot and root parameters of pomegranate under greenhouse condition.}, language = {en}, journal = {International Journal of Chemical Studies}, author = {Pawar, Yogesh and Varma, LR and More, SG and Verma, Piyush and Jat, RK}, pages = {5}, file = {Pawar et al. - Influence of different shoot portion and media on .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\JA6DIESG\\Pawar et al. - Influence of different shoot portion and media on .pdf:application/pdf;OsRR2 Negetif Regulator.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\JLDI4GUI\\OsRR2 Negetif Regulator.pdf:application/pdf}, } @article{jones_auxin_2011, title = {Auxin and cytokinin regulate each other’s levels via a metabolic feedback loop}, volume = {6}, issn = {1559-2324}, url = {http://www.tandfonline.com/doi/abs/10.4161/psb.6.6.15323}, doi = {10.4161/psb.6.6.15323}, language = {en}, number = {6}, urldate = {2021-05-21}, journal = {Plant Signaling \& Behavior}, author = {Jones, Brian and Ljung, Karin}, month = jun, year = {2011}, pages = {901--904}, file = {Jones and Ljung - 2011 - Auxin and cytokinin regulate each other’s levels v.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\H7JUCAS6\\Jones and Ljung - 2011 - Auxin and cytokinin regulate each other’s levels v.pdf:application/pdf}, } @article{ikeuchi_plant_2013-1, title = {Plant {Callus}: {Mechanisms} of {Induction} and {Repression}}, volume = {25}, issn = {1040-4651, 1532-298X}, shorttitle = {Plant {Callus}}, url = {https://academic.oup.com/plcell/article/25/9/3159-3173/6097899}, doi = {10.1105/tpc.113.116053}, language = {en}, number = {9}, urldate = {2021-05-21}, journal = {Plant Cell}, author = {Ikeuchi, Momoko and Sugimoto, Keiko and Iwase, Akira}, month = sep, year = {2013}, pages = {3159--3173}, file = {Ikeuchi et al. - 2013 - Plant Callus Mechanisms of Induction and Repressi.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\STPYS3M5\\Ikeuchi et al. - 2013 - Plant Callus Mechanisms of Induction and Repressi.pdf:application/pdf;ethylen.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\L2ZP3AWG\\ethylen.pdf:application/pdf}, } @article{ma_auxin_2018, title = {Auxin signaling: a big question to be addressed by small molecules}, volume = {69}, issn = {0022-0957, 1460-2431}, shorttitle = {Auxin signaling}, url = {https://academic.oup.com/jxb/article/69/2/313/4641657}, doi = {10.1093/jxb/erx375}, abstract = {Providing a mechanistic understanding of the crucial roles of the phytohormone auxin has been an important and coherent aspect of plant biology research. Since its discovery more than a century ago, prominent advances have been made in the understanding of auxin action, ranging from metabolism and transport to cellular and transcriptional responses. However, there is a long road ahead before a thorough understanding of its complex effects is achieved, because a lot of key information is still missing. The availability of an increasing number of technically advanced scientific tools has boosted the basic discoveries in auxin biology. A plethora of bioactive small molecules, consisting of the synthetic auxin-like herbicides and the more specific auxin-related compounds, developed as a result of the exploration of chemical space by chemical biology, have made the tool box for auxin research more comprehensive. This review mainly focuses on the compounds targeting the auxin co-receptor complex, demonstrates the various ways to use them, and shows clear examples of important basic knowledge obtained by their usage. Application of these precise chemical tools, together with an increasing amount of structural information for the major components in auxin action, will certainly aid in strengthening our insights into the complexity and diversity of auxin response.}, language = {en}, number = {2}, urldate = {2021-05-26}, journal = {Journal of Experimental Botany}, author = {Ma, Qian and Grones, Peter and Robert, Stéphanie}, month = jan, year = {2018}, pages = {313--328}, file = {Ma et al. - 2018 - Auxin signaling a big question to be addressed by.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\KZWMHBM6\\Ma et al. - 2018 - Auxin signaling a big question to be addressed by.pdf:application/pdf}, } @article{tao_role_2015, title = {The {Role} of {Ethylene} in {Plants} {Under} {Salinity} {Stress}}, volume = {6}, issn = {1664-462X}, url = {http://journal.frontiersin.org/Article/10.3389/fpls.2015.01059/abstract}, doi = {10.3389/fpls.2015.01059}, abstract = {Although the roles of ethylene in plant response to salinity and other stresses have been extensively studied, there are still some obscure points left to be clarified. Generally, in Arabidopsis and many other terrestrial plants, ethylene signaling is indispensable for plant rapid response and tolerance to salinity stress. However, a few studies showed that functional knock-out of some ACSs increased plant salinity-tolerance, while overexpression of them caused more sensitivity. This seems to be contradictory to the known opinion that ethylene plays positive roles in salinity response. Differently, ethylene in rice may play negative roles in regulating seedling tolerance to salinity. The main positive ethylene signaling components MHZ7/OsEIN2, MHZ6/OsEIL1, and OsEIL2 all negatively regulate the salinity-tolerance of rice seedlings. Recently, several different research groups all proposed a negative feedback mechanism of coordinating plant growth and ethylene response, in which several ethylene-inducible proteins (including NtTCTP, NEIP2 in tobacco, AtSAUR76/77/78, and AtARGOS) act as inhibitors of ethylene response but activators of plant growth. Therefore, in addition to a summary of the general roles of ethylene biosynthesis and signaling in salinity response, this review mainly focused on discussing (i) the discrepancies between ethylene biosynthesis and signaling in salinity response, (ii) the divergence between rice and Arabidopsis in regulation of salinity response by ethylene, and (iii) the possible negative feedback mechanism of coordinating plant growth and salinity response by ethylene.}, language = {en}, urldate = {2021-05-26}, journal = {Front. Plant Sci.}, author = {Tao, Jian-Jun and Chen, Hao-Wei and Ma, Biao and Zhang, Wan-Ke and Chen, Shou-Yi and Zhang, Jin-Song}, month = nov, year = {2015}, file = {Tao et al. - 2015 - The Role of Ethylene in Plants Under Salinity Stre.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\DFXAUFK9\\Tao et al. - 2015 - The Role of Ethylene in Plants Under Salinity Stre.pdf:application/pdf;baby boom.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\DHCBNX6A\\baby boom.pdf:application/pdf}, } @article{jha_baby_2018, title = {{BABY} {BOOM} ({BBM}): a candidate transcription factor gene in plant biotechnology}, volume = {40}, issn = {0141-5492, 1573-6776}, shorttitle = {{BABY} {BOOM} ({BBM})}, url = {http://link.springer.com/10.1007/s10529-018-2613-5}, doi = {10.1007/s10529-018-2613-5}, abstract = {Plants have evolved a number of transcription factors, many of which are implicated in signaling pathways as well as regulating diverse cellular functions. BABY BOOM (BBM), transcription factors of the AP2/ERF family are key regulators of plant cell totipotency. Ectopic expression of the BBM gene, originally identified in Brassica napus, has diverse functions in plant cell proliferation, growth and development without exogenous growth regulators. The BBM gene has been implicated to play an important role as a gene marker in multiple signaling developmental pathways in plant development. This review focuses on recent advances in our understanding of a member of the AP2 family of transcription factor BBM in plant biotechnology including plant embryogenesis, cell proliferation, regeneration, plant transformation and apogamy. Recent discoveries about the BBM gene will inevitably help to unlock the long-standing mysteries of different biological mechanisms of plant cells.}, language = {en}, number = {11-12}, urldate = {2021-05-26}, journal = {Biotechnol Lett}, author = {Jha, Priyanka and Kumar, Vijay}, month = dec, year = {2018}, pages = {1467--1475}, file = {Jha and Kumar - 2018 - BABY BOOM (BBM) a candidate transcription factor .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\L4JQJGZW\\Jha and Kumar - 2018 - BABY BOOM (BBM) a candidate transcription factor .pdf:application/pdf}, } @article{duan_strigolactone_2019, title = {Strigolactone promotes cytokinin degradation through transcriptional activation of \textit{{CYTOKININ} {OXIDASE}/{DEHYDROGENASE} 9} in rice}, volume = {116}, issn = {0027-8424, 1091-6490}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1810980116}, doi = {10.1073/pnas.1810980116}, abstract = {Strigolactones (SLs), a group of terpenoid lactones derived from carotenoids, are plant hormones that control numerous aspects of plant development. Although the framework of SL signaling that the repressor DWARF 53 (D53) could be SL-dependently degraded via the SL receptor D14 and F-box protein D3 has been established, the downstream response genes to SLs remain to be elucidated. Here we show that the cytokinin (CK) content is dramatically increased in shoot bases of the rice SL signaling mutant d53 . By examining transcript levels of all the CK metabolism-related genes after treatment with SL analog GR24, we identified CYTOKININ OXIDASE/DEHYDROGENASE 9 ( OsCKX9 ) as a primary response gene significantly up-regulated within 1 h of treatment in the wild type but not in d53 . We also found that OsCKX9 functions as a cytosolic and nuclear dual-localized CK catabolic enzyme, and that the overexpression of OsCKX9 suppresses the browning of d53 calli. Both the CRISPR/Cas9-generated OsCKX9 mutants and OsCKX9 -overexpressing transgenic plants showed significant increases in tiller number and decreases in plant height and panicle size, suggesting that the homeostasis of OsCKX9 plays a critical role in regulating rice shoot architecture. Moreover, we identified the CK-inducible rice type-A response regulator OsRR5 as the secondary SL-responsive gene, whose expression is significantly repressed after 4 h of GR24 treatment in the wild type but not in osckx9 . These findings reveal a comprehensive plant hormone cross-talk in which SL can induce the expression of OsCKX9 to down-regulate CK content, which in turn triggers the response of downstream genes.}, language = {en}, number = {28}, urldate = {2021-05-26}, journal = {Proc Natl Acad Sci USA}, author = {Duan, Jingbo and Yu, Hong and Yuan, Kun and Liao, Zhigang and Meng, Xiangbing and Jing, Yanhui and Liu, Guifu and Chu, Jinfang and Li, Jiayang}, month = jul, year = {2019}, pages = {14319--14324}, file = {Duan et al. - 2019 - Strigolactone promotes cytokinin degradation throu.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\ZZNA4L9P\\Duan et al. - 2019 - Strigolactone promotes cytokinin degradation throu.pdf:application/pdf}, } @article{lee_regulation_nodate, title = {Regulation of {Ethylene} {Biosynthesis} by {Phytohormones} in {Etiolated} {Rice} ({Oryza} sativa {L}.) {Seedlings}}, abstract = {The gaseous hormone ethylene influences many aspects of plant growth, development, and responses to a variety of stresses. The biosynthesis of ethylene is tightly regulated by various internal and external stimuli, and the primary target of the regulation is the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS), which catalyzes the rate-limiting step of ethylene biosynthesis. We have previously demonstrated that the regulation of ethylene biosynthesis is a common feature of most of the phytohormones in etiolated Arabidopsis seedlings via the modulation of the protein stability of ACS. Here, we show that various phytohormones also regulate ethylene biosynthesis from etiolated rice seedlings in a similar manner to those in Arabidopsis. Cytokinin, brassinosteroids, and gibberellic acid increase ethylene biosynthesis without changing the transcript levels of neither OsACS nor ACC oxidases (OsACO), a family of enzymes catalyzing the final step of the ethylene biosynthetic pathway. Likewise, salicylic acid and abscisic acid do not alter the gene expression of OsACS, but both hormones downregulate the transcript levels of a subset of ACO genes, resulting in a decrease in ethylene biosynthesis. In addition, we show that the treatment of the phytohormones results in distinct etiolated seedling phenotypes, some of which resemble ethylene-responsive phenotypes, while others display ethylene-independent morphologies, indicating a complicated hormone crosstalk in rice. Together, our study brings a new insight into crosstalk between ethylene biosynthesis and other phytohormones, and provides evidence that rice ethylene biosynthesis could be regulated by the post-transcriptional regulation of ACS proteins.}, language = {en}, author = {Lee, Han Yong and Yoon, Gyeong Mee}, pages = {9}, file = {Lee and Yoon - Regulation of Ethylene Biosynthesis by Phytohormon.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\49ITTYIG\\Lee and Yoon - Regulation of Ethylene Biosynthesis by Phytohormon.pdf:application/pdf}, } @article{binder_ethylene_2020, title = {Ethylene signaling in plants}, volume = {295}, issn = {00219258}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925817494610}, doi = {10.1074/jbc.REV120.010854}, language = {en}, number = {22}, urldate = {2021-05-29}, journal = {Journal of Biological Chemistry}, author = {Binder, Brad M.}, month = may, year = {2020}, pages = {7710--7725}, file = {Binder - 2020 - Ethylene signaling in plants.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\6AXCZVC3\\Binder - 2020 - Ethylene signaling in plants.pdf:application/pdf}, } @article{jiang_correlation_2017, title = {A correlation analysis on chlorophyll content and {SPAD} value in tomato leaves}, volume = {71}, url = {https://doi.org/10.20776/S18808824-71-P37}, abstract = {To investigate relationship between tomato（Solanum lycopersicum）leaf chlorophyll content and Minolta SPAD-502 plus chlorophyll meter, we studied leaves at plant vegetative growth stage and reproductive growth stage, and conducted correlation analysis to establish most optimal function model. The results showed that the correlation of SPAD value and the content of chlorophyll a, chlorophyll b and total chlorophyll content were significantly correlated in tomato leaves. At plant vegetative growth stage, the optimal mathematic function for SPAD value and chlorophyll a, chlorophyll b and total chlorophyll were y = 0.0006x1.924（r = 0.785）, y = 0.0006x1.8009（r = 0.756）and y = 0.2317e0.0406x（r = 0.869）respectively. At reproductive growth stage, the optimal function models were y = 0.0236x － 0.0705（r = 0.856）for chlorophyll a, y = 0.2975e0.0127x（r = 0.793）for chlorophyll b and y = 0.0306x + 0.1443（r = 0.869）for total chlorophyll. All these data proved SPAD-502 can be an effective tool used for rapid and nondestructive estimation of leaf chlorophyll content in tomato.}, language = {en}, urldate = {2021-06-05}, journal = {Hort Research}, author = {Jiang, Chengyao and Johkan, Masahumi and Hohjo, Masaaki and Tsukagoshi, Satoru and Maturo, Toru}, month = mar, year = {2017}, pages = {37--42}, file = {JIANG et al. - 2017 - A correlation analysis on chlorophyll content and .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\GQTISEA7\\JIANG et al. - 2017 - A correlation analysis on chlorophyll content and .pdf:application/pdf}, } @article{sweeney_complex_2007, title = {The {Complex} {History} of the {Domestication} of {Rice}}, volume = {100}, issn = {0305-7364, 1095-8290}, url = {https://academic.oup.com/aob/article-lookup/doi/10.1093/aob/mcm128}, doi = {10.1093/aob/mcm128}, language = {en}, number = {5}, urldate = {2021-06-19}, journal = {Annals of Botany}, author = {Sweeney, M. and McCouch, S.}, month = jul, year = {2007}, pages = {951--957}, file = {Sweeney and McCouch - 2007 - The Complex History of the Domestication of Rice.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\KIMRP4WE\\Sweeney and McCouch - 2007 - The Complex History of the Domestication of Rice.pdf:application/pdf}, } @book{dunna_rice_2018, address = {India}, title = {Rice ({Oryza} sativa {L}.)}, url = {https://www.researchgate.net/publication/281152980}, language = {english}, publisher = {Research Gate}, author = {Dunna, Vijay and Roy, Bidhan}, year = {2018}, note = {ICAR: India Agricultural Research Institute. India : New India Publishing Agency}, } @article{ali_improved_2021, title = {Improved {Anther} {Culture} {Media} for {Enhanced} {Callus} {Formation} and {Plant} {Regeneration} in {Rice} ({Oryza} sativa {L}.)}, volume = {10}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/10/5/839}, doi = {10.3390/plants10050839}, abstract = {Anther culture technique is the most viable and efficient method of producing homozygous doubled haploid plants within a short period. However, the practical application of this technology in rice improvement is still limited by various factors that influence culture efficiency. The present study was conducted to determine the effects of two improved anther culture media, Ali-1 (A1) and Ali-2 (A2), a modified N6 medium, to enhance the callus formation and plant regeneration of japonica, indica, and hybrids of indica and japonica cross. The current study demonstrated that genotype and media had a significant impact (p {\textless} 0.001) on both callus induction frequency and green plantlet regeneration efficiency. The use of the A1 and A2 medium significantly enhanced callus induction frequency of japonica rice type, Nipponbare, and the hybrids of indica × japonica cross (CXY6, CXY24, and Y2) but not the indica rice type, NSIC Rc480. However, the A1 medium is found superior to the N6 medium as it significantly improved the green plantlet regeneration efficiency of CXY6, CXY24, and Y2 by almost 36\%, 118\%, and 277\%, respectively. Furthermore, it substantially reduced the albino plantlet regeneration of the induced callus in two hybrids (CXY6 and Y2). Therefore, the improved anther culture medium A1 can produce doubled haploid rice plants for indica × japonica, which can be useful in different breeding programs that will enable the speedy development of rice varieties for resource-poor farmers.}, language = {en}, number = {5}, urldate = {2021-06-29}, journal = {Plants}, author = {Ali, Jauhar and Nicolas, Katrina Leslie C. and Akther, Shahana and Torabi, Azerkhsh and Ebadi, Ali Akbar and Marfori-Nazarea, Corinne M. and Mahender, Anumalla}, month = apr, year = {2021}, pages = {839}, file = {Ali et al. - 2021 - Improved Anther Culture Media for Enhanced Callus .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\2CBVXKBH\\Ali et al. - 2021 - Improved Anther Culture Media for Enhanced Callus .pdf:application/pdf}, } @article{lardon_natural_2020, title = {Natural {Variation} in {Plant} {Pluripotency} and {Regeneration}}, volume = {9}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/9/10/1261}, doi = {10.3390/plants9101261}, abstract = {Plant regeneration is essential for survival upon wounding and is, hence, considered to be a strong natural selective trait. The capacity of plant tissues to regenerate in vitro, however, varies substantially between and within species and depends on the applied incubation conditions. Insight into the genetic factors underlying this variation may help to improve numerous biotechnological applications that exploit in vitro regeneration. Here, we review the state of the art on the molecular framework of de novo shoot organogenesis from root explants in Arabidopsis, which is a complex process controlled by multiple quantitative trait loci of various effect sizes. Two types of factors are distinguished that contribute to natural regenerative variation: master regulators that are conserved in all experimental systems (e.g., WUSCHEL and related homeobox genes) and conditional regulators whose relative role depends on the explant and the incubation settings. We further elaborate on epigenetic variation and protocol variables that likely contribute to differential explant responsivity within species and conclude that in vitro shoot organogenesis occurs at the intersection between (epi) genetics, endogenous hormone levels, and environmental influences.}, language = {en}, number = {10}, urldate = {2021-06-29}, journal = {Plants}, author = {Lardon, Robin and Geelen, Danny}, month = sep, year = {2020}, pages = {1261}, file = {Lardon and Geelen - 2020 - Natural Variation in Plant Pluripotency and Regene.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\V3EQG7T7\\Lardon and Geelen - 2020 - Natural Variation in Plant Pluripotency and Regene.pdf:application/pdf}, } @article{yang_response_2020, title = {Response of {Photosynthesis} to {High} {Growth} {Temperature} {Was} {Not} {Related} to {Leaf} {Anatomy} {Plasticity} in {Rice} ({Oryza} sativa {L}.)}, volume = {11}, issn = {1664-462X}, url = {https://www.frontiersin.org/article/10.3389/fpls.2020.00026/full}, doi = {10.3389/fpls.2020.00026}, abstract = {Photosynthesis is highly sensitive to high temperature stress, and with the rising global temperature, it is meaningful to investigate the response of photosynthesis to growth temperature and its relationship with leaf anatomy plasticity. We planted 21 cultivars including eight indica cultivars, eight japonica cultivars, and five javanica cultivars in pot experiments under high growth temperature (HT, 38/28°C, day/night) and control treatment (CK, 30/28°C, day/night). Photosynthetic rate (A), stomatal conductance (gs), transpiration rate (E), stomatal density (SD), vein density (VD), minor vein area (SVA), and major vein area (LVA) were measured after 30 treatment days. Results showed HT significantly increased A, gs, and E, while significantly decreased SD and LVA. There was no significant difference in A among the three subspecies both under CK and HT, while the javanica subspecies had higher gs, E, SVA, and LVA under HT, and the indica cultivars had higher VD and SD both under CK and HT. The javanica subspecies had higher relative value (HT/CK) of A, gs, and E, while difference was not observed in the relative value of SD, VD, and LVA among the three subspecies. The relative value of A was positively related to that of gs, while the latter was not correlated with the relative value of SD, VD, SVA, and LVA. Overall, the results suggested the increase of A and gs at HT was not attributed to leaf anatomy plasticity in respect of stomata and vein under HT.}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Yang, Desheng and Peng, Shaobing and Wang, Fei}, month = feb, year = {2020}, pages = {26}, file = {Yang et al. - 2020 - Response of Photosynthesis to High Growth Temperat.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\TQQE74IF\\Yang et al. - 2020 - Response of Photosynthesis to High Growth Temperat.pdf:application/pdf}, } @article{han_highly_2021, title = {Highly efficient and genotype-independent barley gene editing based on anther culture}, volume = {2}, issn = {25903462}, url = {https://linkinghub.elsevier.com/retrieve/pii/S259034622030105X}, doi = {10.1016/j.xplc.2020.100082}, abstract = {Recalcitrance to tissue culture and genetic transformation is the major bottleneck for gene manipulation in crops. In barley, immature embryos of Golden Promise have typically been used as explants for transformation. However, the genotype dependence of this approach limits the genetic modification of commercial varieties. Here, we developed an anther culture-based system that permits the effective creation of transgenic and gene-edited plants from commercial barley varieties. The protocol was tested in Golden Promise and four Australian varieties, which differed in phenology, callus induction, and green plant regeneration responses. Agrobacterium-mediated transformation was performed on microspore-derived callus to target the HvPDS gene, and T0 albinos with targeted mutations were successfully obtained from commercial varieties. Further editing of three targets was achieved with an average mutation rate of 53\% in the five varieties. In 51 analyzed T0 individuals, Cas9 induced a large proportion (69\%) of single-base indels and two-base deletions in the target sites, with variable mutation rates among targets and varieties. Both ontarget and off-target activities were detected in T1 progenies. Compared with immature embryo protocols, this genotype-independent platform can deliver a high editing efficiency and more regenerant plants within a similar time frame. It shows promise for functional genomics and the application of CRISPR technologies for the precise improvement of commercial varieties.}, language = {en}, number = {2}, urldate = {2021-06-29}, journal = {Plant Communications}, author = {Han, Yong and Broughton, Sue and Liu, Li and Zhang, Xiao-Qi and Zeng, Jianbin and He, Xiaoyan and Li, Chengdao}, month = mar, year = {2021}, pages = {100082}, file = {Han et al. - 2021 - Highly efficient and genotype-independent barley g.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\FVVDTWXF\\Han et al. - 2021 - Highly efficient and genotype-independent barley g.pdf:application/pdf}, } @article{indoliya_decoding_2016, title = {Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies}, volume = {6}, issn = {2045-2322}, url = {http://www.nature.com/articles/srep23050}, doi = {10.1038/srep23050}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Sci Rep}, author = {Indoliya, Yuvraj and Tiwari, Poonam and Chauhan, Abhisekh Singh and Goel, Ridhi and Shri, Manju and Bag, Sumit Kumar and Chakrabarty, Debasis}, month = sep, year = {2016}, pages = {23050}, file = {Indoliya et al. - 2016 - Decoding regulatory landscape of somatic embryogen.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\JZZDGJY2\\Indoliya et al. - 2016 - Decoding regulatory landscape of somatic embryogen.pdf:application/pdf}, } @article{tran_effect_2015, title = {Effect of antibiotics on callus regeneration during transformation of {IR} 64 rice}, volume = {7}, issn = {2215017X}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2215017X15000399}, doi = {10.1016/j.btre.2015.06.004}, language = {en}, urldate = {2021-06-29}, journal = {Biotechnology Reports}, author = {Tran, Thanh Ngoc and Sanan-Mishra, Neeti}, month = sep, year = {2015}, pages = {143--149}, file = {Tran and Sanan-Mishra - 2015 - Effect of antibiotics on callus regeneration durin.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\JBABZD53\\Tran and Sanan-Mishra - 2015 - Effect of antibiotics on callus regeneration durin.pdf:application/pdf}, } @article{tian_breeding_2019, title = {Breeding {Rice} lines for physio-functional food through indica ‘{Zhaxima}’ × japonica ‘{Nanjing} 46’ haploid technique}, volume = {1}, issn = {2661-8974}, url = {https://fppn.biomedcentral.com/articles/10.1186/s43014-019-0010-7}, doi = {10.1186/s43014-019-0010-7}, abstract = {Resistant starch (RS) encompasses those forms of starch which are not accessible to human digestive enzymes and are fermented in the colons producing short chain fatty acids. The plant materials containing RS are few in the world. In this contribution, the culture ability of callus from anthers of F1 plants from, landraces, ‘Zhaxima’(Oryza sativa var. indica, high-RS rice line with 7.705 ± 0.142, g/100 g) × ‘Nanjing 46’ (Oryza sativa var. japonica, rice variety with RS content (g/100 g) of 0.200 ± 0.001 crosses were studied for obtaining high RS rice plants. The results showed that when M8 basic induction medium was added with 1.5 mg /L 2,4-D、2 mg /LNAA and 0.3 mg /L KT, the inductivity of callus was high as 32.14\% for 21 d after pretreatment at 4 °C for 3 d; When MS differentiation basic medium was added with 2 mg /LKT and 3 mg /L ABA, the frequency of regeneration for callus was 50.3\% with only a regeneration frequency of 4.55\% grown into green seedlings. The RS content in the seeds was between those of the two parents and was partially normally distributed, the highest RS contents of the regenerated plants was as high as 7.66 ± 1.197\%. This produced an efficient technology for regenerating stable rice lines with high RS and good eating quality using anthers culture.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Food Prod Process and Nutr}, author = {Tian, Q. Q. and Li, X. and Lu, C. M. and Fang, X. W.}, month = dec, year = {2019}, pages = {12}, file = {Tian et al. - 2019 - Breeding Rice lines for physio-functional food thr.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\EZJWD5H8\\Tian et al. - 2019 - Breeding Rice lines for physio-functional food thr.pdf:application/pdf}, } @article{solanki_optimization_2019, title = {Optimization of in vitro culture media for improvement in yield of {Navara} ancient {Indian} medicinal rice}, volume = {9}, issn = {2190-572X, 2190-5738}, url = {http://link.springer.com/10.1007/s13205-019-1797-2}, doi = {10.1007/s13205-019-1797-2}, abstract = {Medicinally important ancient Navara rice (GI Kerala, India 2007) is a very short duration (60–70 days) variety with a yield of only 0.5 tonnes/hectare costing {\textasciitilde} Rs. 400/kg. It is used for indigenous treatment for chronic diseases by local and oral consumption. In this study, scutellum-derived calli were generated from mature Navara seeds and these were inoculated on different CIM-1 to CIM-5 media supplemented with 2.5 mg/l 2,4-dichlorophenoxyacetic acid. Regeneration of calli on different regeneration media RI, RII and RIII media were performed. Regeneration of 30-day-old calli on RI media showed 30\%, for RII it showed no regeneration and on RIII media only 12\% regeneration was obtained. The addition of glutamine and proline showed a 30–40\% improvement in somatic embryogenesis. The 74–88\% callus induction frequency was obtained on CIM-1 to CIM-5. The fresh weight (mg) of 30-day-old calli is CIM-2 {\textless} CIM-3 {\textless} CIM-4 {\textless} CIM-1 {\textless}{\textless} CIM-5 and corresponding size shows CIM-2–CIM-3 {\textless} CIM-5 {\textless} CIM-1 {\textless} CIM-4. A negative correlation between the callus fresh weight and the regeneration efficiency was observed. In CIM-5, 20–25 days 3.4-fold increase and 25–30 days a 1.7-fold increase in fresh weight of calli is noted. The 20-day-old calli transfer to RI media shows 80\% regeneration frequency and 6–7 plantlets/callus, which are twofold higher as compared with 30-day-old calli. The somatic embryogenesis and its regeneration on synthetic media provide an alternative for biotechnological intervention for yield improvement, in turn cost reduction for Navara rice.}, language = {en}, number = {7}, urldate = {2021-06-29}, journal = {3 Biotech}, author = {Solanki, Manish and Sinha, Anshika and Shukla, Lata I.}, month = jul, year = {2019}, pages = {270}, file = {Solanki et al. - 2019 - Optimization of in vitro culture media for improve.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\72A39H7M\\Solanki et al. - 2019 - Optimization of in vitro culture media for improve.pdf:application/pdf}, } @article{juarez-gonzalez_explant_2019, title = {The explant developmental stage profoundly impacts small {RNA}-mediated regulation at the dedifferentiation step of maize somatic embryogenesis}, volume = {9}, issn = {2045-2322}, url = {http://www.nature.com/articles/s41598-019-50962-y}, doi = {10.1038/s41598-019-50962-y}, abstract = {Abstract Maize somatic embryogenesis (SE) requires the induction of embryogenic callus and establishment of proliferation before plant regeneration. The molecular mechanisms underlying callus embryogenic potential are not well understood. Here we explored the role of small RNAs (sRNAs) and the accumulation of their target transcripts in maize SE at the dedifferentiation step using VS-535 zygotic embryos collected at distinct developmental stages and displaying contrasting in vitro embryogenic potential and morphology. MicroRNAs (miRNAs), trans -acting siRNAs (tasiRNAs), heterochromatic siRNAs (hc-siRNAs) populations and their RNA targets were analyzed by high-throughput sequencing. Abundances of specific miRNAs, tasiRNAs and targets were validated by qRT-PCR. Unique accumulation patterns were found for immature embryo at 15 Days After Pollination (DAP) and for the callus induction from this explant, as compared to 23 DAP and mature embryos. miR156, miR164, miR166, tasiARFs and the 24 nt hc-siRNAs displayed the most strikingly different patterns between explants and during dedifferentiation. According to their role in auxin responses and developmental cues, we conclude that sRNA-target regulation operating within the 15 DAP immature embryo explant provides key molecular hints as to why this stage is relevant for callus induction with successful proliferation and plant regeneration.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Sci Rep}, author = {Juárez-González, Vasti T. and López-Ruiz, Brenda A. and Baldrich, Patricia and Luján-Soto, Eduardo and Meyers, Blake C. and Dinkova, Tzvetanka D.}, month = dec, year = {2019}, pages = {14511}, file = {Juárez-González et al. - 2019 - The explant developmental stage profoundly impacts.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\7NLG4B7N\\Juárez-González et al. - 2019 - The explant developmental stage profoundly impacts.pdf:application/pdf}, } @article{xu_atacing_2020, title = {{ATACing} {Somatic} {Embryogenesis}}, volume = {54}, issn = {15345807}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580720307103}, doi = {10.1016/j.devcel.2020.09.008}, language = {en}, number = {6}, urldate = {2021-06-29}, journal = {Developmental Cell}, author = {Xu, Jian}, month = sep, year = {2020}, pages = {689--690}, file = {Xu - 2020 - ATACing Somatic Embryogenesis.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\XV3MV3IL\\Xu - 2020 - ATACing Somatic Embryogenesis.pdf:application/pdf}, } @article{gulzar_genes_2020, title = {Genes, proteins and other networks regulating somatic embryogenesis in plants}, volume = {18}, issn = {2090-5920}, url = {https://jgeb.springeropen.com/articles/10.1186/s43141-020-00047-5}, doi = {10.1186/s43141-020-00047-5}, abstract = {Background: Somatic embryogenesis (SE) is an intricate molecular and biochemical process principally based on cellular totipotency and a model in studying plant development. In this unique embryo-forming process, the vegetative cells acquire embryogenic competence under cellular stress conditions. The stress caused by plant growth regulators (PGRs), nutrient, oxygenic, or other signaling elements makes cellular reprogramming and transforms vegetative cells into embryos through activation/deactivation of a myriad of genes and transcriptional networks. Hundreds of genes have been directly linked to zygotic and somatic embryogeneses; some of them like SOMATIC EMBRYOGENESIS LIKE RECEPTOR KINASE (SERK), LEAFY COTYLEDON (LEC), BABYBOOM (BBM), and AGAMOUSLIKE 15 (AGL15) are very important and are part of molecular network. Main text (observation): This article reviews various genes/orthologs isolated from different plants; encoded proteins and their possible role in regulating somatic embryogenesis of plants have been discussed. The role of SERK in regulating embryogenesis is also summarized. Different SE-related proteins identified through LC–MS at various stages of embryogenesis are also described; a few proteins like 14-3-3, chitinase, and LEA are used as potential SE markers. These networks are interconnected in a complicated manner, posing challenges for their complete elucidation. Conclusions: The various gene networks and factors controlling somatic embryogenesis have been discussed and presented. The roles of stress, PGRs, and other signaling elements have been discussed. In the last two-to-three decades’ progress, the challenges ahead and its future applications in various fields of research have been highlighted. The review also presents the need of high throughput, innovative techniques, and sensitive instruments in unraveling the mystery of SE.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {J Genet Eng Biotechnol}, author = {Gulzar, Basit and Mujib, A. and Malik, Moien Qadir and Sayeed, Rukaya and Mamgain, Jyoti and Ejaz, Bushra}, month = dec, year = {2020}, pages = {31}, file = {Gulzar et al. - 2020 - Genes, proteins and other networks regulating soma.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\H9NL3JUM\\Gulzar et al. - 2020 - Genes, proteins and other networks regulating soma.pdf:application/pdf}, } @article{vercruyssen_growth_2015, title = {{GROWTH} {REGULATING} {FACTOR5} {Stimulates} {Arabidopsis} {Chloroplast} {Division}, {Photosynthesis}, and {Leaf} {Longevity}}, volume = {167}, issn = {1532-2548}, url = {https://academic.oup.com/plphys/article/167/3/817/6113750}, doi = {10.1104/pp.114.256180}, abstract = {Abstract Arabidopsis (Arabidopsis thaliana) leaf development relies on subsequent phases of cell proliferation and cell expansion. During the proliferation phase, chloroplasts need to divide extensively, and during the transition from cell proliferation to expansion, they differentiate into photosynthetically active chloroplasts, providing the plant with energy. The transcription factor GROWTH REGULATING FACTOR5 (GRF5) promotes the duration of the cell proliferation period during leaf development. Here, it is shown that GRF5 also stimulates chloroplast division, resulting in a higher chloroplast number per cell with a concomitant increase in chlorophyll levels in 35S:GRF5 leaves, which can sustain higher rates of photosynthesis. Moreover, 35S:GRF5 plants show delayed leaf senescence and are more tolerant for growth on nitrogen-depleted medium. Cytokinins also stimulate leaf growth in part by extending the cell proliferation phase, simultaneously delaying the onset of the cell expansion phase. In addition, cytokinins are known to be involved in chloroplast development, nitrogen signaling, and senescence. Evidence is provided that GRF5 and cytokinins synergistically enhance cell division and chlorophyll retention after dark-induced senescence, which suggests that they also cooperate to stimulate chloroplast division and nitrogen assimilation. Taken together with the increased leaf size, ectopic expression of GRF5 has great potential to improve plant productivity.}, language = {en}, number = {3}, urldate = {2021-06-29}, journal = {Plant Physiology}, author = {Vercruyssen, Liesbeth and Tognetti, Vanesa B. and Gonzalez, Nathalie and Van Dingenen, Judith and De Milde, Liesbeth and Bielach, Agnieszka and De Rycke, Riet and Van Breusegem, Frank and Inzé, Dirk}, month = feb, year = {2015}, pages = {817--832}, file = {Vercruyssen et al. - 2015 - GROWTH REGULATING FACTOR5 Stimulates Arabidopsis C.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\MVDBLVGI\\Vercruyssen et al. - 2015 - GROWTH REGULATING FACTOR5 Stimulates Arabidopsis C.pdf:application/pdf}, } @article{yasmin_ethylene_2014, title = {Ethylene influences in vitro regeneration frequency in the {FR13A} rice harbouring the {SUB1A} gene}, volume = {72}, issn = {0167-6903, 1573-5087}, url = {http://link.springer.com/10.1007/s10725-013-9840-5}, doi = {10.1007/s10725-013-9840-5}, abstract = {Many studies have examined the effects of ethylene on in vitro plant growth and development, often with controversial results. Ethylene accumulates in culture vessels due to both the release from the tissues and the physical entrapment due to the need for closed containers. This hormone has several effects on plant regeneration, depending on the plant species and even the cultivar. A prerequisite for ethylene use for in vitro culture is thus to formulate a specific protocol for the genotype of interest. In rice, ethylene is a key regulator of adaptation strategies to low oxygen environments. In particular, the SUBMERGENCE1A (SUB1A) gene, when present, drives the acclimation response which when activated by ethylene produced by submerged plants leads to adaptation through reduced plant growth and ethanolic fermentation enhancement. This gene is restricted to a limited number of rice for which a very specific response to ethylene is expected, whatever the source. This paper reports the regeneration differences between a SUB1A rice landrace (indica-aus, FR13A) and a non-SUB1A variety (japonica, Nipponbare). Our results suggest that regeneration protocols with exogenous ethylene precursors supply are required for the FR13A rice harbouring the SUB1A gene to overcome the problem of low regeneration efficiency.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Plant Growth Regul}, author = {Yasmin, Sabina and Mensuali-Sodi, Anna and Perata, Pierdomenico and Pucciariello, Chiara}, month = jan, year = {2014}, pages = {97--103}, file = {Yasmin et al. - 2014 - Ethylene influences in vitro regeneration frequenc.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\RFY2HQ6Z\\Yasmin et al. - 2014 - Ethylene influences in vitro regeneration frequenc.pdf:application/pdf}, } @article{neves_modulation_2021, title = {Modulation of {Organogenesis} and {Somatic} {Embryogenesis} by {Ethylene}: {An} {Overview}}, volume = {10}, issn = {2223-7747}, shorttitle = {Modulation of {Organogenesis} and {Somatic} {Embryogenesis} by {Ethylene}}, url = {https://www.mdpi.com/2223-7747/10/6/1208}, doi = {10.3390/plants10061208}, abstract = {Ethylene is a plant hormone controlling physiological and developmental processes such as fruit maturation, hairy root formation, and leaf abscission. Its effect on regeneration systems, such as organogenesis and somatic embryogenesis (SE), has been studied, and progress in molecular biology techniques have contributed to unveiling the mechanisms behind its effects. The influence of ethylene on regeneration should not be overlooked. This compound affects regeneration differently, depending on the species, genotype, and explant. In some species, ethylene seems to revert recalcitrance in genotypes with low regeneration capacity. However, its effect is not additive, since in genotypes with high regeneration capacity this ability decreases in the presence of ethylene precursors, suggesting that regeneration is modulated by ethylene. Several lines of evidence have shown that the role of ethylene in regeneration is markedly connected to biotic and abiotic stresses as well as to hormonalcrosstalk, in particular with key regeneration hormones and growth regulators of the auxin and cytokinin families. Transcriptional factors of the ethylene response factor (ERF) family are regulated by ethylene and strongly connected to SE induction. Thus, an evident connection between ethylene, stress responses, and regeneration capacity is markedly established. In this review the effect of ethylene and the way it interacts with other players during organogenesis and somatic embryogenesis is discussed. Further studies on the regulation of ERF gene expression induced by ethylene during regeneration can contribute to new insights on the exact role of ethylene in these processes. A possible role in epigenetic modifications should be considered, since some ethylene signaling components are directly related to histone acetylation.}, language = {en}, number = {6}, urldate = {2021-06-29}, journal = {Plants}, author = {Neves, Mariana and Correia, Sandra and Cavaleiro, Carlos and Canhoto, Jorge}, month = jun, year = {2021}, pages = {1208}, file = {Neves et al. - 2021 - Modulation of Organogenesis and Somatic Embryogene.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\L9MRQGBD\\Neves et al. - 2021 - Modulation of Organogenesis and Somatic Embryogene.pdf:application/pdf}, } @article{gao_transcriptome_2020, title = {Transcriptome sequencing and identification of key callus browning-related genes from petiole callus of tree peony ({Paeonia} suffruticosa cv. {Kao}) cultured on media with three browning inhibitors}, volume = {149}, issn = {09819428}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0981942820300371}, doi = {10.1016/j.plaphy.2020.01.029}, abstract = {Abstract: Tree peony (Paeonia suffruticosa Andrews) has ornamental, oil, and medicinal values, and demand in the markets for uniform tree peony seedlings is increasing. Micropropagation could quickly propagate uniform seedlings. However, the heavy browning phenomenon hinders large-scale development of uniform tree peony seedlings. In this paper, we measured the total phenolic compounds content, and sequenced the transcriptomes of tree peony ‘Kao’ petiole calluses cultured on media with three browning antagonist treatments and fresh petioles to identify the key genes involved in callus browning. Polyvinylpyrrolidone (PVP) treatment can reduce production of phenolic compounds and promote callus regeneration. A total of 218,957 unigenes were obtained from fresh petiole and three kinds of browning petiole calluses by transcriptome sequencing. The average sequence length of unigenes was 446 bp with an N50 of 493 bp. Functional annotation analysis revealed that 43,428, 45,357, 31,194, 30,019, and 21,357 unigenes were annotated using the NCBI-NR database, Swiss-Prot, KOG, GO, and KEGG, respectively. In total, 33 differentially expressed genes (DEGs) were identified as potentially associated with callus browning. Among these DEGs, 12 genes were predicted to participate in phenolic compounds biosynthesis, three genes were predicted to be involved in phenolic compounds oxidation, and six genes were predicted to participate in callus regeneration. Moreover, six transcription factors were observed to be differentially expressed in the fresh petiole and three treated petioles in tree peony. This study comprehensively identifies browning-related gene resources and will possibly help in deciphering the molecular mechanisms of callus browning of tree peony in the future.}, language = {en}, urldate = {2021-06-29}, journal = {Plant Physiology and Biochemistry}, author = {Gao, Jie and Xue, Jingqi and Xue, Yuqian and Liu, Rong and Ren, Xiuxia and Wang, Shunli and Zhang, Xiuxin}, month = apr, year = {2020}, pages = {36--49}, file = {Gao et al. - 2020 - Transcriptome sequencing and identification of key.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\REDWX3NB\\Gao et al. - 2020 - Transcriptome sequencing and identification of key.pdf:application/pdf}, } @article{jones_inhibition_2013, title = {Inhibition of {Phenylpropanoid} {Biosynthesis} in {Artemisia} annua {L}.: {A} {Novel} {Approach} to {Reduce} {Oxidative} {Browning} in {Plant} {Tissue} {Culture}}, volume = {8}, issn = {1932-6203}, shorttitle = {Inhibition of {Phenylpropanoid} {Biosynthesis} in {Artemisia} annua {L}.}, url = {https://dx.plos.org/10.1371/journal.pone.0076802}, doi = {10.1371/journal.pone.0076802}, abstract = {Oxidative browning is a common and often severe problem in plant tissue culture systems caused by the accumulation and oxidation of phenolic compounds. The current study was conducted to investigate a novel preventative approach to address this problem by inhibiting the activity of the phenylalanine ammonia lyase enzyme (PAL), thereby reducing the biosynthesis of phenolic compounds. This was accomplished by incorporating 2aminoindane-2-phosphonic acid (AIP), a competitive PAL inhibitor, into culture media of Artemisia annua as a model system. Addition of AIP into culture media resulted in significant reductions in visual tissue browning, a reduction in total phenol content, as well as absorbance and autoflourescence of tissue extracts. Reduced tissue browning was accompanied with a significant increase in growth on cytokinin based medium. Microscopic observations demonstrated that phenolic compounds accumulated in discrete cells and that these cells were more prevalent in brown tissue. These cells were highly plasmolyzed and often ruptured during examination, demonstrating a mechanism in which phenolics are released into media in this system. These data indicate that inhibiting phenylpropanoid biosynthesis with AIP is an effective approach to reduce tissue browning in A. annua. Additional experiments with Ulmus americana and Acer saccharum indicate this approach is effective in many species and it could have a wide application in systems where oxidative browning restricts the development of biotechnologies.}, language = {en}, number = {10}, urldate = {2021-06-29}, journal = {PLoS ONE}, author = {Jones, Andrew Maxwell Phineas and Saxena, Praveen Kumar}, editor = {Liu, Ji-Hong}, month = oct, year = {2013}, pages = {e76802}, file = {Jones and Saxena - 2013 - Inhibition of Phenylpropanoid Biosynthesis in Arte.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\7W45R8V5\\Jones and Saxena - 2013 - Inhibition of Phenylpropanoid Biosynthesis in Arte.pdf:application/pdf}, } @article{watkins_ethylene-induced_2014, title = {Ethylene-{Induced} {Flavonol} {Accumulation} in {Guard} {Cells} {Suppresses} {Reactive} {Oxygen} {Species} and {Moderates} {Stomatal} {Aperture}}, volume = {164}, issn = {0032-0889, 1532-2548}, url = {https://academic.oup.com/plphys/article/164/4/1707-1717/6112792}, doi = {10.1104/pp.113.233528}, language = {en}, number = {4}, urldate = {2021-06-29}, journal = {Plant Physiol.}, author = {Watkins, Justin M. and Hechler, Paul J. and Muday, Gloria K.}, month = apr, year = {2014}, pages = {1707--1717}, file = {Watkins et al. - 2014 - Ethylene-Induced Flavonol Accumulation in Guard Ce.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\QGPXECHM\\Watkins et al. - 2014 - Ethylene-Induced Flavonol Accumulation in Guard Ce.pdf:application/pdf}, } @article{ikeuchi_wounding_2017, title = {Wounding {Triggers} {Callus} {Formation} via {Dynamic} {Hormonal} and {Transcriptional} {Changes}}, volume = {175}, issn = {0032-0889, 1532-2548}, url = {https://academic.oup.com/plphys/article/175/3/1158-1174/6116893}, doi = {10.1104/pp.17.01035}, language = {en}, number = {3}, urldate = {2021-06-29}, journal = {Plant Physiol.}, author = {Ikeuchi, Momoko and Iwase, Akira and Rymen, Bart and Lambolez, Alice and Kojima, Mikiko and Takebayashi, Yumiko and Heyman, Jefri and Watanabe, Shunsuke and Seo, Mitsunori and De Veylder, Lieven and Sakakibara, Hitoshi and Sugimoto, Keiko}, month = nov, year = {2017}, pages = {1158--1174}, file = {Ikeuchi et al. - 2017 - Wounding Triggers Callus Formation via Dynamic Hor.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\6H78HQYX\\Ikeuchi et al. - 2017 - Wounding Triggers Callus Formation via Dynamic Hor.pdf:application/pdf}, } @article{zhang_common_2020-1, title = {A common wild rice-derived {BOC1} allele reduces callus browning in indica rice transformation}, volume = {11}, issn = {2041-1723}, url = {http://www.nature.com/articles/s41467-019-14265-0}, doi = {10.1038/s41467-019-14265-0}, abstract = {Abstract Callus browning, a common trait derived from the indica rice cultivar ( Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 ( BOC1 ) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession ( Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1 , which consequently improves the genetic transformation efficiency. The presence of a Tourist -like miniature inverted-repeat transposable element ( Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Nat Commun}, author = {Zhang, Kun and Su, Jingjing and Xu, Min and Zhou, Zhihui and Zhu, Xiaoyang and Ma, Xin and Hou, Jingjing and Tan, Lubin and Zhu, Zuofeng and Cai, Hongwei and Liu, Fengxia and Sun, Hongying and Gu, Ping and Li, Chen and Liang, Yuntao and Zhao, Wensheng and Sun, Chuanqing and Fu, Yongcai}, month = dec, year = {2020}, pages = {443}, file = {Zhang et al. - 2020 - A common wild rice-derived BOC1 allele reduces cal.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\C2XWM5HJ\\Zhang et al. - 2020 - A common wild rice-derived BOC1 allele reduces cal.pdf:application/pdf}, } @article{binder_ethylene_2020-1, title = {Ethylene signaling in plants}, volume = {295}, issn = {00219258}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925817494610}, doi = {10.1074/jbc.REV120.010854}, language = {en}, number = {22}, urldate = {2021-06-29}, journal = {Journal of Biological Chemistry}, author = {Binder, Brad M.}, month = may, year = {2020}, pages = {7710--7725}, file = {Binder - 2020 - Ethylene signaling in plants.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\7PE4RBQE\\Binder - 2020 - Ethylene signaling in plants.pdf:application/pdf;3. Dunna, 2013.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\6Z7DM9PK\\3. Dunna, 2013.pdf:application/pdf}, } @article{cunha_ethylene-induced_2017, title = {Ethylene-induced transcriptional and hormonal responses at the onset of sugarcane ripening}, volume = {7}, issn = {2045-2322}, url = {http://www.nature.com/articles/srep43364}, doi = {10.1038/srep43364}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Sci Rep}, author = {Cunha, Camila P. and Roberto, Guilherme G. and Vicentini, Renato and Lembke, Carolina G. and Souza, Glaucia M. and Ribeiro, Rafael V. and Machado, Eduardo C. and Lagôa, Ana M. M. A. and Menossi, Marcelo}, month = mar, year = {2017}, pages = {43364}, file = {Cunha et al. - 2017 - Ethylene-induced transcriptional and hormonal resp.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\NMD5E3N4\\Cunha et al. - 2017 - Ethylene-induced transcriptional and hormonal resp.pdf:application/pdf}, } @article{wang_tree1-ein3mediated_2020, title = {{TREE1}-{EIN3}–mediated transcriptional repression inhibits shoot growth in response to ethylene}, volume = {117}, issn = {0027-8424, 1091-6490}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2018735117}, doi = {10.1073/pnas.2018735117}, abstract = {Ethylene is an important plant hormone that regulates plant growth, in which the master transcriptionactivator EIN3 (Ethylene Insensitive 3)-mediated transcriptional activation plays vital roles. However, the EIN3-mediated transcriptional repression in ethylene response is unknown. We report here that a Transcriptional Repressor of EIN3-dependent Ethylene-response 1 (TREE1) interacts with EIN3 to regulate transcriptional repression that leads to an inhibition of shoot growth in response to ethylene. Tissue-specific transcriptome analysis showed that most of the genes are down-regulated by ethylene in shoots, and a DNA binding motif was identified that is important for this transcriptional repression. TREE1 binds to the DNA motif to repress gene expression in an EIN3-dependent manner. Genetic validation demonstrated that repression of TREE1-targeted genes leads to an inhibition of shoot growth. Overall, this work establishes a mechanism by which transcriptional repressor TREE1 interacts with EIN3 to inhibit shoot growth via transcriptional repression in response to ethylene.}, language = {en}, number = {46}, urldate = {2021-06-29}, journal = {Proc Natl Acad Sci USA}, author = {Wang, Likai and Ko, Eun Esther and Tran, Jaclyn and Qiao, Hong}, month = nov, year = {2020}, pages = {29178--29189}, file = {Wang et al. - 2020 - TREE1-EIN3–mediated transcriptional repression inh.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\DYYXZ45W\\Wang et al. - 2020 - TREE1-EIN3–mediated transcriptional repression inh.pdf:application/pdf}, } @article{sharma_modulatory_2017, title = {Modulatory {Effects} of {Exogenously} {Applied} {Polyamines} on {Postharvest} {Physiology}, {Antioxidant} {System} and {Shelf} {Life} of {Fruits}: {A} {Review}}, volume = {18}, issn = {1422-0067}, shorttitle = {Modulatory {Effects} of {Exogenously} {Applied} {Polyamines} on {Postharvest} {Physiology}, {Antioxidant} {System} and {Shelf} {Life} of {Fruits}}, url = {http://www.mdpi.com/1422-0067/18/8/1789}, doi = {10.3390/ijms18081789}, abstract = {Polyamines (PAs) are natural compounds involved in many growth and developmental processes in plants, and, specifically in fruits, play a vital role regulating its development, ripening and senescence processes. Putrescine (PUT), spermine (SPE), and spermidine (SPD) are prominent PAs applied exogenously to extend shelf life of fruits. They also originate endogenously during developmental phases of horticultural crops and simultaneously affect the quality attributes and shelf life. Their anti-ethylene nature is being exploited to enhance the shelf life when exogenously applied on fruits. In growth and development of fruits, PA levels generally fall, which marks the beginning of senescence at postharvest phase. PUT, SPE and SPD treatments are being applied during postharvest phase to prolong the shelf life. They enhance the shelf life of fruits by reducing respiration rate, ethylene release and enhance firmness and quality attributes in fruits. PAs have a mitigating impact on biotic and abiotic stresses including chilling injury (CI) in tropical and sub-tropical fruits. PAs are environment friendly in nature and are biodegradable without showing any negative effect on environment. Biotechnological interventions by using chimeric gene constructs of PA encoding genes has boosted the research to develop transgenic fruits and vegetables which would possess inherent or in situ mechanism of enhanced biosynthesis of PAs at different stages of development and thereby will enhance the shelf life and quality in fruits. Internal and external quality attributes of fruits are improved by modulation of antioxidant system and by strengthening biophysical morphology of fruits by electrostatic interaction between PAs and phospholipids in the cell wall.}, language = {en}, number = {8}, urldate = {2021-06-29}, journal = {IJMS}, author = {Sharma, Sunil and Pareek, Sunil and Sagar, Narashans and Valero, Daniel and Serrano, Maria}, month = aug, year = {2017}, pages = {1789}, file = {Sharma et al. - 2017 - Modulatory Effects of Exogenously Applied Polyamin.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\642KUVQR\\Sharma et al. - 2017 - Modulatory Effects of Exogenously Applied Polyamin.pdf:application/pdf}, } @article{sgamma_ethylene_2015, title = {Ethylene inhibitor silver nitrate enhances regeneration and genetic transformation of {Prunus} avium ({L}.) cv {Stella}}, volume = {120}, issn = {0167-6857, 1573-5044}, url = {http://link.springer.com/10.1007/s11240-014-0581-6}, doi = {10.1007/s11240-014-0581-6}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Plant Cell Tiss Organ Cult}, author = {Sgamma, Tiziana and Thomas, Brian and Muleo, Rosario}, month = jan, year = {2015}, pages = {79--88}, file = {Sgamma et al. - 2015 - Ethylene inhibitor silver nitrate enhances regener.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\F9ZWD9IJ\\Sgamma et al. - 2015 - Ethylene inhibitor silver nitrate enhances regener.pdf:application/pdf}, } @incollection{binder_inhibitors_2017, address = {New York, NY}, title = {Inhibitors of {Ethylene} {Biosynthesis} and {Signaling}}, volume = {1573}, isbn = {978-1-4939-6852-7 978-1-4939-6854-1}, url = {http://link.springer.com/10.1007/978-1-4939-6854-1_15}, abstract = {Ethylene is a gas biosynthesized by plants which has many physiological and developmental effects on their growth. Ethylene affects agriculturally and horticulturally important traits such as fruit ripening, postharvest physiology, senescence, and abscission, and so ethylene action is often inhibited to improve the shelf life of fruits, vegetables, and cut flowers. Chemical inhibitors of ethylene action are also useful for research to characterize the mechanisms of ethylene biosynthesis and signal transduction, and the role that ethylene plays in various physiological processes. Here, we describe the use of three inhibitors commonly used for the study of ethylene action in plants: 2-a­ minoethoxyvinyl glycine (AVG), silver ions (Ag), and the gaseous compound 1-methylcyclopropene (1-MCP). AVG is an inhibitor of 1-aminocyclopropane-1-carboxylic acid (ACC) synthase, a key enzyme involved in ethylene biosynthesis. Silver and 1-MCP are both inhibitors of the ethylene receptors. Inhibitor use as well as off-target effects are described with a focus on ethylene responses in dark-grown Arabidopsis seedlings. Methods for the use of these inhibitors can be applied to other plant growth assays.}, language = {en}, urldate = {2021-06-29}, booktitle = {Ethylene {Signaling}}, publisher = {Springer New York}, author = {Schaller, G. Eric and Binder, Brad M.}, editor = {Binder, Brad M. and Eric Schaller, G.}, year = {2017}, doi = {10.1007/978-1-4939-6854-1_15}, note = {Series Title: Methods in Molecular Biology}, pages = {223--235}, file = {Schaller and Binder - 2017 - Inhibitors of Ethylene Biosynthesis and Signaling.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\EEWTTINJ\\Schaller and Binder - 2017 - Inhibitors of Ethylene Biosynthesis and Signaling.pdf:application/pdf}, } @article{barros_detection_2013, title = {Detection of 1-aminocyclopropane-1-carboxylate oxidase activity in seeds of {Stylosanthes} humilis {H}.{B}.{K}}, issn = {21970025}, url = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S2197-00252013000300008&lng=en&nrm=iso&tlng=en}, doi = {10.1590/S2197-00252013000300008}, abstract = {The activity of 1-aminocyclopropane-1-carboxylate oxidase (ACO) was characterized in seeds of the tropical legume Townsville stylo (Stylosanthes humilis) both in vitro (desalted extract of non-dormant seeds) and in vivo (entire dormant seeds). Optimum conditions for maximum in vitro ACO activity in a Trizma-HCl 100 mM buffered medium were: pH 7.0, temperature 32ºC and cofactors and co-substrate at the following concentrations: NaHCO3 30 mM, sodium ascorbate 30 mM and FeSO4 50 μM. Rates of in vitro reaction catalyzed by ACO were shown to be constant within the interval 15-150 minutes from the onset of the reaction. The apparent Km for in vitro ACO, as determined from the non-linear curve fitting to the Michaelis-Menten equation, was 156±8.3 μM ACC with a Vmax 5.4±0.08 mmol (ET) g-1 h-1 on a fresh matter (FM) basis. In vivo (control basal medium: HCl-KOH 10 mM pH 7.0, 30ºC, reaction time 15 hours) apparent Km was 230±27 μM ACC and Vmax 11.9±0.38 mmol (ET) g-1.h-1 on a FM basis. These data suggest that the enzyme exhibits a relatively low affinity for the substrate. The well-known inhibitors of ACO activity, α-aminoisobutyric acid, salicylic and acetylsalicylic acids, n-propylgallate and cobaltous ions, were highly effective in inhibiting ACO activity of Townsville stylo seeds.}, language = {en}, urldate = {2021-06-29}, journal = {Theor. Exp. Plant Physiol.}, author = {Barros, Raimundo Santos and Araújo Pinheiro, Frank James and Müller, Caroline and Pires, Marcel Viana and Silva, Alexei Gresta Vieira da and Ribeiro, Dimas Mendes}, year = {2013}, file = {Barros et al. - 2013 - Detection of 1-aminocyclopropane-1-carboxylate oxi.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\9VB96RWT\\Barros et al. - 2013 - Detection of 1-aminocyclopropane-1-carboxylate oxi.pdf:application/pdf}, } @article{suekawa_exogenous_2019, title = {Exogenous proline has favorable effects on growth and browning suppression in rice but not in tobacco}, volume = {142}, issn = {09819428}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0981942819302670}, doi = {10.1016/j.plaphy.2019.06.032}, abstract = {Proline is one of the amino acids that compose proteins and has various roles under non-stress and stress conditions. In this study, we investigated the effect of proline on the growth and browning of two plants, tobacco and rice, by exogenous application and endogenous increase of proline. Exogenous proline had a different effect on the growth and browning between tobacco and rice: proline affected negatively the growth of tobacco seedlings and favorably that of rice seedlings. In addition, proline prevented browning only in rice cultured cells, consistent with the increase of proline contents, but not in tobacco BY-2 cells. These results might be due to the difference of exogenous proline uptake activity in these cells. From the Lineweaver-Burk plots, proline inhibited polyphenol oxidase activity in vitro, which is a major factor of enzymatic browning in plants, by affecting the enzyme-substrate complex. Proline could suppress the browning of the plant callus by inhibition of PPO activity.}, language = {en}, urldate = {2021-06-29}, journal = {Plant Physiology and Biochemistry}, author = {Suekawa, Marina and Fujikawa, Yukichi and Esaka, Muneharu}, month = sep, year = {2019}, pages = {1--7}, file = {Suekawa et al. - 2019 - Exogenous proline has favorable effects on growth .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\I2GHYD8Q\\Suekawa et al. - 2019 - Exogenous proline has favorable effects on growth .pdf:application/pdf}, } @article{sun_pyrazinamide_2017, title = {Pyrazinamide and derivatives block ethylene biosynthesis by inhibiting {ACC} oxidase}, volume = {8}, issn = {2041-1723}, url = {http://www.nature.com/articles/ncomms15758}, doi = {10.1038/ncomms15758}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Nat Commun}, author = {Sun, Xiangzhong and Li, Yaxin and He, Wenrong and Ji, Chenggong and Xia, Peixue and Wang, Yichuan and Du, Shuo and Li, Hongjiang and Raikhel, Natasha and Xiao, Junyu and Guo, Hongwei}, month = aug, year = {2017}, pages = {15758}, file = {Sun et al. - 2017 - Pyrazinamide and derivatives block ethylene biosyn.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\25JSB8YP\\Sun et al. - 2017 - Pyrazinamide and derivatives block ethylene biosyn.pdf:application/pdf}, } @article{kuklin_ethylene_1995, title = {Ethylene {Impact} on {Somatic} {Embryogenesis}: {Biotechnological} {Considerations}}, volume = {9}, issn = {1310-2818, 1314-3530}, shorttitle = {Ethylene {Impact} on {Somatic} {Embryogenesis}}, url = {http://www.tandfonline.com/doi/abs/10.1080/13102818.1995.10818856}, doi = {10.1080/13102818.1995.10818856}, abstract = {The gaseous plant hormone ethylene affects somatic emb1yogenesis in various ways depending on the species or explants used. Inclusion of ethylene action inhibitors, name{\textasciitilde}v silver ions in culture media increased somatic embryogenesis in some species. Large scale (bioreactor) yields of somatic emb1yos were less than these ji·01n flask cultures. Ethylene depletion from the bioreactors due to aeration is considered as a possible reason for the decrease in somatic emb1yogenesis. Ethylene is discussed as a physiological marker related to emb1yogenic potential. {\textasciitilde}Vound ethylene evolved after transformation experiments might have some inhibit01:v role on transformation but results are contradictory. Ethylene plays different roles in long term storage (low and ambient temperatures) of emb1yogenic cultures. Use of transgenic technology in ethylene biosynthesis reduction is discussed as a way to understanding ethylene role in somatic emb(vogenesis.}, language = {en}, number = {4}, urldate = {2021-06-29}, journal = {Biotechnology \& Biotechnological Equipment}, author = {Kuklin, A.}, month = jan, year = {1995}, pages = {12--19}, file = {Kuklin - 1995 - Ethylene Impact on Somatic Embryogenesis Biotechn.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\7GV93AGT\\Kuklin - 1995 - Ethylene Impact on Somatic Embryogenesis Biotechn.pdf:application/pdf}, } @article{wang_transcriptomes_2021, title = {Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in {Hevea} brasiliensis}, volume = {22}, issn = {1471-2164}, url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07501-9}, doi = {10.1186/s12864-021-07501-9}, abstract = {Background: Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE are still not well understood. Results: In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92\% of them were mapped to the rubber tree genome. The de novo assembly generated 36,937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions: This study provides important information to elucidate the molecular regulation during rubber tree late SE.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {BMC Genomics}, author = {Wang, Ying and Li, Hui-Liang and Zhou, Yong-Kai and Guo, Dong and Zhu, Jia-Hong and Peng, Shi-Qing}, month = dec, year = {2021}, pages = {183}, file = {Wang et al. - 2021 - Transcriptomes analysis reveals novel insight into.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\R7WIFBMD\\Wang et al. - 2021 - Transcriptomes analysis reveals novel insight into.pdf:application/pdf}, } @article{wojcik_current_2020, title = {Current {Perspectives} on the {Auxin}-{Mediated} {Genetic} {Network} that {Controls} the {Induction} of {Somatic} {Embryogenesis} in {Plants}}, volume = {21}, issn = {1422-0067}, url = {https://www.mdpi.com/1422-0067/21/4/1333}, doi = {10.3390/ijms21041333}, abstract = {Auxin contributes to almost every aspect of plant development and metabolism as well as the transport and signalling of auxin-shaped plant growth and morphogenesis in response to endo- and exogenous signals including stress conditions. Consistently with the common belief that auxin is a central trigger of developmental changes in plants, the auxin treatment of explants was reported to be an indispensable inducer of somatic embryogenesis (SE) in a large number of plant species. Treating in vitro-cultured tissue with auxins (primarily 2,4-dichlorophenoxyacetic acid, which is a synthetic auxin-like plant growth regulator) results in the extensive reprogramming of the somatic cell transcriptome, which involves the modulation of numerous SE-associated transcription factor genes (TFs). A number of SE-modulated TFs that control auxin metabolism and signalling have been identified, and conversely, the regulators of the auxin-signalling pathway seem to control the SE-involved TFs. In turn, the different expression of the genes encoding the core components of the auxin-signalling pathway, the AUXIN/INDOLE-3-ACETIC ACIDs (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs), was demonstrated to accompany SE induction. Thus, the extensive crosstalk between the hormones, in particular, auxin and the TFs, was revealed to play a central role in the SE-regulatory network. Accordingly, LEAFY COTYLEDON (LEC1 and LEC2), BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15) and WUSCHEL (WUS) were found to constitute the central part of the complex regulatory network that directs the somatic plant cell towards embryogenic development in response to auxin. The revealing picture shows a high degree of complexity of the regulatory relationships between the TFs of the SE-regulatory network, which involve direct and indirect interactions and regulatory feedback loops. This review examines the recent advances in studies on the auxin-controlled genetic network, which is involved in the mechanism of SE induction and focuses on the complex regulatory relationships between the down- and up-stream targets of the SE-regulatory TFs. In particular, the outcomes from investigations on Arabidopsis, which became a model plant in research on genetic control of SE, are presented.}, language = {en}, number = {4}, urldate = {2021-06-29}, journal = {IJMS}, author = {Wójcik, Anna M. and Wójcikowska, Barbara and Gaj, Małgorzata D.}, month = feb, year = {2020}, pages = {1333}, file = {Wójcik et al. - 2020 - Current Perspectives on the Auxin-Mediated Genetic.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\QQ9RZY64\\Wójcik et al. - 2020 - Current Perspectives on the Auxin-Mediated Genetic.pdf:application/pdf}, } @article{abiri_enhancing_2017-1, title = {Enhancing somatic embryogenesis of {Malaysian} rice cultivar {MR219} using adjuvant materials in a high-efficiency protocol}, volume = {14}, issn = {1735-1472, 1735-2630}, url = {http://link.springer.com/10.1007/s13762-016-1221-y}, doi = {10.1007/s13762-016-1221-y}, language = {en}, number = {5}, urldate = {2021-06-29}, journal = {Int. J. Environ. Sci. Technol.}, author = {Abiri, R. and Maziah, M. and Shaharuddin, N. A. and Yusof, Z. N. B. and Atabaki, N. and Hanafi, M. M. and Sahebi, M. and Azizi, P. and Kalhori, N. and Valdiani, A.}, month = may, year = {2017}, pages = {1091--1108}, file = {Abiri et al. - 2017 - Enhancing somatic embryogenesis of Malaysian rice .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\KPDMN2XI\\Abiri et al. - 2017 - Enhancing somatic embryogenesis of Malaysian rice .pdf:application/pdf}, } @article{wojcikowska_epigenetic_2020, title = {Epigenetic {Regulation} of {Auxin}-{Induced} {Somatic} {Embryogenesis} in {Plants}}, volume = {21}, issn = {1422-0067}, url = {https://www.mdpi.com/1422-0067/21/7/2307}, doi = {10.3390/ijms21072307}, abstract = {Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.}, language = {en}, number = {7}, urldate = {2021-06-29}, journal = {IJMS}, author = {Wójcikowska, Barbara and Wójcik, Anna M. and Gaj, Małgorzata D.}, month = mar, year = {2020}, pages = {2307}, file = {Wójcikowska et al. - 2020 - Epigenetic Regulation of Auxin-Induced Somatic Emb.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\KY3PCPQ2\\Wójcikowska et al. - 2020 - Epigenetic Regulation of Auxin-Induced Somatic Emb.pdf:application/pdf}, } @article{ma_auxin_2018-1, title = {Auxin signaling: a big question to be addressed by small molecules}, volume = {69}, issn = {0022-0957, 1460-2431}, shorttitle = {Auxin signaling}, url = {https://academic.oup.com/jxb/article/69/2/313/4641657}, doi = {10.1093/jxb/erx375}, abstract = {Providing a mechanistic understanding of the crucial roles of the phytohormone auxin has been an important and coherent aspect of plant biology research. Since its discovery more than a century ago, prominent advances have been made in the understanding of auxin action, ranging from metabolism and transport to cellular and transcriptional responses. However, there is a long road ahead before a thorough understanding of its complex effects is achieved, because a lot of key information is still missing. The availability of an increasing number of technically advanced scientific tools has boosted the basic discoveries in auxin biology. A plethora of bioactive small molecules, consisting of the synthetic auxin-like herbicides and the more specific auxin-related compounds, developed as a result of the exploration of chemical space by chemical biology, have made the tool box for auxin research more comprehensive. This review mainly focuses on the compounds targeting the auxin co-receptor complex, demonstrates the various ways to use them, and shows clear examples of important basic knowledge obtained by their usage. Application of these precise chemical tools, together with an increasing amount of structural information for the major components in auxin action, will certainly aid in strengthening our insights into the complexity and diversity of auxin response.}, language = {en}, number = {2}, urldate = {2021-06-29}, journal = {Journal of Experimental Botany}, author = {Ma, Qian and Grones, Peter and Robert, Stéphanie}, month = jan, year = {2018}, pages = {313--328}, file = {Ma et al. - 2018 - Auxin signaling a big question to be addressed by.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\GRZXTS8J\\Ma et al. - 2018 - Auxin signaling a big question to be addressed by.pdf:application/pdf}, } @article{a_libin_callus_2012-1, title = {Callus induction and plant regeneration of {Sarawak} rice ({Oryza} sativa {L}.) variety {Biris}}, volume = {7}, issn = {1991637X}, url = {http://www.academicjournals.org/ajar/abstracts/abstracts/Abstracts%202012/7Aug/Libin%20et%20al.htm}, doi = {10.5897/AJAR12.587}, abstract = {Sarawak Biris rice is a strong aromatic rice variety which can thrive well in rice fields prone to flood, drought and other soil constraints. Tissue culture of Biris rice is important in producing planting materials and conducting genetic improvement work. The present study was conducted to induce callus from Biris rice seed and assess its regeneration ability. Dehusked mature seeds were used as starting materials for callus induction. Sterilized seeds were cultured onto Murashige and Skoog medium containing various concentrations of 2, 4-dichlorophenoxyacetic acid (2, 4-D). The optimum 2, 4-D concentration for callus induction was 2.0 mg/L with a frequency as high as 97\%. The calli produced were of desired features (creamy in colour, globular) and relatively bigger in size as compared to other treatments. The calli produced were further tested with plant growth regulator, naphthaleneacetic acid (NAA) in combination with kinetin (Kn) for plant regeneration ability. All uncontaminated calli were found to regenerate. Up to nine shoots were induced by a callus treated with 0.5 mg/L NAA in combination with 1.0 mg/L Kn. The present study should be noted as the first attempt to induce callus and regenerate plants from seeds of Biris rice.}, language = {en}, number = {30}, urldate = {2021-06-29}, journal = {Afr. J. Agric. Res.}, author = {{A. Libin,}}, month = aug, year = {2012}, file = {A. Libin, - 2012 - Callus induction and plant regeneration of Sarawak.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\CRDT9SSS\\A. Libin, - 2012 - Callus induction and plant regeneration of Sarawak.pdf:application/pdf}, } @article{sun_genome-wide_2019, title = {Genome-{Wide} {Analysis} of {Cotton} {Auxin} {Early} {Response} {Gene} {Families} and {Their} {Roles} in {Somatic} {Embryogenesis}}, volume = {10}, issn = {2073-4425}, url = {https://www.mdpi.com/2073-4425/10/10/730}, doi = {10.3390/genes10100730}, abstract = {Auxin is well known to regulate growth and development processes. Auxin early response genes serve as a critical component of auxin signaling and mediate auxin regulation of diverse physiological processes. In the present study, a genome-wide identification and comprehensive analysis of auxin early response genes were conducted in upland cotton. A total of 71 auxin response factor (ARF), 86 Auxin/Indole-3-Acetic Acid (Aux/IAA), 63 Gretchen Hagen3 (GH3), and 194 small auxin upregulated RNA (SAUR) genes were identified in upland cotton, respectively. Phylogenetic analysis revealed that the ARF, GH3, and SAUR families were likely subject to extensive evolutionary divergence between Arabidopsis and upland cotton, while the Aux/IAA family was evolutionary conserved. Expression profiles showed that the ARF, Aux/IAA, GH3, and SAUR family genes were extensively involved in embryogenic competence acquisition of upland cotton callus. The Aux/IAA family genes generally showed a higher expression level in the non-embryogenic callus (NEC) of highly embryogenic cultivar CCRI24 than that of recalcitrant cultivar CCRI12, which may be conducive to initializing the embryogenic transformation. Auxin early response genes were tightly co-expressed with most of the known somatic embryogenesis (SE) related genes, indicating that these genes may regulate upland cotton SE by interacting with auxin early response genes.}, language = {en}, number = {10}, urldate = {2021-06-29}, journal = {Genes}, author = {{Sun} and {Wang} and {Ma} and {Li} and {Liu}}, month = sep, year = {2019}, pages = {730}, file = {Sun et al. - 2019 - Genome-Wide Analysis of Cotton Auxin Early Respons.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\M9UFIP8B\\Sun et al. - 2019 - Genome-Wide Analysis of Cotton Auxin Early Respons.pdf:application/pdf}, } @article{antoniadi_cell-surface_2020, title = {Cell-surface receptors enable perception of extracellular cytokinins}, volume = {11}, issn = {2041-1723}, url = {http://www.nature.com/articles/s41467-020-17700-9}, doi = {10.1038/s41467-020-17700-9}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Nat Commun}, author = {Antoniadi, Ioanna and Novák, Ondřej and Gelová, Zuzana and Johnson, Alexander and Plíhal, Ondřej and Simerský, Radim and Mik, Václav and Vain, Thomas and Mateo-Bonmatí, Eduardo and Karady, Michal and Pernisová, Markéta and Plačková, Lenka and Opassathian, Korawit and Hejátko, Jan and Robert, Stéphanie and Friml, Jiří and Doležal, Karel and Ljung, Karin and Turnbull, Colin}, month = dec, year = {2020}, pages = {4284}, file = {Antoniadi et al. - 2020 - Cell-surface receptors enable perception of extrac.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\JTF8QPN7\\Antoniadi et al. - 2020 - Cell-surface receptors enable perception of extrac.pdf:application/pdf}, } @article{li_cytokinins_2021, title = {Cytokinins as central regulators during plant growth and stress response}, volume = {40}, issn = {0721-7714, 1432-203X}, url = {http://link.springer.com/10.1007/s00299-020-02612-1}, doi = {10.1007/s00299-020-02612-1}, abstract = {Key message  Cytokinins are a class of phytohormone that participate in the regulation of the plant growth, development, and stress response. In this review, the potential regulating mechanism during plant growth and stress response are discussed.}, language = {en}, number = {2}, urldate = {2021-06-29}, journal = {Plant Cell Rep}, author = {Li, Si-Min and Zheng, Hong-Xiang and Zhang, Xian-Sheng and Sui, Na}, month = feb, year = {2021}, pages = {271--282}, file = {Li et al. - 2021 - Cytokinins as central regulators during plant grow.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\IUP6BU9C\\Li et al. - 2021 - Cytokinins as central regulators during plant grow.pdf:application/pdf}, } @article{kieber_cytokinins_2014-1, title = {Cytokinins}, volume = {e0168}, issn = {1543-8120}, url = {http://www.bioone.org/doi/10.1199/tab.0168}, doi = {10.1199/tab.0168}, language = {en}, urldate = {2021-06-29}, journal = {The Arabidopsis Book}, author = {Kieber, Joseph J. and Schaller, G. Eric}, month = jan, year = {2014}, pages = {1--35}, file = {Kieber and Schaller - 2014 - Cytokinins.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\2V6U9TIY\\Kieber and Schaller - 2014 - Cytokinins.pdf:application/pdf}, } @article{kroll_cytokinin_2020, title = {Cytokinin {Signaling} {Downstream} of the {His}-{Asp} {Phosphorelay} {Network}: {Cytokinin}-{Regulated} {Genes} and {Their} {Functions}}, volume = {11}, issn = {1664-462X}, shorttitle = {Cytokinin {Signaling} {Downstream} of the {His}-{Asp} {Phosphorelay} {Network}}, url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.604489/full}, doi = {10.3389/fpls.2020.604489}, abstract = {The plant hormone cytokinin, existing in several molecular forms, is perceived by membrane-localized histidine kinases. The signal is transduced to transcription factors of the type-B response regulator family localized in the nucleus by a multi-step histidineaspartate phosphorelay network employing histidine phosphotransmitters as shuttle proteins across the nuclear envelope. The type-B response regulators activate a number of primary response genes, some of which trigger in turn further signaling events and the expression of secondary response genes. Most genes activated in both rounds of transcription were identified with high confidence using different transcriptomic toolkits and meta analyses of multiple individual published datasets. In this review, we attempt to summarize the existing knowledge about the primary and secondary cytokinin response genes in order to try connecting gene expression with the multitude of effects that cytokinin exerts within the plant body and throughout the lifespan of a plant.}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Kroll, Carlo K. and Brenner, Wolfram G.}, month = nov, year = {2020}, pages = {604489}, file = {Kroll and Brenner - 2020 - Cytokinin Signaling Downstream of the His-Asp Phos.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\K4TZVLUX\\Kroll and Brenner - 2020 - Cytokinin Signaling Downstream of the His-Asp Phos.pdf:application/pdf}, } @article{an_kinetin_2017, title = {Kinetin {Improves} {Barrier} {Function} of the {Skin} by {Modulating} {Keratinocyte} {Differentiation} {Markers}}, volume = {29}, issn = {1013-9087, 2005-3894}, url = {https://anndermatol.org/DOIx.php?id=10.5021/ad.2017.29.1.6}, doi = {10.5021/ad.2017.29.1.6}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Ann Dermatol}, author = {An, Sungkwan and Cha, Hwa Jun and Ko, Jung-Min and Han, Hyunjoo and Kim, Su Young and Kim, Kyung-Suk and Lee, Song Jeong and An, In-Sook and Kim, Sangwon and Youn, Hae Jeong and Ahn, Kyu Joong and Kim, Soo-Yeon}, year = {2017}, pages = {6}, file = {An et al. - 2017 - Kinetin Improves Barrier Function of the Skin by M.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\2D9GYU4U\\An et al. - 2017 - Kinetin Improves Barrier Function of the Skin by M.pdf:application/pdf}, } @article{rose_somatic_2019, title = {Somatic {Embryogenesis} in the {Medicago} truncatula {Model}: {Cellular} and {Molecular} {Mechanisms}}, volume = {10}, issn = {1664-462X}, shorttitle = {Somatic {Embryogenesis} in the {Medicago} truncatula {Model}}, url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00267/full}, doi = {10.3389/fpls.2019.00267}, abstract = {Medicago truncatula is now widely regarded as a legume model where there is an increasing range of genomic resources. Highly regenerable lines have been developed from the wildtype Jemalong cultivar, most likely due to epigenetic changes. These lines with high rates of somatic embryogenesis (SE) can be compared with wild-type where SE is rare. Much of the research has been with the high SE genotype Jemalong 2HA (2HA). SE can be induced from leaf tissue explants or isolated mesophyll protoplasts. In 2HA, the exogenous phytohormones 1-naphthaleneacetic acid (NAA) and 6-benzylaminopurine (BAP) are central to SE. However, there are interactions with ethylene, abscisic acid (ABA), and gibberellic acid (GA) which produce maximum SE. In the main, somatic embryos are derived from dedifferentiated cells, undergo organellar changes, and produce stem-like cells. There is evidence that the SE is induced as a result of a stress and hormone interaction and this is discussed. In M. truncatula, there are connections between stress and specific up-regulated genes and specific hormones and up-regulated genes during the SE induction phase. Some of the transcription factors have been knocked down using RNAi to show they are critical for SE induction (MtWUSCHEL, MtSERF1). SE research in M. truncatula has utilized high throughput transcriptomic and proteomic studies and the more detailed investigation of some individual genes. In this review, these studies are integrated to suggest a framework and timeline for some of the key events of SE induction in M. truncatula.}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Rose, Ray J.}, month = mar, year = {2019}, pages = {267}, file = {Rose - 2019 - Somatic Embryogenesis in the Medicago truncatula M.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\KH3D4QEH\\Rose - 2019 - Somatic Embryogenesis in the Medicago truncatula M.pdf:application/pdf}, } @article{li_identification_2017, title = {Identification of novel {miRNAs} and {miRNA} expression profiling in embryogenic tissues of {Picea} balfouriana treated by 6-benzylaminopurine}, volume = {12}, issn = {1932-6203}, url = {https://dx.plos.org/10.1371/journal.pone.0176112}, doi = {10.1371/journal.pone.0176112}, abstract = {Here, we compared miRNA expression profiles in embryonic cell cultures of the conifer Picea balfouriana following application of the synthetic cytokinin 6-benzylaminopurine (6-BAP). We used next-generation sequencing to analyze three libraries of small RNAs from the treated embryogenic cell cultures and generated 24,000,000 raw reads from each of the libraries. Over 70 differentially regulated micro RNA (miRNA) families (!2 fold change in expression) were identified between pairs of treatments. A quantitative analysis showed that miR3633 and miR1026 were upregulated in tissues with the highest embryogenic ability. These two miRNAs were predicted to target genes encoding receptor-like protein kinase and GAMYB transcription factors, respectively. In one library, miR1160, miR5638, miR1315, and miR5225 were downregulated. These four miRNAs were predicted to target genes encoding APETALA2, calmodulin-binding protein, and calciumdependent protein kinase transcription factors. The expression patterns of the miRNAs and their targets were negatively correlated. Approximately 181 potentially novel P. balfouriana miRNAs were predicted from the three libraries, and seven were validated during the quantitative analysis. This study is the first report of differential miRNA regulation in tissues treated with 6-BAP during somatic embryogenesis. The differentially expressed miRNAs will be of value for investigating the mechanisms of embryogenic processes that are responsive to 6-BAP in P. balfouriana.}, language = {en}, number = {5}, urldate = {2021-06-29}, journal = {PLoS ONE}, author = {Li, Qingfen and Deng, Cheng and Xia, Yan and Kong, Lisheng and Zhang, Hanguo and Zhang, Shougong and Wang, Junhui}, editor = {Zheng, Yun}, month = may, year = {2017}, pages = {e0176112}, file = {Li et al. - 2017 - Identification of novel miRNAs and miRNA expressio.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\2FHYQT27\\Li et al. - 2017 - Identification of novel miRNAs and miRNA expressio.pdf:application/pdf}, } @article{ming_combination_2019-1, title = {Combination of {Plant} {Growth} {Regulators}, {Maltose}, and {Partial} {Desiccation} {Treatment} {Enhance} {Somatic} {Embryogenesis} in {Selected} {Malaysian} {Rice} {Cultivar}}, volume = {8}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/8/6/144}, doi = {10.3390/plants8060144}, abstract = {The development of efficient tissue culture protocol for somatic embryo would facilitate the genetic modification breeding program. The callus induction and regeneration were studied by using different parameters i.e., auxins, cytokinins, and desiccation treatment. Scanning electron microscopy and histological analysis were performed to identify the embryogenic callus for regeneration. The callus percentage results showed that MS (Murashige and Skoog) basal medium supplemented with 3 mg/L 2, 4-D and 30g/L maltose were the optimal callus induction medium for MR220 (80\%) and MR220-CL2 (95\%). The morphology of the embryogenic callus was confirmed by the SEM (Scanning Electron Microscopy) (presence of extracellular matrix surface network) and later by histological analysis. Finally, MS media supplemented with 0.5 mg/L NAA (Naphthalene Acetic Acid), 2 mg/L kin, and 1 mg/L BAP were selected as the optimum regeneration media treatment while callus desiccated for 48 h was proved to produce more plantlets in MR220 (60\%) and MR220-CL2 (73.33\%) compared to control treatment (without desiccation). The protocol presented here showed the necessity for the inclusion of partial desiccation as an important step in the tissue culture protocol of Malaysian indica rice genotypes in order to enhance their regeneration potential.}, language = {en}, number = {6}, urldate = {2021-06-29}, journal = {Plants}, author = {Ming, NG Ja and Binte Mostafiz, Suraiya and Johon, Nur Syafiqoh and Abdullah Zulkifli, Nur Saliha and Wagiran, Alina}, month = may, year = {2019}, pages = {144}, file = {Ming et al. - 2019 - Combination of Plant Growth Regulators, Maltose, a.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\83CBEPNI\\Ming et al. - 2019 - Combination of Plant Growth Regulators, Maltose, a.pdf:application/pdf}, } @article{yang_ethylene_2015, title = {Ethylene {Signaling} in {Rice} and {Arabidopsis}: {Conserved} and {Diverged} {Aspects}}, volume = {8}, issn = {16742052}, shorttitle = {Ethylene {Signaling} in {Rice} and {Arabidopsis}}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205215000908}, doi = {10.1016/j.molp.2015.01.003}, abstract = {Ethylene as a gas phytohormone plays significant roles in the whole life cycle of plants, ranging from growth and development to stress responses. A linear ethylene signaling pathway has been established in the dicotyledonous model plant Arabidopsis. However, the ethylene signaling mechanism in monocotyledonous plants such as rice is largely unclear. In this review, we compare the ethylene response phenotypes of dark-grown seedlings of Arabidopsis, rice, and other monocotyledonous plants (maize, wheat, sorghum, and Brachypodium distachyon) and pinpoint that rice has a distinct phenotype of root inhibition but coleoptile promotion in etiolated seedlings upon ethylene treatment. We further summarize the homologous genes of Arabidopsis ethylene signaling components in these monocotyledonous plants and discuss recent progress. Although conserved in most aspects, ethylene signaling in rice has evolved new features compared with that in Arabidopsis. These analyses provide novel insights into the understanding of ethylene signaling in the dicotyledonous Arabidopsis and monocotyledonous plants, particularly rice. Further characterization of rice ethylene-responsive mutants and their corresponding genes will help us better understand the whole picture of ethylene signaling mechanisms in plants.}, language = {en}, number = {4}, urldate = {2021-06-29}, journal = {Molecular Plant}, author = {Yang, Chao and Lu, Xiang and Ma, Biao and Chen, Shou-Yi and Zhang, Jin-Song}, month = apr, year = {2015}, pages = {495--505}, file = {Yang et al. - 2015 - Ethylene Signaling in Rice and Arabidopsis Conser.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\GWJVZASM\\Yang et al. - 2015 - Ethylene Signaling in Rice and Arabidopsis Conser.pdf:application/pdf}, } @article{khanday_male-expressed_2019, title = {A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds}, volume = {565}, issn = {0028-0836, 1476-4687}, url = {http://www.nature.com/articles/s41586-018-0785-8}, doi = {10.1038/s41586-018-0785-8}, language = {en}, number = {7737}, urldate = {2021-06-29}, journal = {Nature}, author = {Khanday, Imtiyaz and Skinner, Debra and Yang, Bing and Mercier, Raphael and Sundaresan, Venkatesan}, month = jan, year = {2019}, pages = {91--95}, file = {Khanday et al. - 2019 - A male-expressed rice embryogenic trigger redirect.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\7WI89E82\\Khanday et al. - 2019 - A male-expressed rice embryogenic trigger redirect.pdf:application/pdf}, } @article{lowe_morphogenic_2016, title = {Morphogenic {Regulators} \textit{{Baby} boom} and \textit{{Wuschel}} {Improve} {Monocot} {Transformation}}, volume = {28}, issn = {1040-4651, 1532-298X}, url = {https://academic.oup.com/plcell/article/28/9/1998-2015/6098336}, doi = {10.1105/tpc.16.00124}, language = {en}, number = {9}, urldate = {2021-06-29}, journal = {Plant Cell}, author = {Lowe, Keith and Wu, Emily and Wang, Ning and Hoerster, George and Hastings, Craig and Cho, Myeong-Je and Scelonge, Chris and Lenderts, Brian and Chamberlin, Mark and Cushatt, Josh and Wang, Lijuan and Ryan, Larisa and Khan, Tanveer and Chow-Yiu, Julia and Hua, Wei and Yu, Maryanne and Banh, Jenny and Bao, Zhongmeng and Brink, Kent and Igo, Elizabeth and Rudrappa, Bhojaraja and Shamseer, Pm and Bruce, Wes and Newman, Lisa and Shen, Bo and Zheng, Peizhong and Bidney, Dennis and Falco, Carl and Register, Jim and Zhao, Zuo-Yu and Xu, Deping and Jones, Todd and Gordon-Kamm, William}, month = sep, year = {2016}, pages = {1998--2015}, file = {Lowe et al. - 2016 - Morphogenic Regulators Baby boom and Wus.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\XYRHYKFJ\\Lowe et al. - 2016 - Morphogenic Regulators Baby boom and Wus.pdf:application/pdf}, } @article{nic-can_new_2013, title = {New {Insights} into {Somatic} {Embryogenesis}: {LEAFY} {COTYLEDON1}, {BABY} {BOOM1} and {WUSCHEL}-{RELATED} {HOMEOBOX4} {Are} {Epigenetically} {Regulated} in {Coffea} canephora}, volume = {8}, issn = {1932-6203}, shorttitle = {New {Insights} into {Somatic} {Embryogenesis}}, url = {https://dx.plos.org/10.1371/journal.pone.0072160}, doi = {10.1371/journal.pone.0072160}, abstract = {Plant cells have the capacity to generate a new plant without egg fertilization by a process known as somatic embryogenesis (SE), in which differentiated somatic cells can form somatic embryos able to generate a functional plant. Although there have been advances in understanding the genetic basis of SE, the epigenetic mechanism that regulates this process is still unknown. Here, we show that the embryogenic development of Coffea canephora proceeds through a crosstalk between DNA methylation and histone modifications during the earliest embryogenic stages of SE. We found that low levels of DNA methylation, histone H3 lysine 9 dimethylation (H3K9me2) and H3K27me3 change according to embryo development. Moreover, the expression of LEAFY COTYLEDON1 (LEC1) and BABY BOOM1 (BBM1) are only observed after SE induction, whereas WUSCHEL-RELATED HOMEOBOX4 (WOX4) decreases its expression during embryo maturation. Using a pharmacological approach, it was found that 5-Azacytidine strongly inhibits the embryogenic response by decreasing both DNA methylation and gene expression of LEC1 and BBM1. Therefore, in order to know whether these genes were epigenetically regulated, we used Chromatin Immunoprecipitation (ChIP) assays. It was found that WOX4 is regulated by the repressive mark H3K9me2, while LEC1 and BBM1 are epigenetically regulated by H3K27me3. We conclude that epigenetic regulation plays an important role during somatic embryogenic development, and a molecular mechanism for SE is proposed.}, language = {en}, number = {8}, urldate = {2021-06-29}, journal = {PLoS ONE}, author = {Nic-Can, Geovanny I. and López-Torres, Adolfo and Barredo-Pool, Felipe and Wrobel, Kazimierz and Loyola-Vargas, Víctor M. and Rojas-Herrera, Rafael and De-la-Peña, Clelia}, editor = {Candela, Hector}, month = aug, year = {2013}, pages = {e72160}, file = {Nic-Can et al. - 2013 - New Insights into Somatic Embryogenesis LEAFY COT.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\DSLMJ4WJ\\Nic-Can et al. - 2013 - New Insights into Somatic Embryogenesis LEAFY COT.pdf:application/pdf}, } @article{duan_strigolactone_2019-1, title = {Strigolactone promotes cytokinin degradation through transcriptional activation of \textit{{CYTOKININ} {OXIDASE}/{DEHYDROGENASE} 9} in rice}, volume = {116}, issn = {0027-8424, 1091-6490}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1810980116}, doi = {10.1073/pnas.1810980116}, abstract = {Strigolactones (SLs), a group of terpenoid lactones derived from carotenoids, are plant hormones that control numerous aspects of plant development. Although the framework of SL signaling that the repressor DWARF 53 (D53) could be SL-dependently degraded via the SL receptor D14 and F-box protein D3 has been established, the downstream response genes to SLs remain to be elucidated. Here we show that the cytokinin (CK) content is dramatically increased in shoot bases of the rice SL signaling mutant d53 . By examining transcript levels of all the CK metabolism-related genes after treatment with SL analog GR24, we identified CYTOKININ OXIDASE/DEHYDROGENASE 9 ( OsCKX9 ) as a primary response gene significantly up-regulated within 1 h of treatment in the wild type but not in d53 . We also found that OsCKX9 functions as a cytosolic and nuclear dual-localized CK catabolic enzyme, and that the overexpression of OsCKX9 suppresses the browning of d53 calli. Both the CRISPR/Cas9-generated OsCKX9 mutants and OsCKX9 -overexpressing transgenic plants showed significant increases in tiller number and decreases in plant height and panicle size, suggesting that the homeostasis of OsCKX9 plays a critical role in regulating rice shoot architecture. Moreover, we identified the CK-inducible rice type-A response regulator OsRR5 as the secondary SL-responsive gene, whose expression is significantly repressed after 4 h of GR24 treatment in the wild type but not in osckx9 . These findings reveal a comprehensive plant hormone cross-talk in which SL can induce the expression of OsCKX9 to down-regulate CK content, which in turn triggers the response of downstream genes.}, language = {en}, number = {28}, urldate = {2021-06-29}, journal = {Proc Natl Acad Sci USA}, author = {Duan, Jingbo and Yu, Hong and Yuan, Kun and Liao, Zhigang and Meng, Xiangbing and Jing, Yanhui and Liu, Guifu and Chu, Jinfang and Li, Jiayang}, month = jul, year = {2019}, pages = {14319--14324}, file = {Duan et al. - 2019 - Strigolactone promotes cytokinin degradation throu.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\PFS6UKJU\\Duan et al. - 2019 - Strigolactone promotes cytokinin degradation throu.pdf:application/pdf}, } @article{mou_ethylene-independent_2020, title = {Ethylene-independent signaling by the ethylene precursor {ACC} in {Arabidopsis} ovular pollen tube attraction}, volume = {11}, issn = {2041-1723}, url = {http://www.nature.com/articles/s41467-020-17819-9}, doi = {10.1038/s41467-020-17819-9}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Nat Commun}, author = {Mou, Wangshu and Kao, Yun-Ting and Michard, Erwan and Simon, Alexander A. and Li, Dongdong and Wudick, Michael M. and Lizzio, Michael A. and Feijó, José A. and Chang, Caren}, month = dec, year = {2020}, pages = {4082}, file = {Mou et al. - 2020 - Ethylene-independent signaling by the ethylene pre.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\9BYU4EUC\\Mou et al. - 2020 - Ethylene-independent signaling by the ethylene pre.pdf:application/pdf}, } @article{zhang_common_2020-2, title = {A common wild rice-derived {BOC1} allele reduces callus browning in indica rice transformation}, volume = {11}, issn = {2041-1723}, url = {http://www.nature.com/articles/s41467-019-14265-0}, doi = {10.1038/s41467-019-14265-0}, abstract = {Abstract Callus browning, a common trait derived from the indica rice cultivar ( Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 ( BOC1 ) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession ( Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1 , which consequently improves the genetic transformation efficiency. The presence of a Tourist -like miniature inverted-repeat transposable element ( Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Nat Commun}, author = {Zhang, Kun and Su, Jingjing and Xu, Min and Zhou, Zhihui and Zhu, Xiaoyang and Ma, Xin and Hou, Jingjing and Tan, Lubin and Zhu, Zuofeng and Cai, Hongwei and Liu, Fengxia and Sun, Hongying and Gu, Ping and Li, Chen and Liang, Yuntao and Zhao, Wensheng and Sun, Chuanqing and Fu, Yongcai}, month = dec, year = {2020}, pages = {443}, file = {Zhang et al. - 2020 - A common wild rice-derived BOC1 allele reduces cal.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\HUYT2QD5\\Zhang et al. - 2020 - A common wild rice-derived BOC1 allele reduces cal.pdf:application/pdf}, } @article{wambugu_genetics_2021, title = {Genetics and {Genomics} of {African} {Rice} ({Oryza} glaberrima {Steud}) {Domestication}}, volume = {14}, issn = {1939-8425, 1939-8433}, url = {https://thericejournal.springeropen.com/articles/10.1186/s12284-020-00449-6}, doi = {10.1186/s12284-020-00449-6}, abstract = {African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Rice}, author = {Wambugu, Peterson W. and Ndjiondjop, Marie-Noelle and Henry, Robert}, month = dec, year = {2021}, pages = {6}, file = {Wambugu et al. - 2021 - Genetics and Genomics of African Rice (Oryza glabe.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\GBMG6KER\\Wambugu et al. - 2021 - Genetics and Genomics of African Rice (Oryza glabe.pdf:application/pdf}, } @article{rodrigo_risk_2021, title = {Risk of {Bacillus} cereus in {Relation} to {Rice} and {Derivatives}}, volume = {10}, issn = {2304-8158}, url = {https://www.mdpi.com/2304-8158/10/2/302}, doi = {10.3390/foods10020302}, abstract = {Rice is a very popular food throughout the world and the basis of the diet of the citizens of many countries. It is used as a raw material for the preparation of many complex dishes in which different ingredients are involved. Rice, as a consequence of their cultivation, harvesting, and handling, is often contaminated with spores of Bacillus cereus, a ubiquitous microorganism found mainly in the soil. B. cereus can multiply under temperature conditions as low as 4 ◦C in foods that contain rice and have been cooked or subjected to treatments that do not produce commercial sterility. B. cereus produces diarrhoeal or emetic foodborne toxin when the consumer eats food in which a sufficient number of cells have grown. These circumstances mean that every year many outbreaks of intoxication or intestinal problems related to this microorganism are reported. This work is a review from the perspective of risk assessment of the risk posed by B. cereus to the health of consumers and of some control measures that can be used to mitigate such a risk.}, language = {en}, number = {2}, urldate = {2021-06-29}, journal = {Foods}, author = {Rodrigo, Dolores and Rosell, Cristina M. and Martinez, Antonio}, month = feb, year = {2021}, pages = {302}, file = {Rodrigo et al. - 2021 - Risk of Bacillus cereus in Relation to Rice and De.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\MMXLQ65F\\Rodrigo et al. - 2021 - Risk of Bacillus cereus in Relation to Rice and De.pdf:application/pdf}, } @article{ciulu_extraction_2018, title = {Extraction and {Analysis} of {Phenolic} {Compounds} in {Rice}: {A} {Review}}, volume = {23}, issn = {1420-3049}, shorttitle = {Extraction and {Analysis} of {Phenolic} {Compounds} in {Rice}}, url = {http://www.mdpi.com/1420-3049/23/11/2890}, doi = {10.3390/molecules23112890}, abstract = {Rice represents the main source of calorie intake in many world countries and about 60\% of the world population include rice in their staple diet. Whole grain rice, also called brown rice, represent the unpolished version of the more common white rice including bran, germ, and endosperm. Many health-promoting properties have been associated to the consumption of whole grain rice and, for this reason, great attention has been paid by the scientific community towards the identification and the quantification of bioactive compounds in this food item. In this contribution, the last five years progresses in the quali-quantitative determination of phenolic compounds in rice have been highlighted. Special attention has been devoted to the most recent strategies for the extraction of the target compounds from rice along with the analytical approaches adopted for the separation, identification and quantification of phenolic acids, flavonoids, anthocyanins, and proanthocyanidins. More specifically, the main features of the “traditional” extraction methods (i.e., maceration, ultrasound-assisted extraction) have been described, as well as the more innovative protocols involving advanced extraction techniques, such as MAE (microwave-assisted extraction). The predominant role of HPLC in the definition of the phenolic profile has been examined also presenting the most recent results obtained by using mass spectrometry-based detection systems. In addition, the most common procedures aimed to the quantification of the total amount of the cited classes of phenolic compounds have been described together with the spectrophotometric protocols aimed to the evaluation of the antioxidant properties of rice phenolic extracts (i.e., FRAP, DPPH, ABTS and ORAC).}, language = {en}, number = {11}, urldate = {2021-06-29}, journal = {Molecules}, author = {Ciulu, Marco and Cádiz-Gurrea, Maria and Segura-Carretero, Antonio}, month = nov, year = {2018}, pages = {2890}, file = {Ciulu et al. - 2018 - Extraction and Analysis of Phenolic Compounds in R.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\LHWCJQP5\\Ciulu et al. - 2018 - Extraction and Analysis of Phenolic Compounds in R.pdf:application/pdf}, } @article{efferth_biotechnology_2019, title = {Biotechnology {Applications} of {Plant} {Callus} {Cultures}}, volume = {5}, issn = {20958099}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2095809918306131}, doi = {10.1016/j.eng.2018.11.006}, abstract = {In ethnopharmacology, and especially in traditional Chinese medicine, medicinal plants have been used for thousands of years. Similarly, agricultural plants have been used throughout the history of mankind. The recent development of the genetic engineering of plants to produce plants with desirable features adds a new and growing dimension to humanity’s usage of plants. The biotechnology of plants has come of age and a plethora of bioengineering applications in this context have been delineated during the past few decades. Callus cultures and suspension cell cultures offer a wide range of usages in pharmacology and pharmacy (including Chinese medicine), as well as in agriculture and horticulture. This review provides a timely overview of the advancements that have been made with callus cultures in these scientific fields. Genetically modified callus cultures by gene technological techniques can be used for the synthesis of bioactive secondary metabolites and for the generation of plants with improved resistance against salt, draft, diseases, and pests. Although the full potential of callus plant culture technology has not yet been exploited, the time has come to develop and market more callus culture-based products.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Engineering}, author = {Efferth, Thomas}, month = feb, year = {2019}, pages = {50--59}, file = {Efferth - 2019 - Biotechnology Applications of Plant Callus Culture.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\DI27V4AH\\Efferth - 2019 - Biotechnology Applications of Plant Callus Culture.pdf:application/pdf}, } @article{mendez-hernandez_signaling_2019, title = {Signaling {Overview} of {Plant} {Somatic} {Embryogenesis}}, volume = {10}, issn = {1664-462X}, url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00077/full}, doi = {10.3389/fpls.2019.00077}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Méndez-Hernández, Hugo A. and Ledezma-Rodríguez, Maharshi and Avilez-Montalvo, Randy N. and Juárez-Gómez, Yary L. and Skeete, Analesa and Avilez-Montalvo, Johny and De-la-Peña, Clelia and Loyola-Vargas, Víctor M.}, month = feb, year = {2019}, pages = {77}, file = {Méndez-Hernández et al. - 2019 - Signaling Overview of Plant Somatic Embryogenesis.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\AD9TBYW4\\Méndez-Hernández et al. - 2019 - Signaling Overview of Plant Somatic Embryogenesis.pdf:application/pdf}, } @article{martinez_holm_2019, title = {Holm {Oak} {Somatic} {Embryogenesis}: {Current} {Status} and {Future} {Perspectives}}, volume = {10}, issn = {1664-462X}, shorttitle = {Holm {Oak} {Somatic} {Embryogenesis}}, url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00239/full}, doi = {10.3389/fpls.2019.00239}, abstract = {Quercus ilex (holm oak) is one of the most representative trees in the Mediterranean basin, but now the sustainability of its ecosystems is at serious risk due to the lack of natural regeneration and to the presence of a severe disease called oak decline that has caused the death of thousands of trees. The application of biotechnological tools, such as somatic embryogenesis, allows programs of genetic improvement of the species to be speeded up and helps in the conservation of its ecosystems. Somatic embryogenesis is currently considered one of the main biotechnological techniques that has demonstrated significant benefits when has applied to forest tree species, providing significant advantages such as mass propagation, genetic transformation, application of synthetic seed, and cryopreservation of elite genotypes. In this report, the state of the art of somatic embryogenesis in holm oak is reviewed. Factors affecting the induction (plant donor age, type of explant, or plant growth regulators) and maintenance and proliferation of the embryogenic cultures are summarized. Advances on the conversion of somatic embryos into plants and on the acclimatization of these plantlets, as well as the results obtained on the application of the genetic transformation and the cryopreservation procedures to holm oak embryogenic cultures, are also presented.}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Martínez, María Teresa and San-José, María del Carmen and Arrillaga, Isabel and Cano, Vanesa and Morcillo, Marián and Cernadas, María José and Corredoira, Elena}, month = mar, year = {2019}, pages = {239}, file = {Martínez et al. - 2019 - Holm Oak Somatic Embryogenesis Current Status and.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\YX9VHDSW\\Martínez et al. - 2019 - Holm Oak Somatic Embryogenesis Current Status and.pdf:application/pdf}, } @article{nic-can_somatic_2015, title = {Somatic {Embryogenesis}: {Identified} {Factors} that {Lead} to {Embryogenic} {Repression}. {A} {Case} of {Species} of the {Same} {Genus}}, volume = {10}, issn = {1932-6203}, shorttitle = {Somatic {Embryogenesis}}, url = {https://dx.plos.org/10.1371/journal.pone.0126414}, doi = {10.1371/journal.pone.0126414}, abstract = {Somatic embryogenesis is a powerful biotechnological tool for the mass production of economically important cultivars. Due to the cellular totipotency of plants, somatic cells under appropriate conditions are able to develop a complete functional embryo. During the induction of somatic embryogenesis, there are different factors involved in the success or failure of the somatic embryogenesis response. Among these factors, the origin of the explant, the culture medium and the in vitro environmental conditions have been the most studied. However, the secretion of molecules into the media has not been fully addressed. We found that the somatic embryogenesis of Coffea canephora, a highly direct embryogenic species, is disrupted by the metabolites secreted from C. arabica, a poorly direct embryogenic species. These metabolites also affect DNA methylation. Our results show that the abundance of two major phenolic compounds, caffeine and chlorogenic acid, are responsible for inhibiting somatic embryogenesis in C. canephora.}, language = {en}, number = {6}, urldate = {2021-06-29}, journal = {PLoS ONE}, author = {Nic-Can, Geovanny I. and Galaz-Ávalos, Rosa M. and De-la-Peña, Clelia and Alcazar-Magaña, Armando and Wrobel, Kazimierz and Loyola-Vargas, Víctor M.}, editor = {Candela, Hector}, month = jun, year = {2015}, pages = {e0126414}, file = {Nic-Can et al. - 2015 - Somatic Embryogenesis Identified Factors that Lea.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\NZFY2VYQ\\Nic-Can et al. - 2015 - Somatic Embryogenesis Identified Factors that Lea.pdf:application/pdf}, } @article{berenguer_inhibition_2017, title = {Inhibition of {Histone} {H3K9} {Methylation} by {BIX}-01294 {Promotes} {Stress}-{Induced} {Microspore} {Totipotency} and {Enhances} {Embryogenesis} {Initiation}}, volume = {8}, issn = {1664-462X}, url = {http://journal.frontiersin.org/article/10.3389/fpls.2017.01161/full}, doi = {10.3389/fpls.2017.01161}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Berenguer, Eduardo and Bárány, Ivett and Solís, María-Teresa and Pérez-Pérez, Yolanda and Risueño, María C. and Testillano, Pilar S.}, month = jun, year = {2017}, pages = {1161}, file = {Berenguer et al. - 2017 - Inhibition of Histone H3K9 Methylation by BIX-0129.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\WZ9KH6RA\\Berenguer et al. - 2017 - Inhibition of Histone H3K9 Methylation by BIX-0129.pdf:application/pdf}, } @article{pais_somatic_2019, title = {Somatic {Embryogenesis} {Induction} in {Woody} {Species}: {The} {Future} {After} {OMICs} {Data} {Assessment}}, volume = {10}, issn = {1664-462X}, shorttitle = {Somatic {Embryogenesis} {Induction} in {Woody} {Species}}, url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00240/full}, doi = {10.3389/fpls.2019.00240}, abstract = {Very early somatic embryogenesis has been recognized as a powerful method to propagate plants in vitro. For some woody species and in particular for some coniferous trees, somatic embryogenesis induction has become a routine procedure. For the majority, the application of this technology presents yet many limitations especially due to the genotype, the induction conditions, the number of embryos produced, maturation, and conversion, among other factors that compromise the systematic use of somatic embryogenesis for commercial purposes especially of woody species and forest trees in particular. The advancements obtained on somatic embryogenesis in Arabidopsis and the development of OMIC technologies allowed the characterization of genes and the corresponding proteins that are conserved in woody species. This knowledge will help in understanding the molecular mechanisms underlying the complex regulatory networks that control somatic embryogenesis in woody plants. In this revision, we report on developments of OMICs (genomics, transcriptomics, metabolomics, and proteomics) applied to somatic embryogenesis induction and its contribution for understanding the change of fate giving rise to the expression of somatic embryogenesis competence.}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Pais, Maria Salomé}, month = mar, year = {2019}, pages = {240}, file = {Pais - 2019 - Somatic Embryogenesis Induction in Woody Species .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\PGHMUWKI\\Pais - 2019 - Somatic Embryogenesis Induction in Woody Species .pdf:application/pdf;leva annarita, 2012.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\HH3TV3KN\\leva annarita, 2012.pdf:application/pdf}, } @article{mendez-hernandez_signaling_2019-1, title = {Signaling {Overview} of {Plant} {Somatic} {Embryogenesis}}, volume = {10}, issn = {1664-462X}, url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00077/full}, doi = {10.3389/fpls.2019.00077}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Méndez-Hernández, Hugo A. and Ledezma-Rodríguez, Maharshi and Avilez-Montalvo, Randy N. and Juárez-Gómez, Yary L. and Skeete, Analesa and Avilez-Montalvo, Johny and De-la-Peña, Clelia and Loyola-Vargas, Víctor M.}, month = feb, year = {2019}, pages = {77}, file = {Méndez-Hernández et al. - 2019 - Signaling Overview of Plant Somatic Embryogenesis.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\IWFSZGPU\\Méndez-Hernández et al. - 2019 - Signaling Overview of Plant Somatic Embryogenesis.pdf:application/pdf}, } @incollection{leva_prerequisite_2012, title = {The {Prerequisite} of the {Success} in {Plant} {Tissue} {Culture}: {High} {Frequency} {Shoot} {Regeneration}}, isbn = {978-953-51-0787-3}, shorttitle = {The {Prerequisite} of the {Success} in {Plant} {Tissue} {Culture}}, url = {http://www.intechopen.com/books/recent-advances-in-plant-in-vitro-culture/the-prerequisite-of-the-success-in-plant-tissue-culture-high-frequency-shoot-regeneration}, language = {en}, urldate = {2021-06-30}, booktitle = {Recent {Advances} in {Plant} in vitro {Culture}}, publisher = {InTech}, author = {Yildiz, Mustafa}, editor = {Leva, Annarita}, month = oct, year = {2012}, doi = {10.5772/51097}, file = {Yildiz - 2012 - The Prerequisite of the Success in Plant Tissue Cu.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\5NQNCB9X\\Yildiz - 2012 - The Prerequisite of the Success in Plant Tissue Cu.pdf:application/pdf}, } @book{wen_ethylene_2015, address = {Dordrecht}, title = {Ethylene in {Plants}}, isbn = {978-94-017-9483-1 978-94-017-9484-8}, url = {http://link.springer.com/10.1007/978-94-017-9484-8}, language = {en}, urldate = {2021-07-01}, publisher = {Springer Netherlands}, editor = {Wen, Chi-Kuang}, year = {2015}, doi = {10.1007/978-94-017-9484-8}, file = {Wen - 2015 - Ethylene in Plants.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\GRBXW9CW\\Wen - 2015 - Ethylene in Plants.pdf:application/pdf}, } @article{jha_baby_2018-1, title = {{BABY} {BOOM} ({BBM}): a candidate transcription factor gene in plant biotechnology}, volume = {40}, issn = {0141-5492, 1573-6776}, shorttitle = {{BABY} {BOOM} ({BBM})}, url = {http://link.springer.com/10.1007/s10529-018-2613-5}, doi = {10.1007/s10529-018-2613-5}, abstract = {Plants have evolved a number of transcription factors, many of which are implicated in signaling pathways as well as regulating diverse cellular functions. BABY BOOM (BBM), transcription factors of the AP2/ERF family are key regulators of plant cell totipotency. Ectopic expression of the BBM gene, originally identified in Brassica napus, has diverse functions in plant cell proliferation, growth and development without exogenous growth regulators. The BBM gene has been implicated to play an important role as a gene marker in multiple signaling developmental pathways in plant development. This review focuses on recent advances in our understanding of a member of the AP2 family of transcription factor BBM in plant biotechnology including plant embryogenesis, cell proliferation, regeneration, plant transformation and apogamy. Recent discoveries about the BBM gene will inevitably help to unlock the long-standing mysteries of different biological mechanisms of plant cells.}, language = {en}, number = {11-12}, urldate = {2021-07-04}, journal = {Biotechnol Lett}, author = {Jha, Priyanka and Kumar, Vijay}, month = dec, year = {2018}, pages = {1467--1475}, file = {Jha and Kumar - 2018 - BABY BOOM (BBM) a candidate transcription factor .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\WJ6C97MY\\Jha and Kumar - 2018 - BABY BOOM (BBM) a candidate transcription factor .pdf:application/pdf}, } @article{inoue_identifcation_2001, title = {Identifcation of {CRE1} as {A} {Cytokinin} {Receptor} from {Arabidopsis}}, volume = {409 (6823)}, doi = {doi:10.1038/35059117}, abstract = {Cytokinins are a class of plant hormones that are central to the regulation of cell division and differentiation in plants1,2. It has been proposed that they are detected by a two-component system, because overexpression of the histidine kinase gene CKI1 induces typical cytokinin responses3 and genes for a set of response regulators of two-component systems can be induced by cytokinins4,5. Two-component systems use a histidine kinase as an environmental sensor and rely on a phosphorelay for signal transduction. They are common in microorganisms, and are also emerging as important signal detection routes in plants6±9. Here we report the identi®cation of a cytokinin receptor. We identi®ed Arabidopsis cre1 (cytokinin response 1) mutants, which exhibited reduced responses to cytokinins. The mutated gene CRE1 encodes a histidine kinase. CRE1 expression conferred a cytokinindependent growth phenotype on a yeast mutant that lacked the endogenous histidine kinase SLN1 (ref. 10), providing direct evidence that CRE1 is a cytokinin receptor. We also provide evidence that cytokinins can activate CRE1 to initiate phosphorelay signalling.}, journal = {Nature}, author = {Inoue, Tsutomu and Higuchi, Masayuki and Hashimoto, Yukari and Seki, Motoaki and Kobayashi, Masatomo and Kato, Tomohiko and Tabata, Satoshi and Shinozak, Kazuo and Kakimoto, Tatsuo}, month = feb, year = {2001}, pages = {1060--1063}, } @article{anderson_zygotic_2017, title = {The {Zygotic} {Transition} {Is} {Initiated} in {Unicellular} {Plant} {Zygotes} with {Asymmetric} {Activation} of {Parental} {Genomes}}, volume = {43}, issn = {15345807}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580717308183}, doi = {10.1016/j.devcel.2017.10.005}, abstract = {The zygotic transition, from a fertilized egg to an embryo, is central to animal and plant reproduction. Animal embryos depend upon maternally provided factors until zygotic genome activation (ZGA). In plants, the timing and parental genome contributions to ZGA are unresolved. Here, we use the flowering plant Oryza sativa (rice) to characterize transcriptomes of time-staged isogenic and hybrid zygotes following fertilization. Large-scale transcriptomic changes were observed in unicellular zygotes, including upregulation of S-phase genes, a characteristic of ZGA. The parental contributions to ZGA were highly asymmetric. Zygotic transcription was primarily from the maternal genome and included genes for basic cellular processes. Transcription of the paternal genome was highly restricted but unexpectedly included genes encoding putative pluripotency factors expressed at the onset of ZGA. Thus, distinct transcriptional activities are exhibited by the parental genomes during the initiation of embryogenesis, which presumptively derive from divergent pre-zygotic transcriptional states established in the gametes.}, language = {en}, number = {3}, urldate = {2021-07-07}, journal = {Developmental Cell}, author = {Anderson, Sarah N. and Johnson, Cameron S. and Chesnut, Joshua and Jones, Daniel S. and Khanday, Imtiyaz and Woodhouse, Margaret and Li, Chenxin and Conrad, Liza J. and Russell, Scott D. and Sundaresan, Venkatesan}, month = nov, year = {2017}, pages = {349--358.e4}, file = {Anderson et al. - 2017 - The Zygotic Transition Is Initiated in Unicellular.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\QRC6HYT3\\Anderson et al. - 2017 - The Zygotic Transition Is Initiated in Unicellular.pdf:application/pdf}, } @article{anderson_zygotic_2017-1, title = {The {Zygotic} {Transition} {Is} {Initiated} in {Unicellular} {Plant} {Zygotes} with {Asymmetric} {Activation} of {Parental} {Genomes}}, volume = {43}, issn = {15345807}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580717308183}, doi = {10.1016/j.devcel.2017.10.005}, abstract = {The zygotic transition, from a fertilized egg to an embryo, is central to animal and plant reproduction. Animal embryos depend upon maternally provided factors until zygotic genome activation (ZGA). In plants, the timing and parental genome contributions to ZGA are unresolved. Here, we use the flowering plant Oryza sativa (rice) to characterize transcriptomes of time-staged isogenic and hybrid zygotes following fertilization. Large-scale transcriptomic changes were observed in unicellular zygotes, including upregulation of S-phase genes, a characteristic of ZGA. The parental contributions to ZGA were highly asymmetric. Zygotic transcription was primarily from the maternal genome and included genes for basic cellular processes. Transcription of the paternal genome was highly restricted but unexpectedly included genes encoding putative pluripotency factors expressed at the onset of ZGA. Thus, distinct transcriptional activities are exhibited by the parental genomes during the initiation of embryogenesis, which presumptively derive from divergent pre-zygotic transcriptional states established in the gametes.}, language = {en}, number = {3}, urldate = {2021-07-07}, journal = {Developmental Cell}, author = {Anderson, Sarah N. and Johnson, Cameron S. and Chesnut, Joshua and Jones, Daniel S. and Khanday, Imtiyaz and Woodhouse, Margaret and Li, Chenxin and Conrad, Liza J. and Russell, Scott D. and Sundaresan, Venkatesan}, month = nov, year = {2017}, pages = {349--358.e4}, file = {Anderson et al. - 2017 - The Zygotic Transition Is Initiated in Unicellular.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\KQPILEYE\\Anderson et al. - 2017 - The Zygotic Transition Is Initiated in Unicellular.pdf:application/pdf}, } @article{panda_biochemical_2018, title = {Biochemical and molecular characterisation of exogenous cytokinin application on grain filling in rice}, doi = {https://doi.org/10.1186/s12870-018-1279-4}, abstract = {Abstract Background: Poor filling of grains in the basal spikelets of large size panicles bearing numerous spikelets has been a major limitation in attempts to increase the rice production to feed the world’s increasing population. Considering that biotechnological intervention could play important role in overcoming this limitation, the role of cytokinin in grain filling was investigated based on the information on cell proliferating potential of the hormone and reports of its high accumulation in immature seeds. Results: A comparative study considering two rice varieties differing in panicle compactness, lax-panicle Upahar and compact-panicle OR-1918, revealed significant difference in grain filling, cytokinin oxidase (CKX) activity and expression, and expression of cell cycle regulators and cytokinin signaling components between the basal and apical spikelets of OR-1918, but not of Upahar. Exogenous application of cytokinin (6-Benzylaminopurine, BAP) to OR-1918 improved grain filling significantly, and this was accompanied by a significant decrease in expression and activity of CKX, particularly in the basal spikelets where the activity of CKX was significantly higher than that in the apical spikelets. Cytokinin application also resulted in significant increase in expression of cell cycle regulators like cyclin dependent kinases and cyclins in the basal spikelets that might be facilitating cell division in the endosperm cells by promoting G1/S phase and G2/M phase transition leading to improvement in grain filling. Expression studies of type-A response regulator (RR) component of cytokinin signaling indicated possible role of OsRR3, OsRR4 and OsRR6 as repressors of CKX expression, much needed for an increased accumulation of CK in cells. Furthermore, the observed effect of BAP might not be solely because of it, but also because of induced synthesis of trans-zeatin (tZ) and N 6 2 -(Δ -isopentenyl)adenine (iP), as reflected from accumulation of tZR (tZ riboside) and iPR (iP riboside), and significantly enhanced expression of an isopentenyl transferase (IPT) isoform. Conclusion: The results suggested that seed-specific overexpression of OsRR4 and OsRR6, and more importantly of IPT9 could be an effective biotechnological intervention towards improving the CK level of the developing caryopses leading to enhanced grain filling in rice cultivars bearing large panicles with numerous spikelets, and thereby increasing their yield potential. Keywords: Cytokinin oxidase, Cytokinin treatment, 6-Benzylaminopurine, Cell cycle regulators, Chromosomal endoreduplication, Oryza sativa}, language = {english}, journal = {BMC Plant Biology}, author = {Panda, Binay Bhushan and {1} and {Sudhanshu Sekhar} and {2} and {, Sushant Kumar Dash} and {2} and {, Lamboder Behera} and {and Birendra Prasad Shaw}}, year = {2018}, pages = {19}, } @article{shaopei_cytokinin_2014, title = {{CYTOKININ} {OXIDASE}/{DEHYDROGENASE4} {Integrates} {Cytokinin} and {Auxin} {Signaling} to {Control} {Rice} {Crown} {Root} {Formation}}, volume = {165}, url = {www.plantphyshiol.com}, abstract = {Crown roots constitute the majority of the rice (Oryza sativa) root system and play an important role in rice growth and development. However, the molecular mechanism of crown root formation in rice is not well understood. Here, we characterized a rice dominant mutant, root enhancer1 (ren1-D), which was observed to exhibit a more robust root system, increased crown root number, and reduced plant height. Molecular and genetic analyses revealed that these phenotypes are caused by the activation of a cytokinin oxidase/dehydrogenase (CKX) family gene, OsCKX4. Subcellular localization demonstrated that OsCKX4 is a cytosolic isoform of CKX. OsCKX4 is predominantly expressed in leaf blades and roots. It is the dominant CKX, preferentially expressed in the shoot base where crown root primordia are produced, underlining its role in root initiation. OsCKX4 is induced by exogenous auxin and cytokinin in the roots. Furthermore, one-hybrid assays revealed that OsCKX4 is a direct binding target of both the auxin response factor OsARF25 and the cytokinin response regulators OsRR2 and OsRR3. Overexpression and RNA interference of OsCKX4 confi rmed that OsCKX4 plays a positive role in crown root formation. Moreover, expression analysis revealed a signifi cant alteration in the expression of auxin-related genes in the ren1-D mutants, indicating that the OsCKX4 mediates crown root development by integrating the interaction between cytokinin and auxin. Transgenic plants harboring OsCKX4 under the control of the root-specifi c promoter RCc3 displayed enhanced root development without affecting their shoot parts, suggesting that this strategy could be a powerful tool in rice root engineering}, journal = {Plant Physiology}, author = {Shaopei, Gao and {, FanXu, WeiWang, Xiaohong Sun, JinfangChu,BaodongCai,} and {Yuqi Feng, and Chengcai Chu}}, month = jul, year = {2014}, pages = {1035--1046}, } @article{noauthor_notitle_nodate-1, } @article{fraiture_biotech_2016, title = {Biotech rice: {Current} developments and future detection challenges in food and feed chain}, volume = {52}, issn = {09242244}, shorttitle = {Biotech rice}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0924224415302028}, doi = {10.1016/j.tifs.2016.03.011}, abstract = {Background: To improve agricultural practices and the food/feed security, plant breeding techniques were developed, including transgenesis commonly using Agrobacterium tumefaciens or biolistic technologies. To guarantee the traceability of GMO in food/feed chain and the consumer's freedom of choice, regulatory frameworks were established in many countries around the world, such as in Europe. Their implementations, including detection systems usually based on qPCR, are becoming complex and expensive regarding the number of analysis to perform. Moreover, the dispersion of publicly available information about developed GMO prevents to accurately estimate the efficiency of the standard detection system applied to unauthorized GMO.}, language = {en}, urldate = {2021-10-15}, journal = {Trends in Food Science \& Technology}, author = {Fraiture, Marie-Alice and Roosens, Nancy H.C. and Taverniers, Isabel and De Loose, Marc and Deforce, Dieter and Herman, Philippe}, month = jun, year = {2016}, pages = {66--79}, file = {Fraiture et al. - 2016 - Biotech rice Current developments and future dete.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\DSQHSDZZ\\Fraiture et al. - 2016 - Biotech rice Current developments and future dete.pdf:application/pdf}, } @article{kieber_cytokinins_2014-2, title = {Cytokinins}, volume = {e0168}, issn = {1543-8120}, url = {http://www.bioone.org/doi/10.1199/tab.0168}, doi = {10.1199/tab.0168}, language = {en}, urldate = {2021-10-15}, journal = {The Arabidopsis Book}, author = {Kieber, Joseph J. and Schaller, G. Eric}, month = jan, year = {2014}, pages = {1--35}, file = {Kieber and Schaller - 2014 - Cytokinins.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\T3LGNAHV\\Kieber and Schaller - 2014 - Cytokinins.pdf:application/pdf}, } @article{yamburenko_functional_2020, title = {Functional {Analysis} of the {Rice} {Type}-{B} {Response} {Regulator} {RR22}}, volume = {11}, issn = {1664-462X}, url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.577676/full}, doi = {10.3389/fpls.2020.577676}, language = {en}, urldate = {2021-10-15}, journal = {Front. Plant Sci.}, author = {Yamburenko, Maria V. and Worthen, Jennifer M. and Zeenat, Asyia and Azhar, Beenish J. and Swain, Swadhin and Couitt, Adam R. and Shakeel, Samina N. and Kieber, Joseph J. and Schaller, G. Eric}, month = nov, year = {2020}, pages = {577676}, file = {Yamburenko et al. - 2020 - Functional Analysis of the Rice Type-B Response Re.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\CRV7G6GD\\Yamburenko et al. - 2020 - Functional Analysis of the Rice Type-B Response Re.pdf:application/pdf}, } @article{fanata_n-glycan_2013, title = {N-glycan maturation is crucial for cytokinin-mediated development and cellulose synthesis in \textit{{Oryza} sativa}}, volume = {73}, issn = {09607412}, url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.12087}, doi = {10.1111/tpj.12087}, abstract = {To explore the physiological significance of N-glycan maturation in the plant Golgi apparatus, gnt1, a mutant with loss of N-acetylglucosaminyltransferase I (GnTI) function, was isolated in Oryza sativa. gnt1 exhibited complete inhibition of N-glycan maturation and accumulated high-mannose N-glycans. Phenotypic analyses revealed that gnt1 shows defective post-seedling development and incomplete cell wall biosynthesis, leading to symptoms such as failure in tiller formation, brittle leaves, reduced cell wall thickness, and decreased cellulose content. The developmental defects of gnt1 ultimately resulted in early lethality without transition to the reproductive stage. However, callus induced from gnt1 seeds could be maintained for periods, although it exhibited a low proliferation rate, small size, and hypersensitivity to salt stress. Shoot regeneration and dark-induced leaf senescence assays indicated that the loss of GnTI function results in reduced sensitivity to cytokinin in rice. Reduced expression of A-type O. sativa response regulators that are rapidly induced by cytokinins in gnt1 confirmed that cytokinin signaling is impaired in the mutant. These results strongly support the proposed involvement of N-glycan maturation in transport as well as in the function of membrane proteins that are synthesized via the endomembrane system.}, language = {en}, number = {6}, urldate = {2021-10-15}, journal = {Plant J}, author = {Fanata, Wahyu Indra Duwi and Lee, Kyoung Hwan and Son, Bo Hwa and Yoo, Jae Yong and Harmoko, Rikno and Ko, Ki Seong and Ramasamy, Nirmal Kumar and Kim, Kyung Hwa and Oh, Doo-Byoung and Jung, Hyun Suk and Kim, Jae-Yean and Lee, Sang Yeol and Lee, Kyun Oh}, month = mar, year = {2013}, pages = {966--979}, file = {Fanata et al. - 2013 - N-glycan maturation is crucial for cytokinin-media.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\4L3XJZUF\\Fanata et al. - 2013 - N-glycan maturation is crucial for cytokinin-media.pdf:application/pdf}, } @article{arisandi_effect_2020, title = {Effect of ethylene inhibitor, type of auxin, and type of sugar on anther culture of local {East} {Java} aromatic rice varieties}, volume = {23}, issn = {1975-9479, 2005-8276}, url = {https://link.springer.com/10.1007/s12892-020-00045-6}, doi = {10.1007/s12892-020-00045-6}, abstract = {Breeding using the double haploid approach has been used in accelerating the rice breeding process. However, the main obstacle in the application of this technique in rice is the low level of callus formation and their regeneration into haploid plants. Based on these issues, this research is aimed at developing the best method for obtaining double haploid plants through anther culture using three kinds of aromatic rice of Indonesian local varieties. Anthers of Pendok, Genjah Arum, and Merah Wangi varieties were cultured in callus induction media which were either supplemented with different types of carbon sources, or auxins and ethylene inhibitors. However, the application of different sugar types did not significantly affect callus formation of Pendok and Genjah Arum. However, auxin treatment showed NAA to be more efficient for the callus induction of Pendok, while 2,4-D had no effect on callus induction in all tested varieties. The addition of ethylene inhibitor successfully induced callus formation of Merah Wangi varieties, while the rates of Pendok and Genjah Arum were not significantly affected. Callus of three plant lines were then regenerated into plantlet in regeneration media. Of the three callus varieties used, only Pendok could regenerate into plantlets and grow into adult haploid plants.}, language = {en}, number = {4}, urldate = {2021-10-15}, journal = {J. Crop Sci. Biotechnol.}, author = {Arisandi, Dewi Puspa and Paradisa, Fragaria Vesca and Sugiharto, Bambang and Avivi, Sholeh and Fanata, Wahyu Indra Duwi}, month = sep, year = {2020}, pages = {367--373}, file = {Arisandi et al. - 2020 - Effect of ethylene inhibitor, type of auxin, and t.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\99PX8565\\Arisandi et al. - 2020 - Effect of ethylene inhibitor, type of auxin, and t.pdf:application/pdf}, } @article{dewi_role_2008, title = {{ROLE} {OF} {POLYAMINES} {IN} {INHIBITION} {OF} {ETHYLENE} {BIOSYNTHESIS} {AND} {THEIR} {EFFECTS} {ON} {RICE} {ANTHER} {CULTURE} {DEVELOPMENT}}, abstract = {The polyamines such as putrescine, spermidine, and spermine were reported to increase green plant regeneration in rice anther culture. Low response of anther culture of rice sub-species indica may be improved with the addition of putrescine in the culture media. Four experiments were conducted to study the role of polyamines in inhibition of ethylene biosynthesis and their effects on rice anther culture development. Anthers of two subspecies of rice, indica (IR64, Krowal, Jatiluhur) and japonica (Taipei 309) were cultured onto media supplemented with putrescine (N6P) and without putrescine (N6). Young panicles containing the anthers at mid-to-late nucleate microspores were cold pretreated at 5 + 2°C and incubated in the dark for 8 days before the anthers were cultured. Results showed that medium without putrescine produced an earlier senescence of indica rice anther than that of japonica. The addition of 10-3 M putrescine into the culture media inhibited ethylene biosynthesis as anther senescence delayed, increased the three polyamines contents, and decreased the ACC content as well as ACC oxydase activity in anther-derived calli. In the anther and anther-derived calli of subspecies indica, the total polyamines content was lower (10.14 nM g-1 anther and 8.48 nM g-1 calli) than that of subspecies japonica (12.61 nM g-1 anther and 10.16 nM g-1 calli), whereas the ethylene production was higher (32.31 nM g-1 anther and 2.48 nM g-1 calli) than the japonica (31.68 nM g-1 anther and 1.76 nM g-1 calli). This study suggests that application of 10-3 M putrescine in anther culture of rice subspecies indica improves androgenesis by inhibiting early senescence of cultured anthers and enhancing embryo or callus formation from microspores.}, language = {en}, author = {Dewi, Iswari S and Purwoko, Bambang S}, year = {2008}, pages = {8}, file = {Dewi and Purwoko - ROLE OF POLYAMINES IN INHIBITION OF ETHYLENE BIOSY.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\FZLTQSJU\\Dewi and Purwoko - ROLE OF POLYAMINES IN INHIBITION OF ETHYLENE BIOSY.pdf:application/pdf}, } @article{khanday_rice_2020, title = {Rice embryogenic trigger {BABY} {BOOM1} promotes somatic embryogenesis by upregulation of auxin biosynthesis genes}, url = {http://biorxiv.org/lookup/doi/10.1101/2020.08.24.265025}, abstract = {ABSTRACT Somatic embryogenesis, a powerful tool for clonal propagation and for plant transformation, involves cellular reprogramming of differentiated somatic cells to acquire pluripotency. Somatic embryogenesis can be induced by treating explants with plant growth regulators. However, several plant species including agronomically important cereal crops remain recalcitrant to dedifferentiation and transformation except from embryonic tissues. Somatic embryogenesis can also be induced by ectopic expression of select embryonic factors, including in cereals by BABY BOOM (BBM) transcription factors. How BBM genes bypass the need for exogenous hormones is not well understood. Here, we investigated downstream targets during induction of somatic embryogenesis in rice by OsBBM1 (( Oryza sativa BABY BOOM1 ). Transient induction of OsBBM1 led to the upregulation of auxin biosynthesis OsYUCCA genes. Continued induction of OsBBM1 resulted in somatic embryogenesis without the need for exogenous auxins. Genetic mutant analysis of OsBBM1 downstream targets, OsYUCCA6, OsYUCCA7 and OsYUCCA9 , show that they are required for normal rice development including root and shoot development. Somatic embryogenic potential of OsYUCCA triple mutants was highly compromised despite the presence of exogenous auxin. Additionally, we show that somatic embryogenesis induction by exogenous auxin in rice requires functional BBM genes. Thus, OsBBM1 mediated cellular reprogramming and somatic embryogenesis likely involves increased localized auxin through direct upregulation of OsYUCCA genes. This study reveals mechanistic details of how somatic embryogenesis is established in differentiated tissues in rice, a monocot model and agronomically important cereal crop, with the potential utility to improve regeneration from tissue culture for recalcitrant plants in future. One-sentence summary Rice BABY BOOM1 induces somatic embryogenesis from differentiated tissues by promoting auxin biosynthesis through direct upregulation of YUCCA genes.}, language = {en}, urldate = {2021-10-15}, author = {Khanday, Imtiyaz and Santos-Medellín, Christian and Sundaresan, Venkatesan}, month = aug, year = {2020}, doi = {10.1101/2020.08.24.265025}, file = {Khanday et al. - 2020 - Rice embryogenic trigger BABY BOOM1 promotes somat.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\4Y82NYD8\\Khanday et al. - 2020 - Rice embryogenic trigger BABY BOOM1 promotes somat.pdf:application/pdf}, } @article{fanata_daya_2020-1, title = {{DAYA} {REGENERASI} {KALUS} {DAN} {TUNAS} {IN} {VITRO} {PADI} {VARIETAS} {TARABAS} {PADA} {BERBAGAI} {KONSENTRASI} 2,4-{D}}, volume = {7}, issn = {2548-611X, 2442-2606}, url = {http://ejurnal.bppt.go.id/index.php/JBBI/article/view/4404}, doi = {10.29122/jbbi.v7i2.4404}, abstract = {The Agricultural Research and Development Agency and the West Java Provincial Government are developing new superior varieties with Japonica rice standards, namely the Tarabas variety. However, the equivalence of somatic embryogenesis ability of Tarabas rice with original Japonica variety has not been reported. In this study, the frequency of callus regeneration of Tarabas vs Hwayoung rice varieties was compared. Induction of callus from mature embryos with several concentrations of 2,4-D showed the same extent of callus formation in both rice varieties. Callus induced by 1 ppm of 2,4-D showed the higher rate of shoot formation. On the other hand, percentage of callus formation of Tarabas rice was not affected by the increase of 2,4-D concentrations and was able to show 100\% regeneration rate at the fourth week in the regeneration medium, although the shoot growth was not as fast as those from medium with 1 ppm 2,4-D. Therefore, these results suggest that Tarabas variety has a somatic embryogenesis capacity equivalent to that of japonica rice and has the potential as research objects in the field of biotechnology.}, language = {id}, number = {2}, urldate = {2021-10-15}, journal = {J Bioteknol Biosains Indones}, author = {Fanata, Wahyu Indra Duwi and Qudsiyah, Dalliyah Hadrotul}, month = dec, year = {2020}, pages = {250--258}, file = {Fanata and Qudsiyah - 2020 - DAYA REGENERASI KALUS DAN TUNAS IN VITRO PADI VARI.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\QFBIH3CL\\Fanata and Qudsiyah - 2020 - DAYA REGENERASI KALUS DAN TUNAS IN VITRO PADI VARI.pdf:application/pdf}, } @article{ali_improved_2021-1, title = {Improved {Anther} {Culture} {Media} for {Enhanced} {Callus} {Formation} and {Plant} {Regeneration} in {Rice} ({Oryza} sativa {L}.)}, volume = {10}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/10/5/839}, doi = {10.3390/plants10050839}, abstract = {Anther culture technique is the most viable and efficient method of producing homozygous doubled haploid plants within a short period. However, the practical application of this technology in rice improvement is still limited by various factors that influence culture efficiency. The present study was conducted to determine the effects of two improved anther culture media, Ali-1 (A1) and Ali-2 (A2), a modified N6 medium, to enhance the callus formation and plant regeneration of japonica, indica, and hybrids of indica and japonica cross. The current study demonstrated that genotype and media had a significant impact (p {\textless} 0.001) on both callus induction frequency and green plantlet regeneration efficiency. The use of the A1 and A2 medium significantly enhanced callus induction frequency of japonica rice type, Nipponbare, and the hybrids of indica × japonica cross (CXY6, CXY24, and Y2) but not the indica rice type, NSIC Rc480. However, the A1 medium is found superior to the N6 medium as it significantly improved the green plantlet regeneration efficiency of CXY6, CXY24, and Y2 by almost 36\%, 118\%, and 277\%, respectively. Furthermore, it substantially reduced the albino plantlet regeneration of the induced callus in two hybrids (CXY6 and Y2). Therefore, the improved anther culture medium A1 can produce doubled haploid rice plants for indica × japonica, which can be useful in different breeding programs that will enable the speedy development of rice varieties for resource-poor farmers.}, language = {en}, number = {5}, urldate = {2021-10-27}, journal = {Plants}, author = {Ali, Jauhar and Nicolas, Katrina Leslie C. and Akther, Shahana and Torabi, Azerkhsh and Ebadi, Ali Akbar and Marfori-Nazarea, Corinne M. and Mahender, Anumalla}, month = apr, year = {2021}, pages = {839}, file = {Ali et al. - 2021 - Improved Anther Culture Media for Enhanced Callus .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\WRCUGBFP\\Ali et al. - 2021 - Improved Anther Culture Media for Enhanced Callus .pdf:application/pdf}, } @article{amer_relationship_1997, title = {The relationship between green spot initiation and plantlet regeneration of wheat callus grown under short-term conditions}, volume = {50}, doi = {https://doi.org/10.1023/A:1005855912655}, abstract = {Six wheat genotypes (three varieties and three whole chromosome substitution lines) were used to analyse the relationship between the initiation of green spots and plant regeneration under short-term tissue culture conditions. The highest percentage of green spot initiation was observed after one week culture on maintenance medium (M-Med.). The calluses producing green spots at the end of the first and second week on M-Med. were highest in regeneration frequency compared to late green spot producing ones. A significant positive correlation between green spot initiation and plantlet regeneration was observed for calluses showing green spots within the first two weeks on M-Med. and was decreased for calluses producing green spots afterwards. The results suggest that by selecting only calluses producing early green spots the experimental efficiency will be increased.}, language = {en}, author = {Amer, I M Ben and Borner, A}, year = {1997}, pages = {67--69}, file = {Amer and Borner - The relationship between green spot initiation and.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\T2QG63RP\\Amer and Borner - The relationship between green spot initiation and.pdf:application/pdf}, } @article{rezaei-moghadam_effect_2012, title = {Effect of {Turmeric} and {Carrot} {Seed} {Extracts} on {Serum} {Liver} {Biomarkers} and {Hepatic} {Lipid} {Peroxidation}, {Antioxidant} {Enzymes} and {Total} {Antioxidant} {Status} in {Rats}}, url = {http://bi.tbzmed.ac.ir/JournalIssues/AllIssues/Volume2Issue3/4201223.aspx}, doi = {10.5681/BI.2012.020}, abstract = {Introduction: Pathogenic role of free radicals are well known in various metabolic diseases. They originate from internal and external sources of body. Essential roles of antioxidant defense system for cellular redox regulation and free radical scavenging activity were described in this study. Many in vitro investigations have shown that turmeric (TE) and carrot seed extract (CSE) exhibits to possess antioxidant activities. In this study, we evaluated the antioxidant potentials of ethanolic TE and CSE based on in vivo experiment in the rats. Methods: Animals were assigned to six groups: the 1st and 2nd groups were control groups and 2nd group received 0.2 ml dimethyl sulphoxide as vehicle treated group; other four experimental groups received different doses of TE (100, 200 mg/kg b.w.) and CSE (200, 400 mg/kg b.w.) by gavages, respectively for a period of one month. The indicators of oxidative stress, lipids peroxidation, markers of hepatocyte injury and biliary function markers were measured. Results: The levels of superoxide dismutase, catalase, and glutathione peroxidase were significantly stimulated in the hepatic tissue of treatment groups. The malondialdehyde contents of liver tissue were significantly reduced in the groups fed with TE and CSE. Serum levels of alanine aminotransferase, aspartate aminotransferase and alkaline phosphatase, in treated groups were found to be significantly decreased, whereas albumin and total protein increased as compared to the control groups (P less than 0.05). Conclusion: this study showed that the regular intake of TE and CSE through the diet can improve antioxidant status and inhibit peroxidation activity in the liver tissue so that using these extracts may protect tissue oxidative stress.}, language = {en}, urldate = {2021-11-03}, journal = {BioImpacts; ISSN 2228-5660}, author = {Rezaei-Moghadam, Adel and Mohajeri, Daryoush and Rafiei, Behnam and Dizaji, Rana and Azhdari, Asghar and Yeganehzad, Mahdi and Shahidi, Maryamossadat and Mazani, Mohammad}, year = {2012}, note = {Medium: text/html Publisher: Tabriz University of Medical Sciences}, keywords = {610 Medical sciences; Medicine}, annote = {SeriesInformation BioImpacts; ISSN 2228-5660}, file = {Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\ZDLZI3ZE\\Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:application/pdf}, } @article{rezaei-moghadam_effect_2012-1, title = {Effect of {Antioxidants} and {Carbohydrates} in {Callus} {Cultures} of {Taxus} brevifolia: {Evaluation} of {Browning}, {Callus} {Growth}, {Total} {Phenolics} and {Paclitaxel} {Production}}, volume = {1}, url = {http://bi.tbzmed.ac.ir/JournalIssues/AllIssues/Volume2Issue3/4201223.aspx}, doi = {10.5681/BI.2012.020}, abstract = {Introduction: Pathogenic role of free radicals are well known in various metabolic diseases. They originate from internal and external sources of body. Essential roles of antioxidant defense system for cellular redox regulation and free radical scavenging activity were described in this study. Many in vitro investigations have shown that turmeric (TE) and carrot seed extract (CSE) exhibits to possess antioxidant activities. In this study, we evaluated the antioxidant potentials of ethanolic TE and CSE based on in vivo experiment in the rats. Methods: Animals were assigned to six groups: the 1st and 2nd groups were control groups and 2nd group received 0.2 ml dimethyl sulphoxide as vehicle treated group; other four experimental groups received different doses of TE (100, 200 mg/kg b.w.) and CSE (200, 400 mg/kg b.w.) by gavages, respectively for a period of one month. The indicators of oxidative stress, lipids peroxidation, markers of hepatocyte injury and biliary function markers were measured. Results: The levels of superoxide dismutase, catalase, and glutathione peroxidase were significantly stimulated in the hepatic tissue of treatment groups. The malondialdehyde contents of liver tissue were significantly reduced in the groups fed with TE and CSE. Serum levels of alanine aminotransferase, aspartate aminotransferase and alkaline phosphatase, in treated groups were found to be significantly decreased, whereas albumin and total protein increased as compared to the control groups (P less than 0.05). Conclusion: this study showed that the regular intake of TE and CSE through the diet can improve antioxidant status and inhibit peroxidation activity in the liver tissue so that using these extracts may protect tissue oxidative stress.}, language = {en}, urldate = {2021-11-03}, journal = {BioImpacts; ISSN 2228-5660}, author = {Rezaei-Moghadam, Adel and Mohajeri, Daryoush and Rafiei, Behnam and Dizaji, Rana and Azhdari, Asghar and Yeganehzad, Mahdi and Shahidi, Maryamossadat and Mazani, Mohammad}, year = {2012}, note = {Medium: text/html Publisher: Tabriz University of Medical Sciences}, keywords = {610 Medical sciences; Medicine}, pages = {37--45}, annote = {SeriesInformation BioImpacts; ISSN 2228-5660}, file = {Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\FF6QIVAX\\Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:application/pdf}, } @article{rezaei-moghadam_effect_2012-2, title = {Effect of {Turmeric} and {Carrot} {Seed} {Extracts} on {Serum} {Liver} {Biomarkers} and {Hepatic} {Lipid} {Peroxidation}, {Antioxidant} {Enzymes} and {Total} {Antioxidant} {Status} in {Rats}}, url = {http://bi.tbzmed.ac.ir/JournalIssues/AllIssues/Volume2Issue3/4201223.aspx}, doi = {10.5681/BI.2012.020}, abstract = {Introduction: Pathogenic role of free radicals are well known in various metabolic diseases. They originate from internal and external sources of body. Essential roles of antioxidant defense system for cellular redox regulation and free radical scavenging activity were described in this study. Many in vitro investigations have shown that turmeric (TE) and carrot seed extract (CSE) exhibits to possess antioxidant activities. In this study, we evaluated the antioxidant potentials of ethanolic TE and CSE based on in vivo experiment in the rats. Methods: Animals were assigned to six groups: the 1st and 2nd groups were control groups and 2nd group received 0.2 ml dimethyl sulphoxide as vehicle treated group; other four experimental groups received different doses of TE (100, 200 mg/kg b.w.) and CSE (200, 400 mg/kg b.w.) by gavages, respectively for a period of one month. The indicators of oxidative stress, lipids peroxidation, markers of hepatocyte injury and biliary function markers were measured. Results: The levels of superoxide dismutase, catalase, and glutathione peroxidase were significantly stimulated in the hepatic tissue of treatment groups. The malondialdehyde contents of liver tissue were significantly reduced in the groups fed with TE and CSE. Serum levels of alanine aminotransferase, aspartate aminotransferase and alkaline phosphatase, in treated groups were found to be significantly decreased, whereas albumin and total protein increased as compared to the control groups (P less than 0.05). Conclusion: this study showed that the regular intake of TE and CSE through the diet can improve antioxidant status and inhibit peroxidation activity in the liver tissue so that using these extracts may protect tissue oxidative stress.}, language = {en}, urldate = {2021-11-03}, journal = {BioImpacts; ISSN 2228-5660}, author = {Rezaei-Moghadam, Adel and Mohajeri, Daryoush and Rafiei, Behnam and Dizaji, Rana and Azhdari, Asghar and Yeganehzad, Mahdi and Shahidi, Maryamossadat and Mazani, Mohammad}, year = {2012}, note = {Medium: text/html Publisher: Tabriz University of Medical Sciences}, keywords = {610 Medical sciences; Medicine}, annote = {SeriesInformation BioImpacts; ISSN 2228-5660}, file = {Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\IH36XH3J\\Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:application/pdf}, } @article{khosroushahi_effect_2011, title = {Effect of {Antioxidants} and {Carbohydrates} in {Callus} {Cultures} of {Taxus} brevifolia: {Evaluation} of {Browning}, {Callus} {Growth}, {Total} {Phenolics} and {Paclitaxel} {Production}}, volume = {1(1)}, url = {http://bi.tbzmed.ac.ir/JournalIssues/AllIssues/Volume2Issue3/4201223.aspx}, doi = {10.5681/BI.2012.020}, abstract = {Introduction: To control the tissue browning phenomenon, callus growth, total phenolics and paclitaxel production, in the current investigation, we evaluated the effects of citric acid and ascorbic acid (as antioxidants) and glucose, fructose and sucrose in callus cultures of Taxus brevifolia. Methods: To obtain healthy callus/cell lines of Taxus brevifolia, the effects of two antioxidants ascorbic acid (100-1000 mg/L) and citric acid (50-500 mg/L), and three carbohydrates (glucose, fructose and sucrose (5-10 g/L)) were studied evaluating activities of polyphenol oxidase (PPO) and peroxidase (PO) enzymes, callus growth/browning, total phenolics and paclitaxel production. Results: These antioxidants (ascorbic acid and citric acid) failed to show significant effects on callus growth, browning intensity or paclitaxel production. However, the carbohydrates imposed significant effects on the parameters studied. High concentrations of both glucose and sucrose increased the browning intensity, thus decreased callus growth. Glucose increased paclitaxel production, but sucrose decreased it. Conclusion: These results revealed that the browning phenomenon can be controlled through supplementation of the growth media with glucose, sucrose (5 g/L) and fructose (10 g/L), while increased paclitaxel production can be obtain by the optimized media supplemented with glucose (10 g/L), sucrose and fructose (5 g/L).}, language = {en}, urldate = {2021-11-03}, journal = {BioImpacts; ISSN 2228-5660}, author = {Khosroushahi, Ahmad Yari and Hossein, Naderi-Manesh and Henrik, Toft Simonsen}, year = {2011}, note = {Medium: text/html Publisher: Tabriz University of Medical Sciences}, keywords = {610 Medical sciences; Medicine}, pages = {37--45}, annote = {SeriesInformation BioImpacts; ISSN 2228-5660}, file = {Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\779TCQT3\\Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:application/pdf}, } @article{dewi_role_2008-1, title = {Role of {Polyamines} in {Inhibition} {Of} {Ethylene} {Biosynthesis} and {Their} {Effects} on {Rice} {Anther} {Culture} {Development}}, volume = {9 (2)}, doi = {DOI: 10.21082/ijas.v9n2.2008.p60-67}, abstract = {The polyamines such as putrescine, spermidine, and spermine were reported to increase green plant regeneration in rice anther culture. Low response of anther culture of rice sub-species indica may be improved with the addition of putrescine in the culture media. Four experiments were conducted to study the role of polyamines in inhibition of ethylene biosynthesis and their effects on rice anther culture development. Anthers of two subspecies of rice, indica (IR64, Krowal, Jatiluhur) and japonica (Taipei 309) were cultured onto media supplemented with putrescine (N6P) and without putrescine (N6). Young panicles containing the anthers at mid-to-late nucleate microspores were cold pretreated at 5 + 2°C and incubated in the dark for 8 days before the anthers were cultured. Results showed that medium without putrescine produced an earlier senescence of indica rice anther than that of japonica. The addition of 10-3 M putrescine into the culture media inhibited ethylene biosynthesis as anther senescence delayed, increased the three polyamines contents, and decreased the ACC content as well as ACC oxydase activity in anther-derived calli. In the anther and anther-derived calli of subspecies indica, the total polyamines content was lower (10.14 nM g-1 anther and 8.48 nM g-1 calli) than that of subspecies japonica (12.61 nM g-1 anther and 10.16 nM g-1 calli), whereas the ethylene production was higher (32.31 nM g-1 anther and 2.48 nM g-1 calli) than the japonica (31.68 nM g-1 anther and 1.76 nM g-1 calli). This study suggests that application of 10-3 M putrescine in anther culture of rice subspecies indica improves androgenesis by inhibiting early senescence of cultured anthers and enhancing embryo or callus formation from microspores.}, language = {en}, author = {Dewi, Iswari S and Bambang, S. Purwoko}, year = {2008}, pages = {60--67}, file = {Dewi and Purwoko - ROLE OF POLYAMINES IN INHIBITION OF ETHYLENE BIOSY.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\SH2W73MG\\Dewi and Purwoko - ROLE OF POLYAMINES IN INHIBITION OF ETHYLENE BIOSY.pdf:application/pdf}, } @article{yasmin_ethylene_2013, title = {Ethylene influences in vitro regeneration frequency in the {FR13A} rice harbouring the {SUB1A} gene}, volume = {72}, issn = {0167-6903, 1573-5087}, url = {http://link.springer.com/10.1007/s10725-013-9840-5}, doi = {10.1007/s10725-013-9840-5}, abstract = {Many studies have examined the effects of ethylene on in vitro plant growth and development, often with controversial results. Ethylene accumulates in culture vessels due to both the release from the tissues and the physical entrapment due to the need for closed containers. This hormone has several effects on plant regeneration, depending on the plant species and even the cultivar. A prerequisite for ethylene use for in vitro culture is thus to formulate a specific protocol for the genotype of interest. In rice, ethylene is a key regulator of adaptation strategies to low oxygen environments. In particular, the SUBMERGENCE1A (SUB1A) gene, when present, drives the acclimation response which when activated by ethylene produced by submerged plants leads to adaptation through reduced plant growth and ethanolic fermentation enhancement. This gene is restricted to a limited number of rice for which a very specific response to ethylene is expected, whatever the source. This paper reports the regeneration differences between a SUB1A rice landrace (indica-aus, FR13A) and a non-SUB1A variety (japonica, Nipponbare). Our results suggest that regeneration protocols with exogenous ethylene precursors supply are required for the FR13A rice harbouring the SUB1A gene to overcome the problem of low regeneration efficiency.}, language = {en}, number = {1}, urldate = {2021-11-03}, journal = {Plant Growth Regul}, author = {Yasmin, Sabina and Mensuali-Sodi, Anna and Perata, Pierdomenico and Pucciariello, Chiara}, month = jan, year = {2013}, pages = {97--103}, file = {Yasmin et al. - 2014 - Ethylene influences in vitro regeneration frequenc.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\TMNDRJWZ\\Yasmin et al. - 2014 - Ethylene influences in vitro regeneration frequenc.pdf:application/pdf}, } @article{kakimoto_ckll_1996, title = {{CKll}, a {Histidine} {Kinase} {Homolog} {Implicated} in {Cytokinin} {Signal} {Transduction}}, volume = {274 (5289)}, doi = {doi:10.1126/science.274.5289.982}, abstract = {Although cytokinin plays a central role in plant development, little is known about cytokinin signal transduction. Five Arabidopsis thaliana mutants that exhibit typical cytokinin responses, including rapid cell division and shoot formation in tissue culture in the absence of exogenous cytokinin, were isolated by activation transferred DNA tagging. A gene, CKI1, which was tagged in four of the five mutants and induced typical cytokinin responses after introduction and overexpression in plants, was cloned. CKll encodes a protein similar to the two-component regulators. These results suggest that CKll is involved in cytokinin signal transduction, possibly as a cytokinin receptor.}, journal = {Science}, author = {Kakimoto, Tatsuo}, year = {1996}, pages = {982--985}, } @article{hirose_overexpression_2007, title = {Overexpression of a {Type}-{A} {Response} {Regulator} {Alters} {Rice} {Morphology} and {Cytokinin} {Metabolism}}, volume = {48}, issn = {0032-0781, 1471-9053}, url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcm022}, doi = {10.1093/pcp/pcm022}, language = {en}, number = {3}, urldate = {2021-11-03}, journal = {Plant and Cell Physiology}, author = {Hirose, N. and Makita, N. and Kojima, M. and Kamada-Nobusada, T. and Sakakibara, H.}, month = jan, year = {2007}, pages = {523--539}, file = {Hirose et al. - 2007 - Overexpression of a Type-A Response Regulator Alte.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\ETVJKFI3\\Hirose et al. - 2007 - Overexpression of a Type-A Response Regulator Alte.pdf:application/pdf}, } @article{ren_genome-wide_2009, title = {Genome-{Wide} {Comparative} {Analysis} of {Type}-{A} {Arabidopsis} {Response} {Regulator} {Genes} by {Overexpression} {Studies} {Reveals} {Their} {Diverse} {Roles} and {Regulatory} {Mechanisms} in {Cytokinin} {Signaling}}, volume = {19}, issn = {1001-0602, 1748-7838}, url = {http://www.nature.com/articles/cr200988}, doi = {10.1038/cr.2009.88}, abstract = {Cytokinin is a critical growth regulator for various aspects of plant growth and development. In Arabidopsis, cytokinin signaling is mediated by a two-component system-based phosphorelay that transmits a signal from the receptors, through histidine phosphotransfer proteins, to the downstream response regulators (ARRs). Of these ARRs, type-A ARR genes, whose transcription can be rapidly induced by cytokinin, act as negative regulators of cytokinin signaling. However, because of functional redundancy, the function of type-A ARR genes in plant growth and development is not well understood by analyzing loss-of-function mutants. In this study, we performed a comparative functional study on all ten type-A ARR genes by analyzing transgenic plants overexpressing these ARR genes fused to a MYC epitope tag. Overexpression of ARR genes results in a variety of cytokinin-associated phenotypes. Notably, overexpression of different ARR transgenes causes diverse phenotypes, even between phylogenetically closely-related gene pairs, such as within the ARR3-ARR4 and ARR5-ARR6 pairs. We found that the accumulation of a subset of ARR proteins (ARR3, ARR5, ARR7, ARR16 and ARR17; possibly ARR8 and ARR15) is increased by MG132, a specific proteasomal inhibitor, indicating that stability of these proteins is regulated by proteasomal degradation. Moreover, similar to that of previously characterized ARR5, ARR6 and ARR7, stability of ARR16 and ARR17, possibly including ARR8 and ARR15, is regulated by cytokinin. These results suggest that type-A ARR proteins are regulated by a combinatorial mechanism involving both the cytokinin and proteasome pathways, thereby executing distinctive functions in plant growth and development.}, language = {en}, number = {10}, urldate = {2021-11-03}, journal = {Cell Res}, author = {Ren, Bo and Liang, Yan and Deng, Yan and Chen, Qingguo and Zhang, Jian and Yang, Xiaohui and Zuo, Jianru}, month = oct, year = {2009}, pages = {1178--1190}, file = {Ren et al. - 2009 - Genome-wide comparative analysis of type-A Arabido.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\N5S3TELR\\Ren et al. - 2009 - Genome-wide comparative analysis of type-A Arabido.pdf:application/pdf}, } @article{chatfield_ethylene_2008, title = {Ethylene and shoot regeneration: hookless1 modulates de novo shoot organogenesis in {Arabidopsis} thaliana}, volume = {27}, issn = {0721-7714, 1432-203X}, shorttitle = {Ethylene and shoot regeneration}, url = {http://link.springer.com/10.1007/s00299-007-0496-3}, doi = {10.1007/s00299-007-0496-3}, abstract = {We have investigated the role of ethylene in shoot regeneration from cotyledon explants of Arabidopsis thaliana. We examined the ethylene sensitivity of five ecotypes representing both poor and prolific shoot regenerators and identified Dijon-G, a poor regenerator, as an ecotype with dramatically enhanced ethylene sensitivity. However, inhibiting ethylene action with silver nitrate generally reduced shoot organogenesis in ecotypes capable of regeneration. In ecotype Col-0, we found that ethyleneinsensitive mutants (etr1-1, ein2-1, ein4, ein7) exhibited reduced shoot regeneration rates, whereas constitutive ethylene response mutants (ctr1-1, ctr1-12) increased the proportion of explants producing shoots. Our experiments with ethylene over-production mutants (eto1, eto2 and eto3) indicate that the ethylene biosynthesis inhibitor gene, ETO1, can act as an inhibitor of shoot regeneration. Pharmacological elevation of ethylene levels was also found to significantly increase the proportion of explants regenerating shoots. We determined that the hookless1 (hls1-1) mutant, a suppressor of the ethylene response phenotypes of ctr1 and eto1 mutants, is capable of dramatically enhancing shoot organogenesis. The effects of ACC and loss of HLS1 function on shoot organogenesis were found to be largely additive.}, language = {en}, number = {4}, urldate = {2021-11-03}, journal = {Plant Cell Rep}, author = {Chatfield, Steven P. and Raizada, Manish N.}, month = apr, year = {2008}, pages = {655--666}, file = {Chatfield and Raizada - 2008 - Ethylene and shoot regeneration hookless1 modulat.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\ELJEHUGH\\Chatfield and Raizada - 2008 - Ethylene and shoot regeneration hookless1 modulat.pdf:application/pdf}, } @article{adkins_rice_1990, title = {Rice {Callus} {Physiology} - {Identification} of {Volatile} {Emissions} and {Their} {Effects} on {Culture} {Growth}}, volume = {78}, issn = {0031-9317, 1399-3054}, url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1399-3054.1990.tb05237.x}, doi = {10.1111/j.1399-3054.1990.tb05237.x}, language = {en}, number = {4}, urldate = {2021-11-03}, journal = {Physiol Plant}, author = {Adkins, S. W. and Shiraishi, T. and McComb, J. A.}, month = apr, year = {1990}, pages = {526--531}, file = {Adkins et al. - 1990 - Rice callus physiology - Identification of volatil.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\MQ34B3F8\\Adkins et al. - 1990 - Rice callus physiology - Identification of volatil.pdf:application/pdf}, } @article{kobayashi_effect_nodate, title = {Effect of {Carbon} {Dioxide} and {Ethylene} on {Berberine} {Production} and {Cell} {Browning} {In} {Thalictrum} {Minus} {Cell} {Cultures}}, volume = {9}, doi = {DOI: 10.1007/BF00232104}, language = {en}, journal = {Plant Cell Reports}, author = {Kobayashi, Y and Fukui, H and Tabata, M}, pages = {496--499}, file = {Kobayashi et al. - Effect of carbon dioxide and ethylene on berberine.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\443SC2XX\\Kobayashi et al. - Effect of carbon dioxide and ethylene on berberine.pdf:application/pdf}, } @article{boutilier_ectopic_2002, title = {Ectopic {Expression} of {BABY} {BOOM} {Triggers} a {Conversion} from {Vegetative} to {Embryonic} {Growth}}, volume = {14}, issn = {1040-4651, 1532-298X}, url = {https://academic.oup.com/plcell/article/14/8/1737-1749/6009796}, doi = {10.1105/tpc.001941}, language = {en}, number = {8}, urldate = {2021-11-03}, journal = {Plant Cell}, author = {Boutilier, Kim and Offringa, Remko and Sharma, Vijay K. and Kieft, Henk and Ouellet, Thérèse and Zhang, Lemin and Hattori, Jiro and Liu, Chun-Ming and van Lammeren, André A. M. and Miki, Brian L. A. and Custers, Jan B. M. and van Lookeren Campagne, Michiel M.}, month = aug, year = {2002}, pages = {1737--1749}, file = {Boutilier et al. - 2002 - Ectopic Expression of BABY BOOM Triggers a Convers.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\CJIC9FTQ\\Boutilier et al. - 2002 - Ectopic Expression of BABY BOOM Triggers a Convers.pdf:application/pdf}, } @article{lowe_morphogenic_2016-1, title = {Morphogenic {Regulators} {Baby} {Boom} and {Wuschel} {Improve} {Monocot} {Transformation}}, volume = {28}, issn = {1040-4651, 1532-298X}, url = {https://academic.oup.com/plcell/article/28/9/1998-2015/6098336}, doi = {10.1105/tpc.16.00124}, language = {en}, number = {9}, urldate = {2021-11-03}, journal = {Plant Cell}, author = {Lowe, Keith and Wu, Emily and Wang, Ning and Hoerster, George and Hastings, Craig and Cho, Myeong-Je and Scelonge, Chris and Lenderts, Brian and Chamberlin, Mark and Cushatt, Josh and Wang, Lijuan and Ryan, Larisa and Khan, Tanveer and Chow-Yiu, Julia and Hua, Wei and Yu, Maryanne and Banh, Jenny and Bao, Zhongmeng and Brink, Kent and Igo, Elizabeth and Rudrappa, Bhojaraja and Shamseer, Pm and Bruce, Wes and Newman, Lisa and Shen, Bo and Zheng, Peizhong and Bidney, Dennis and Falco, Carl and Register, Jim and Zhao, Zuo-Yu and Xu, Deping and Jones, Todd and Gordon-Kamm, William}, month = sep, year = {2016}, pages = {1998--2015}, file = {Lowe et al. - 2016 - Morphogenic Regulators Baby boom and Wus.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\53K9K5VQ\\Lowe et al. - 2016 - Morphogenic Regulators Baby boom and Wus.pdf:application/pdf}, } @article{noauthor_notitle_nodate-2, } @article{mostafiz_efficient_2018-2, title = {Efficient {Callus} {Induction} and {Regeneration} in {Selected} {Indica} {Rice}}, volume = {8}, issn = {2073-4395}, url = {http://www.mdpi.com/2073-4395/8/5/77}, doi = {10.3390/agronomy8050077}, abstract = {An efficient callus induction and in vitro regeneration were developed using plant growth regulators, carbon sources, and basal media for three selected Malaysian wetland rice varieties (MR220, MR220-CL2, and MR232) and one upland variety (Bario). Effect of plant growth regulator (PGR) was carried out using four different concentrations (1–4 mg/L) of 2,4-D (2, 4-dichlorophenoxyacetic acid), and NAA (1-naphthalene acetic acid) (2.5, 5.0, 7.5, and 10 mg/L) with optimized 2,4-D. Effects of carbon sources (maltose and sorbitol), and basal media (MS, N6, and LS) were also studied with optimized PGR to maximize the induction of regenerable calli. This study found that all four varieties exhibited high frequency of callus induction on MS (Murashige and Skoog) medium that was supplemented with 3 mg/L 2,4-D and 30 g/L maltose. Callus induction frequencies in the cases of MR220, MR220-CL2, MR232, and Bario were found to be 76\%, 94\%, 85\%, and 42\% respectively. Morphological analysis through scanning electron microscopy (SEM) and histological analysis revealed the embryogenicity of the induced callus. In the regeneration study, it was observed that combination of 2 mg/L BAP (6-benzylaminopurine), 2 mg/L Kin (Kinetin) and 0.5 mg/L NAA supplemented MS medium has the potential to promote regeneration of selected indica rice varieties with higher regeneration percentage, i.e., 82\% (MR220-CL2), 68\% (both in MR220 and MR232), and 40\% (Bario). The optimized conditions for callus formation and regeneration can be useful for biotechnological practices for the genetic improvement of Malaysian indica rice.}, language = {en}, number = {5}, urldate = {2021-04-22}, journal = {Agronomy}, author = {Mostafiz, Suraiya Binte and Wagiran, Alina}, month = may, year = {2018}, pages = {77}, file = {agronomy-08-00077 (1).pdf:C\:\\Users\\Syafira\\Zotero\\storage\\V45G5I85\\agronomy-08-00077 (1).pdf:application/pdf}, } @article{zhang_common_2020-3, title = {A common wild rice-derived {BOC1} allele reduces callus browning in indica rice transformation}, volume = {11}, issn = {2041-1723}, url = {http://www.nature.com/articles/s41467-019-14265-0}, doi = {10.1038/s41467-019-14265-0}, abstract = {Abstract Callus browning, a common trait derived from the indica rice cultivar ( Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 ( BOC1 ) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession ( Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1 , which consequently improves the genetic transformation efficiency. The presence of a Tourist -like miniature inverted-repeat transposable element ( Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation.}, language = {en}, number = {1}, urldate = {2021-04-22}, journal = {Nat Commun}, author = {Zhang, Kun and Su, Jingjing and Xu, Min and Zhou, Zhihui and Zhu, Xiaoyang and Ma, Xin and Hou, Jingjing and Tan, Lubin and Zhu, Zuofeng and Cai, Hongwei and Liu, Fengxia and Sun, Hongying and Gu, Ping and Li, Chen and Liang, Yuntao and Zhao, Wensheng and Sun, Chuanqing and Fu, Yongcai}, month = dec, year = {2020}, pages = {443}, file = {boc browning of callus.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\MEH95BSK\\boc browning of callus.pdf:application/pdf}, } @article{cai_synergistic_2020-1, title = {Synergistic {Effect} of {NaCl} {Pretreatment} and {PVP} on {Browning} {Suppression} and {Callus} {Induction} from {Petal} {Explants} of {Paeonia} {Lactiflora} {Pall}. ‘{Festival} {Maxima}’}, volume = {9}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/9/3/346}, doi = {10.3390/plants9030346}, abstract = {Browning is prevalent in tissue cultures of Paeonia lactiflora Pall. (herbaceous peony), and severely affects and restricts the growth and differentiation of the explants. In this study, dipping excised explants in a sodium chloride (NaCl) solution as a pretreatment, adding polyvinyl pyrrolidone (PVP) to the culture medium, storing planted explants at 4 ◦C for 24 h, and transferring planted explants to a new medium after 24 h were considered as browning-suppression methods in tissue cultures of herbaceous peony ‘Festival Maxima’. The treated petal explants were cultured in a culture room with a 16-hour photoperiod, 25 ◦C temperature, and 80\% relative humidity in darkness for 4 to 8 weeks. The results demonstrated that dipping excised explants in a 0.5 g·L−1 NaCl solution, adding 0.5 g·L−1 PVP to the medium, storing planted explants at 4 ◦C for 24 h, and transferring planted explants to the same fresh medium after 24 h could effectively inhibit browning. Adding PVP to the medium led to the greatest browning suppression percentage of 95\%. Storing planted explants at 4 ◦C for 24 h reduced the effectiveness of other treatments in suppressing browning. After 8 weeks, dipping excised explants in a NaCl solution resulted in the highest callus induction percentage of 75\%, while storing explants at 4 ◦C for 24 h suppressed callus formation. It was observed in all treatments that decreases in browning was accompanied with higher levels of phenols and lower activities of phenylalanine ammonia-lyase (PAL) and polyphenoloxidase (PPO). Overall, the results suggest that dipping in a NaCl solution was effective in alleviating the browning issues of herbaceous peony tissue cultures, and had positive synergistic effects with PVP on browning suppression and callus induction.}, language = {en}, number = {3}, urldate = {2021-04-23}, journal = {Plants}, author = {Cai, Xuan and Wei, Hao and Liu, Chen and Ren, Xiuxia and Thi, Luc The and Jeong, Byoung Ryong}, month = mar, year = {2020}, pages = {346}, file = {Cai et al. - 2020 - Synergistic Effect of NaCl Pretreatment and PVP on.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\7VR7DP5N\\Cai et al. - 2020 - Synergistic Effect of NaCl Pretreatment and PVP on.pdf:application/pdf;ethylene and interaction with other.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\3V94RUSH\\ethylene and interaction with other.pdf:application/pdf}, } @article{liang_effects_2019-1, title = {Effects of {Sucrose} and {Browning} {Inhibitors} on {Callus} {Proliferation} and {Anti}-{Browning} of {Chinese} {Kale}}, volume = {252}, issn = {1755-1315}, url = {https://iopscience.iop.org/article/10.1088/1755-1315/252/2/022018}, doi = {10.1088/1755-1315/252/2/022018}, abstract = {The hypocotyl of Chinese kale ‘Cutiaoyusun’ was used as explants, the effects of the different concentrations of sucrose and different browning inhibitors (activated carbon, polyvinylpyrrolidone, and ascorbic acid) on the callus proliferation and anti-browning of Chinese kale were studied in this study. The results showed that the proliferation medium with 20 gꞏL-1 sucrose had the best effects on the proliferation and anti-browning of Chinese kale callus, and its proliferation rate was the highest, reaching 213.5\%, and the browning rate was as low as 27.77\%. In addition, adding 0.2 gꞏL-1 ascorbic acid to the culture medium can significantly promote callus proliferation and reduce browning rate. In this treatment, the callus had the lowest browning rate of 19.45\% and the highest proliferation rate of 266.98\%, and the morphology of the callus was friable. This study lays a foundation for future research in molecular biology and genetic improvement in Chinese kale.}, language = {en}, urldate = {2021-04-23}, journal = {IOP Conf. Ser.: Earth Environ. Sci.}, author = {Liang, Sha and He, Ying and Zheng, Hao and Yuan, Qiao and Zhang, Fen and Sun, Bo}, month = jul, year = {2019}, pages = {022018}, file = {Liang et al. - 2019 - Effects of Sucrose and Browning Inhibitors on Call.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\MUQY2CKB\\Liang et al. - 2019 - Effects of Sucrose and Browning Inhibitors on Call.pdf:application/pdf}, } @article{centre_national_de_recherche_agronomique_cnra_laboratoire_central_de_biotechnologies_lcb_km_17_adiopodoume_01_bp_1740_abidjan_01_cote_divoire_effect_2017, title = {Effect of antioxidants on the callus induction and the development of somatic embryogenesis of cocoa [{Theobroma} cacao ({L}.)]}, volume = {11}, issn = {18352693, 18352707}, url = {http://www.cropj.com/kouassi_11_1_2017_25_31.pdf}, doi = {10.21475/ajcs.2017.11.01.pne174}, abstract = {The browning of plant tissue and organs is a major constraint in tissue culture of cocoa (Theobroma cacao L.). This study aims to evaluate callogenic and embryogenic potentialities of three genotypes cocoa on culture media supplemented with different types and concentrations of antioxidants. Polyvinylpyrrolidone (PVP), ascorbic acid, silver nitrate and cysteine were used as antioxidant agents. The explants staminode and petal were excised from immature buds of the flowers of genotypes cocoa C1, C8 and C14. The results showed that the induction rate of callus derived from the petal and the staminode varied with the genotypes tested. Except 21 mg/l of silver nitrate, the others antioxidants used namely ascorbic acid, PVP and cysteine have enhanced the callus induction of the genotype C8. In comparison with the control, the callus browning of the three genotypes was reduced two to three times when the culture media were supplemented with various concentrations of the silver nitrate. After 72 days of culture, somatic embryos were induced on callus derived from the petal explants with all the studied genotypes. Addition of PVP (300 mg/l) in the induction medium improved the rate of somatic embryos of the genotypes C1 and C14. The improvement of responses to somatic embryogenesis in reducing the rate of browning of cultures will allow a mass production of the high-yield cocoa genotypes.}, language = {en}, number = {1}, urldate = {2021-04-23}, journal = {Aust J Crop Sci}, author = {{Centre National de Recherche Agronomique (CNRA), Laboratoire Central de Biotechnologies (LCB), KM 17 Adiopodoumé, 01 BP 1740 Abidjan 01, Côte d’Ivoire} and Modeste, Kouassi Kan and Eliane, Manlé Tokpapon and {Centre National de Recherche Agronomique (CNRA), Laboratoire Central de Biotechnologies (LCB), KM 17 Adiopodoumé, 01 BP 1740 Abidjan 01, Côte d’Ivoire} and {Université Nangui Abrogoua, UFR Sciences de la Nature, Laboratoire de Biologie et Amélioration des Productions Végétales, 02 BP 801 Abidjan 02, Côte d’Ivoire} and Daouda, Koné and {Université Félix Houphouët-Boigny, UFR Biosciences, Laboratoire de Génétique, 22 BP 582 Abidjan 22, Côte d’Ivoire} and Brahima, Soumahoro André and {Université Nangui Abrogoua, UFR Sciences de la Nature, Laboratoire de Biologie et Amélioration des Productions Végétales, 02 BP 801 Abidjan 02, Côte d’Ivoire} and Tchoa, Koné and {Université Nangui Abrogoua, UFR Sciences de la Nature, Laboratoire de Biologie et Amélioration des Productions Végétales, 02 BP 801 Abidjan 02, Côte d’Ivoire} and Kouablan, Koffi Edmond and {Centre National de Recherche Agronomique (CNRA), Laboratoire Central de Biotechnologies (LCB), KM 17 Adiopodoumé, 01 BP 1740 Abidjan 01, Côte d’Ivoire} and Mongomaké, Koné and {Université Nangui Abrogoua, UFR Sciences de la Nature, Laboratoire de Biologie et Amélioration des Productions Végétales, 02 BP 801 Abidjan 02, Côte d’Ivoire}}, month = jan, year = {2017}, pages = {25--31}, file = {antioksidan rendah pada browning callus.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\4I95SV3I\\antioksidan rendah pada browning callus.pdf:application/pdf}, } @article{modeste_effect_2017-1, title = {Effect of antioxidants on the callus induction and the development of somatic embryogenesis of cocoa [{Theobroma} cacao ({L}.)]}, volume = {11}, issn = {18352693, 18352707}, url = {http://www.cropj.com/kouassi_11_1_2017_25_31.pdf}, doi = {10.21475/ajcs.2017.11.01.pne174}, abstract = {The browning of plant tissue and organs is a major constraint in tissue culture of cocoa (Theobroma cacao L.). This study aims to evaluate callogenic and embryogenic potentialities of three genotypes cocoa on culture media supplemented with different types and concentrations of antioxidants. Polyvinylpyrrolidone (PVP), ascorbic acid, silver nitrate and cysteine were used as antioxidant agents. The explants staminode and petal were excised from immature buds of the flowers of genotypes cocoa C1, C8 and C14. The results showed that the induction rate of callus derived from the petal and the staminode varied with the genotypes tested. Except 21 mg/l of silver nitrate, the others antioxidants used namely ascorbic acid, PVP and cysteine have enhanced the callus induction of the genotype C8. In comparison with the control, the callus browning of the three genotypes was reduced two to three times when the culture media were supplemented with various concentrations of the silver nitrate. After 72 days of culture, somatic embryos were induced on callus derived from the petal explants with all the studied genotypes. Addition of PVP (300 mg/l) in the induction medium improved the rate of somatic embryos of the genotypes C1 and C14. The improvement of responses to somatic embryogenesis in reducing the rate of browning of cultures will allow a mass production of the high-yield cocoa genotypes.}, language = {en}, number = {1}, urldate = {2021-04-23}, journal = {Aust J Crop Sci}, author = {Modeste, Kouassi Kan and Eliane, Manlé Tokpapon and Daouda, Kone and Brahima, Soumahoro André and Tchoa, Kone and Kouablan, Koffi Edmond and Mongomake, Koné}, month = jan, year = {2017}, pages = {25--31}, file = {antioksidan rendah pada browning callus.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\4NTJQLKY\\antioksidan rendah pada browning callus.pdf:application/pdf}, } @article{kuklin_ethylene_2014-1, title = {Ethylene {Impact} on {Somatic} {Embryogenesis}: {Biotechnological} {Considerations}}, volume = {9}, issn = {1310-2818, 1314-3530}, shorttitle = {Ethylene {Impact} on {Somatic} {Embryogenesis}}, url = {http://www.tandfonline.com/doi/abs/10.1080/13102818.1995.10818856}, doi = {10.1080/13102818.1995.10818856}, abstract = {The gaseous plant hormone ethylene affects somatic emb1yogenesis in various ways depending on the species or explants used. Inclusion of ethylene action inhibitors, name{\textbackslash}textasciitildev silver ions in culture media increased somatic embryogenesis in some species. Large scale (bioreactor) yields of somatic emb1yos were less than these ji·01n flask cultures. Ethylene depletion from the bioreactors due to aeration is considered as a possible reason for the decrease in somatic emb1yogenesis. Ethylene is discussed as a physiological marker related to emb1yogenic potential. {\textbackslash}textasciitildeVound ethylene evolved after transformation experiments might have some inhibit01:v role on transformation but results are contradictory. Ethylene plays different roles in long term storage (low and ambient temperatures) of emb1yogenic cultures. Use of transgenic technology in ethylene biosynthesis reduction is discussed as a way to understanding ethylene role in somatic emb(vogenesis.}, language = {en}, number = {4}, urldate = {2021-04-23}, journal = {Biotechnology \& Biotechnological Equipment}, author = {Kuklin, A.}, month = apr, year = {2014}, pages = {12--19}, file = {Kuklin - 1995 - Ethylene Impact on Somatic Embryogenesis Biotechn.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\ANG5PWNP\\Kuklin - 1995 - Ethylene Impact on Somatic Embryogenesis Biotechn.pdf:application/pdf;ethylen.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\DRIS8ZQA\\ethylen.pdf:application/pdf}, } @article{illyas_ahmad_effect_2013-1, title = {Effect of 2,4-{D} on {Embryogenic} {Callus} {Induction} of {Malaysian} indica {Rice} ({Oryza} sativa {L}.) {Cultivars} {MR123} and {MR127}}, volume = {64}, issn = {2180-3722, 0127-9696}, url = {https://journals.utm.my/index.php/jurnalteknologi/article/view/2048}, doi = {10.11113/jt.v64.2048}, abstract = {The aim of this study is to study the effect of various concentrations of 2,4-D on embryogenic callus induction of indica rice MR123 cultivar and MR127 cultivar using mature seeds. Optimal media for induction of callus of both cultivars was MS basal media supplemented with 30g/L sucrose, 500mg/L glutamine and 500mg/L proline supplemented with 2.5 mg/L 2,4-D. The highest percentage of callus induction was 70\% and 76\% for MR123 and MR127 respectively. Both cultivars produced an embryogenic callus from scutellum after a week in culture with white-yellowish in color. The viability tested using Evans blue show callus obtained was embryogenic. This simple protocol using staining method could be used for screening embryogenic callus before further experiments can be conducted.}, language = {en}, number = {2}, urldate = {2021-04-23}, journal = {Jurnal Teknologi}, author = {Illyas Ahmad, Fauziah and Johan, Nur Shafiqoh and Wagiran, Alina}, month = aug, year = {2013}, file = {Illyas Ahmad et al. - 2013 - Effect of 2,4-D on Embryogenic Callus Induction of.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\JW87YW9V\\Illyas Ahmad et al. - 2013 - Effect of 2,4-D on Embryogenic Callus Induction of.pdf:application/pdf}, } @article{ikeuchi_plant_2013-2, title = {Plant {Callus}: {Mechanisms} of {Induction} and {Repression}}, volume = {25}, issn = {1040-4651, 1532-298X}, shorttitle = {Plant {Callus}}, url = {https://academic.oup.com/plcell/article/25/9/3159-3173/6097899}, doi = {10.1105/tpc.113.116053}, language = {en}, number = {9}, urldate = {2021-04-23}, journal = {Plant Cell}, author = {Ikeuchi, Momoko and Sugimoto, Keiko and Iwase, Akira}, month = sep, year = {2013}, pages = {3159--3173}, file = {Ikeuchi et al. - 2013 - Plant Callus Mechanisms of Induction and Repressi.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\7UZM4GR9\\Ikeuchi et al. - 2013 - Plant Callus Mechanisms of Induction and Repressi.pdf:application/pdf;zhang2020 indica japonica hybrid.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\A54A7A7S\\zhang2020 indica japonica hybrid.pdf:application/pdf}, } @article{a_libin_callus_2012-2, title = {Callus induction and plant regeneration of {Sarawak} rice ({Oryza} sativa {L}.) variety {Biris}}, volume = {7}, issn = {1991637X}, url = {http://www.academicjournals.org/ajar/abstracts/abstracts/Abstracts%202012/7Aug/Libin%20et%20al.htm}, doi = {10.5897/AJAR12.587}, abstract = {Sarawak Biris rice is a strong aromatic rice variety which can thrive well in rice fields prone to flood, drought and other soil constraints. Tissue culture of Biris rice is important in producing planting materials and conducting genetic improvement work. The present study was conducted to induce callus from Biris rice seed and assess its regeneration ability. Dehusked mature seeds were used as starting materials for callus induction. Sterilized seeds were cultured onto Murashige and Skoog medium containing various concentrations of 2, 4-dichlorophenoxyacetic acid (2, 4-D). The optimum 2, 4-D concentration for callus induction was 2.0 mg/L with a frequency as high as 97\%. The calli produced were of desired features (creamy in colour, globular) and relatively bigger in size as compared to other treatments. The calli produced were further tested with plant growth regulator, naphthaleneacetic acid (NAA) in combination with kinetin (Kn) for plant regeneration ability. All uncontaminated calli were found to regenerate. Up to nine shoots were induced by a callus treated with 0.5 mg/L NAA in combination with 1.0 mg/L Kn. The present study should be noted as the first attempt to induce callus and regenerate plants from seeds of Biris rice.}, language = {en}, number = {30}, urldate = {2021-04-23}, journal = {Afr. J. Agric. Res.}, author = {{A. Libin,}}, month = aug, year = {2012}, file = {A. Libin, - 2012 - Callus induction and plant regeneration of Sarawak.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\LSTRW8Q6\\A. Libin, - 2012 - Callus induction and plant regeneration of Sarawak.pdf:application/pdf}, } @article{mostafiz_efficient_2018-3, title = {Efficient {Callus} {Induction} and {Regeneration} in {Selected} {Indica} {Rice}}, volume = {8}, issn = {2073-4395}, url = {http://www.mdpi.com/2073-4395/8/5/77}, doi = {10.3390/agronomy8050077}, abstract = {An efficient callus induction and in vitro regeneration were developed using plant growth regulators, carbon sources, and basal media for three selected Malaysian wetland rice varieties (MR220, MR220-CL2, and MR232) and one upland variety (Bario). Effect of plant growth regulator (PGR) was carried out using four different concentrations (1–4 mg/L) of 2,4-D (2, 4-dichlorophenoxyacetic acid), and NAA (1-naphthalene acetic acid) (2.5, 5.0, 7.5, and 10 mg/L) with optimized 2,4-D. Effects of carbon sources (maltose and sorbitol), and basal media (MS, N6, and LS) were also studied with optimized PGR to maximize the induction of regenerable calli. This study found that all four varieties exhibited high frequency of callus induction on MS (Murashige and Skoog) medium that was supplemented with 3 mg/L 2,4-D and 30 g/L maltose. Callus induction frequencies in the cases of MR220, MR220-CL2, MR232, and Bario were found to be 76\%, 94\%, 85\%, and 42\% respectively. Morphological analysis through scanning electron microscopy (SEM) and histological analysis revealed the embryogenicity of the induced callus. In the regeneration study, it was observed that combination of 2 mg/L BAP (6-benzylaminopurine), 2 mg/L Kin (Kinetin) and 0.5 mg/L NAA supplemented MS medium has the potential to promote regeneration of selected indica rice varieties with higher regeneration percentage, i.e., 82\% (MR220-CL2), 68\% (both in MR220 and MR232), and 40\% (Bario). The optimized conditions for callus formation and regeneration can be useful for biotechnological practices for the genetic improvement of Malaysian indica rice.}, language = {en}, number = {5}, urldate = {2021-04-23}, journal = {Agronomy}, author = {Mostafiz, Suraiya Binte and Wagiran, Alina}, month = may, year = {2018}, pages = {77}, file = {Binte Mostafiz and Wagiran - 2018 - Efficient Callus Induction and Regeneration in Sel.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\2KQM2CIM\\Binte Mostafiz and Wagiran - 2018 - Efficient Callus Induction and Regeneration in Sel.pdf:application/pdf;ETILEN LEE 2018.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\UVU53BNK\\ETILEN LEE 2018.pdf:application/pdf}, } @article{bevitori_morpho-anatomical_2013-1, title = {Morpho-anatomical characterization of mature embryo-derived callus of rice ({Oryza} sativa {L}.) suitable for transformation}, issn = {0033-183X, 1615-6102}, url = {http://link.springer.com/10.1007/s00709-013-0553-4}, doi = {10.1007/s00709-013-0553-4}, language = {en}, urldate = {2021-04-23}, journal = {Protoplasma}, author = {Bevitori, R. and Popielarska-Konieczna, M. and dos Santos, E. M. and Grossi-de-Sá, M. F. and Petrofeza, S.}, month = oct, year = {2013}, file = {Bevitori et al. - 2013 - Morpho-anatomical characterization of mature embry.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\ZR2LP9WM\\Bevitori et al. - 2013 - Morpho-anatomical characterization of mature embry.pdf:application/pdf}, } @article{wang_genotype-by-environment_2019-1, title = {Genotype-by-environment interactions inferred from genetic effects on phenotypic variability in the {UK} {Biobank}}, language = {en}, journal = {SCIENCE ADVANCES}, author = {Wang, Huanwei and Zhang, Futao and Zeng, Jian and Wu, Yang and Kemper, Kathryn E and Xue, Angli and Zhang, Min and Powell, Joseph E and Goddard, Michael E and Wray, Naomi R and Visscher, Peter M and McRae, Allan F and Yang, Jian}, year = {2019}, pages = {13}, file = {Wang et al. - 2019 - Genotype-by-environment interactions inferred from.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\75MG6ZY6\\Wang et al. - 2019 - Genotype-by-environment interactions inferred from.pdf:application/pdf}, } @article{umar_effect_2017-1, title = {Effect of {Medium} {Compositions} on {The} {Growth} of {Rice} ({Oryza} sativa {L}. cv. {Ciherang}) {Callus}}, abstract = {The efficiency of in-vitro regeneration of rice is spesific, which means a suitable medium for the regeneration of one variety may not be similar to other varieties. In this study, eksplan was derived from sterile radical of Ciherang var. This experiment consist two steps. First, induction of callus, and the second step was callus regeneration. The formulation for calli induction consists of three levels, such as i1 (2.4 D 2 ppm), i2 (2.4 D 3 ppm + BAP 0.25 ppm + Casein Hydrolisate 300 ppm + Proline 600 ppm) and i3 (2.4 D 2 ppm + Kinetin 0.5 ppm + Casein Hydrolisate 500 ppm + Proline 500 ppm) with N6 as a basic medium. Callus generated from those media then used in the next experiments for shoot regeneration which consists of two factors, the first factor was concentration of hormones BAP (r) (1 ppm, 2 ppm) and the second factor was concentration of the hormone Kinetin (k) (1 ppm, 2 ppm) with MS as a basic medium. The results showed that the highest embryogenic callus was obtained from i3 treatment by 62,96\%. The fastest rate of greeny callus and the emergence of shoots were found in i2r2k2 and i2r2k1 treatments. The results indicated that the media supplemented with high concentration of Kinetin (2 ppm) was more effective to induce the greeny of callus, and slightly lower concentration (1 ppm) leads to the formation of shoots.}, language = {en}, journal = {2017}, author = {Umar, Ruliana and Wibisono, Yossi and Ermawati, Netty}, year = {2017}, pages = {4}, file = {Umar et al. - Effect of Medium Compositions on The Growth of Ric.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\8Y9VLNK8\\Umar et al. - Effect of Medium Compositions on The Growth of Ric.pdf:application/pdf}, } @article{fanata_daya_2020-2, title = {{DAYA} {REGENERASI} {KALUS} {DAN} {TUNAS} {IN} {VITRO} {PADI} {VARIETAS} {TARABAS} {PADA} {BERBAGAI} {KONSENTRASI} 2,4-{D}}, volume = {7}, issn = {2548-611X, 2442-2606}, url = {http://ejurnal.bppt.go.id/index.php/JBBI/article/view/4404}, doi = {10.29122/jbbi.v7i2.4404}, abstract = {The Agricultural Research and Development Agency and the West Java Provincial Government are developing new superior varieties with Japonica rice standards, namely the Tarabas variety. However, the equivalence of somatic embryogenesis ability of Tarabas rice with original Japonica variety has not been reported. In this study, the frequency of callus regeneration of Tarabas vs Hwayoung rice varieties was compared. Induction of callus from mature embryos with several concentrations of 2,4-D showed the same extent of callus formation in both rice varieties. Callus induced by 1 ppm of 2,4-D showed the higher rate of shoot formation. On the other hand, percentage of callus formation of Tarabas rice was not affected by the increase of 2,4-D concentrations and was able to show 100\% regeneration rate at the fourth week in the regeneration medium, although the shoot growth was not as fast as those from medium with 1 ppm 2,4-D. Therefore, these results suggest that Tarabas variety has a somatic embryogenesis capacity equivalent to that of japonica rice and has the potential as research objects in the field of biotechnology.}, language = {id}, number = {2}, urldate = {2021-04-24}, journal = {J Bioteknol Biosains Indones}, author = {Fanata, Wahyu Indra Duwi and Qudsiyah, Dalliyah Hadrotul}, month = dec, year = {2020}, pages = {250--258}, file = {Fanata and Qudsiyah - 2020 - DAYA REGENERASI KALUS DAN TUNAS IN VITRO PADI VARI.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\WIHMABZA\\Fanata and Qudsiyah - 2020 - DAYA REGENERASI KALUS DAN TUNAS IN VITRO PADI VARI.pdf:application/pdf}, } @article{ming_combination_2019-2, title = {Combination of {Plant} {Growth} {Regulators}, {Maltose}, and {Partial} {Desiccation} {Treatment} {Enhance} {Somatic} {Embryogenesis} in {Selected} {Malaysian} {Rice} {Cultivar}}, volume = {8}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/8/6/144}, doi = {10.3390/plants8060144}, abstract = {The development of efficient tissue culture protocol for somatic embryo would facilitate the genetic modification breeding program. The callus induction and regeneration were studied by using different parameters i.e., auxins, cytokinins, and desiccation treatment. Scanning electron microscopy and histological analysis were performed to identify the embryogenic callus for regeneration. The callus percentage results showed that MS (Murashige and Skoog) basal medium supplemented with 3 mg/L 2, 4-D and 30g/L maltose were the optimal callus induction medium for MR220 (80\%) and MR220-CL2 (95\%). The morphology of the embryogenic callus was confirmed by the SEM (Scanning Electron Microscopy) (presence of extracellular matrix surface network) and later by histological analysis. Finally, MS media supplemented with 0.5 mg/L NAA (Naphthalene Acetic Acid), 2 mg/L kin, and 1 mg/L BAP were selected as the optimum regeneration media treatment while callus desiccated for 48 h was proved to produce more plantlets in MR220 (60\%) and MR220-CL2 (73.33\%) compared to control treatment (without desiccation). The protocol presented here showed the necessity for the inclusion of partial desiccation as an important step in the tissue culture protocol of Malaysian indica rice genotypes in order to enhance their regeneration potential.}, language = {en}, number = {6}, urldate = {2021-04-24}, journal = {Plants}, author = {Ming, NG Ja and Binte Mostafiz, Suraiya and Johon, Nur Syafiqoh and Abdullah Zulkifli, Nur Saliha and Wagiran, Alina}, month = may, year = {2019}, pages = {144}, file = {Ming et al. - 2019 - Combination of Plant Growth Regulators, Maltose, a.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\B9887TVT\\Ming et al. - 2019 - Combination of Plant Growth Regulators, Maltose, a.pdf:application/pdf}, } @article{iqbal_ethylene_2017-1, title = {Ethylene {Role} in {Plant} {Growth}, {Development} and {Senescence}: {Interaction} with {Other} {Phytohormones}}, volume = {08}, issn = {1664-462X}, shorttitle = {Ethylene {Role} in {Plant} {Growth}, {Development} and {Senescence}}, url = {http://journal.frontiersin.org/article/10.3389/fpls.2017.00475/full}, doi = {10.3389/fpls.2017.00475}, abstract = {The complex juvenile/maturity transition during a plant’s life cycle includes growth, reproduction, and senescence of its fundamental organs: leaves, flowers, and fruits. Growth and senescence of leaves, flowers, and fruits involve several genetic networks where the phytohormone ethylene plays a key role, together with other hormones, integrating different signals and allowing the onset of conditions favorable for stage progression, reproductive success and organ longevity. Changes in ethylene level, its perception, and the hormonal crosstalk directly or indirectly regulate the lifespan of plants. The present review focused on ethylene’s role in the development and senescence processes in leaves, flowers and fruits, paying special attention to the complex networks of ethylene crosstalk with other hormones. Moreover, aspects with limited information have been highlighted for future research, extending our understanding on the importance of ethylene during growth and senescence and boosting future research with the aim to improve the qualitative and quantitative traits of crops.}, language = {en}, urldate = {2021-04-24}, journal = {Front. Plant Sci.}, author = {Iqbal, Noushina and Khan, Nafees A. and Ferrante, Antonio and Trivellini, Alice and Francini, Alessandra and Khan, M. I. R.}, month = apr, year = {2017}, file = {Iqbal et al. - 2017 - Ethylene Role in Plant Growth, Development and Sen.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\MC942UJG\\Iqbal et al. - 2017 - Ethylene Role in Plant Growth, Development and Sen.pdf:application/pdf}, } @article{lee_cytokinin_2013-1, title = {Cytokinin, auxin, and abscisic acid affects sucrose metabolism conduce to de novo shoot organogenesis in rice ({Oryza} sativa {L}.) callus}, volume = {54}, issn = {1999-3110}, url = {https://as-botanicalstudies.springeropen.com/articles/10.1186/1999-3110-54-5}, doi = {10.1186/1999-3110-54-5}, abstract = {Background: Shoot regeneration frequency in rice callus is still low and highly diverse among rice cultivars. This study aimed to investigate the association of plant hormone signaling and sucrose uptake and metabolism in rice during callus induction and early shoot organogenesis. The immatured seeds of two rice cultivars, Ai-Nan-Tsao 39 (ANT39) and Tainan 11 (TN11) are used in this study. Results: Callus formation is earlier, callus fresh weight is higher, but water content is significant lower in ANT39 than in TN11 while their explants are inoculated on callus induction medium (CIM). Besides, the regeneration frequency is prominently higher in ANT39 ({\textbackslash}textasciitilde80\%) compared to TN11 callus (0\%). Levels of glucose, sucrose, and starch are all significant higher in ANT39 than in TN11 either at callus induction or early shoot organogenesis stage. Moreover, high expression levels of Cell wall-bound invertase 1, Sucrose transporter 1 (OsSUT1) and OsSUT2 are detected in ANT39 at the fourth-day in CIM but it cannot be detected in TN11 until the tenth-day. It suggested that ANT39 has higher callus growth rate and shoot regeneration ability may cause from higher activity of sucrose uptake and metabolism. As well, the expression levels of ORYZA SATIVA RESPONSE REGULATOR 1 (ORR1), PIN-formed 1 and Late embryogenesis-abundant 1, representing endogenous cytokinin, auxin and ABA signals, respectively, were also up-regulated in highly regenerable callus, ANT39, but only ORR1 was greatly enhanced in TN11 at the tenth-day in CIM. Conclusion: Thus, phytohormone signals may affect sucrose metabolism to trigger callus initiation and further de novo shoot regeneration in rice culture.}, language = {en}, number = {1}, urldate = {2021-04-24}, journal = {Bot Stud}, author = {Lee, Shiang-Ting and Huang, Wen-Lii}, month = dec, year = {2013}, pages = {5}, file = {Lee and Huang - 2013 - Cytokinin, auxin, and abscisic acid affects sucros.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\VG4C23UY\\Lee and Huang - 2013 - Cytokinin, auxin, and abscisic acid affects sucros.pdf:application/pdf}, } @incollection{sharma_abiotic_2019, edition = {1}, title = {Abiotic {Stress} {Management} in {Plants}: {Role} of {Ethylene}}, isbn = {978-1-119-46369-6 978-1-119-46366-5}, shorttitle = {Abiotic {Stress} {Management} in {Plants}}, url = {https://onlinelibrary.wiley.com/doi/10.1002/9781119463665.ch10}, language = {en}, urldate = {2021-04-24}, booktitle = {Molecular {Plant} {Abiotic} {Stress}}, publisher = {Wiley}, author = {Sharma, Anket and Kumar, Vinod and Sidhu, Gagan Preet Singh and Kumar, Rakesh and Kohli, Sukhmeen Kaur and Yadav, Poonam and Kapoor, Dhriti and Bali, Aditi Shreeya and Shahzad, Babar and Khanna, Kanika and Kumar, Sandeep and Thukral, Ashwani Kumar and Bhardwaj, Renu}, editor = {Roychoudhury, Aryadeep and Tripathi, Durgesh}, month = aug, year = {2019}, doi = {10.1002/9781119463665.ch10}, pages = {185--208}, file = {Sharma et al. - 2019 - Abiotic Stress Management in Plants Role of Ethyl.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\LJCWEUUC\\Sharma et al. - 2019 - Abiotic Stress Management in Plants Role of Ethyl.pdf:application/pdf}, } @article{abiri_enhancing_2017-2, title = {Enhancing somatic embryogenesis of {Malaysian} rice cultivar {MR219} using adjuvant materials in a high-efficiency protocol}, volume = {14}, issn = {1735-1472, 1735-2630}, url = {http://link.springer.com/10.1007/s13762-016-1221-y}, doi = {10.1007/s13762-016-1221-y}, language = {en}, number = {5}, urldate = {2021-04-25}, journal = {Int. J. Environ. Sci. Technol.}, author = {Abiri, R. and Maziah, M. and Shaharuddin, N. A. and Yusof, Z. N. B. and Atabaki, N. and Hanafi, M. M. and Sahebi, M. and Azizi, P. and Kalhori, N. and Valdiani, A.}, month = may, year = {2017}, pages = {1091--1108}, file = {Abiri et al. - 2017 - Enhancing somatic embryogenesis of Malaysian rice .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\S2T7SKEW\\Abiri et al. - 2017 - Enhancing somatic embryogenesis of Malaysian rice .pdf:application/pdf;Jha-Kumar2018_Article_BABYBOOMBBMACandidateTranscrip.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\PK4K3GDX\\Jha-Kumar2018_Article_BABYBOOMBBMACandidateTranscrip.pdf:application/pdf}, } @article{kieber_cytokinins_2014-3, title = {Cytokinins}, volume = {12}, issn = {1543-8120}, url = {http://www.bioone.org/doi/10.1199/tab.0168}, doi = {10.1199/tab.0168}, language = {en}, urldate = {2021-04-25}, journal = {The Arabidopsis Book}, author = {Kieber, Joseph J. and Schaller, G. Eric}, month = jan, year = {2014}, pages = {e0168}, file = {Kieber and Schaller - 2014 - Cytokinins.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\QBMAQBDE\\Kieber and Schaller - 2014 - Cytokinins.pdf:application/pdf}, } @article{pawar_influence_nodate-1, title = {Influence of different shoot portion and media on vegetative propagation of pomegranate ({Punica} granatum)}, abstract = {An experiment entitled, influence of different shoot portion and media on vegetative propagation of pomegranate was carried out with two factors viz; shoot portion with three levels and media with seven levels making total twenty one treatment combinations. Experiment was laid out in Factorial Completely Randomized Design with three replications. The results of the present investigation on the basis of pooled data revealed that, minimum days to sprouting (11.33) was recorded with treatment s1 (Apical) whereas, significantly highest length of shoot (9.79 cm), maximum number of roots (8.92) and length of root (8.96 cm) was recorded with treatment s2 (Sub-apical). Among different treatments of media, significantly early sprouting (11.14 days), maximum number of roots per cutting (8.40) and highest length of roots per cutting (8.81 cm) and highest shoot length (9.36 cm) at 60 DAP were observed with treatment m4 (Vermiculite: Poultry Manure [1:1]+ Pseudomonas). Use of sub-apical cutting with Vermiculite: Poultry Manure [1:1]+ Pseudomonas media in plug tray for early sprouting, highest shoot and root parameters of pomegranate under greenhouse condition.}, language = {en}, journal = {International Journal of Chemical Studies}, author = {Pawar, Yogesh and Varma, LR and More, SG and Verma, Piyush and Jat, RK}, pages = {5}, file = {Pawar et al. - Influence of different shoot portion and media on .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\XWSTWQE2\\Pawar et al. - Influence of different shoot portion and media on .pdf:application/pdf;OsRR2 Negetif Regulator.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\TP75NAT8\\OsRR2 Negetif Regulator.pdf:application/pdf}, } @article{jones_auxin_2011-1, title = {Auxin and cytokinin regulate each other’s levels via a metabolic feedback loop}, volume = {6}, issn = {1559-2324}, url = {http://www.tandfonline.com/doi/abs/10.4161/psb.6.6.15323}, doi = {10.4161/psb.6.6.15323}, language = {en}, number = {6}, urldate = {2021-05-21}, journal = {Plant Signaling \& Behavior}, author = {Jones, Brian and Ljung, Karin}, month = jun, year = {2011}, pages = {901--904}, file = {Jones and Ljung - 2011 - Auxin and cytokinin regulate each other’s levels v.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\2IJ2E4G6\\Jones and Ljung - 2011 - Auxin and cytokinin regulate each other’s levels v.pdf:application/pdf}, } @article{ikeuchi_plant_2013-3, title = {Plant {Callus}: {Mechanisms} of {Induction} and {Repression}}, volume = {25}, issn = {1040-4651, 1532-298X}, shorttitle = {Plant {Callus}}, url = {https://academic.oup.com/plcell/article/25/9/3159-3173/6097899}, doi = {10.1105/tpc.113.116053}, language = {en}, number = {9}, urldate = {2021-05-21}, journal = {Plant Cell}, author = {Ikeuchi, Momoko and Sugimoto, Keiko and Iwase, Akira}, month = sep, year = {2013}, pages = {3159--3173}, file = {Ikeuchi et al. - 2013 - Plant Callus Mechanisms of Induction and Repressi.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\NBLUH84E\\Ikeuchi et al. - 2013 - Plant Callus Mechanisms of Induction and Repressi.pdf:application/pdf;ethylen.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\JHWDHXBJ\\ethylen.pdf:application/pdf}, } @article{ma_auxin_2018-2, title = {Auxin signaling: a big question to be addressed by small molecules}, volume = {69}, issn = {0022-0957, 1460-2431}, shorttitle = {Auxin signaling}, url = {https://academic.oup.com/jxb/article/69/2/313/4641657}, doi = {10.1093/jxb/erx375}, abstract = {Providing a mechanistic understanding of the crucial roles of the phytohormone auxin has been an important and coherent aspect of plant biology research. Since its discovery more than a century ago, prominent advances have been made in the understanding of auxin action, ranging from metabolism and transport to cellular and transcriptional responses. However, there is a long road ahead before a thorough understanding of its complex effects is achieved, because a lot of key information is still missing. The availability of an increasing number of technically advanced scientific tools has boosted the basic discoveries in auxin biology. A plethora of bioactive small molecules, consisting of the synthetic auxin-like herbicides and the more specific auxin-related compounds, developed as a result of the exploration of chemical space by chemical biology, have made the tool box for auxin research more comprehensive. This review mainly focuses on the compounds targeting the auxin co-receptor complex, demonstrates the various ways to use them, and shows clear examples of important basic knowledge obtained by their usage. Application of these precise chemical tools, together with an increasing amount of structural information for the major components in auxin action, will certainly aid in strengthening our insights into the complexity and diversity of auxin response.}, language = {en}, number = {2}, urldate = {2021-05-26}, journal = {Journal of Experimental Botany}, author = {Ma, Qian and Grones, Peter and Robert, Stéphanie}, month = jan, year = {2018}, pages = {313--328}, file = {Ma et al. - 2018 - Auxin signaling a big question to be addressed by.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\NPG3RLK7\\Ma et al. - 2018 - Auxin signaling a big question to be addressed by.pdf:application/pdf}, } @article{tao_role_2015-1, title = {The {Role} of {Ethylene} in {Plants} {Under} {Salinity} {Stress}}, volume = {6}, issn = {1664-462X}, url = {http://journal.frontiersin.org/Article/10.3389/fpls.2015.01059/abstract}, doi = {10.3389/fpls.2015.01059}, abstract = {Although the roles of ethylene in plant response to salinity and other stresses have been extensively studied, there are still some obscure points left to be clarified. Generally, in Arabidopsis and many other terrestrial plants, ethylene signaling is indispensable for plant rapid response and tolerance to salinity stress. However, a few studies showed that functional knock-out of some ACSs increased plant salinity-tolerance, while overexpression of them caused more sensitivity. This seems to be contradictory to the known opinion that ethylene plays positive roles in salinity response. Differently, ethylene in rice may play negative roles in regulating seedling tolerance to salinity. The main positive ethylene signaling components MHZ7/OsEIN2, MHZ6/OsEIL1, and OsEIL2 all negatively regulate the salinity-tolerance of rice seedlings. Recently, several different research groups all proposed a negative feedback mechanism of coordinating plant growth and ethylene response, in which several ethylene-inducible proteins (including NtTCTP, NEIP2 in tobacco, AtSAUR76/77/78, and AtARGOS) act as inhibitors of ethylene response but activators of plant growth. Therefore, in addition to a summary of the general roles of ethylene biosynthesis and signaling in salinity response, this review mainly focused on discussing (i) the discrepancies between ethylene biosynthesis and signaling in salinity response, (ii) the divergence between rice and Arabidopsis in regulation of salinity response by ethylene, and (iii) the possible negative feedback mechanism of coordinating plant growth and salinity response by ethylene.}, language = {en}, urldate = {2021-05-26}, journal = {Front. Plant Sci.}, author = {Tao, Jian-Jun and Chen, Hao-Wei and Ma, Biao and Zhang, Wan-Ke and Chen, Shou-Yi and Zhang, Jin-Song}, month = nov, year = {2015}, file = {Tao et al. - 2015 - The Role of Ethylene in Plants Under Salinity Stre.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\CISGQPSD\\Tao et al. - 2015 - The Role of Ethylene in Plants Under Salinity Stre.pdf:application/pdf;baby boom.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\84NSI6L7\\baby boom.pdf:application/pdf}, } @article{jha_baby_2018-2, title = {{BABY} {BOOM} ({BBM}): a candidate transcription factor gene in plant biotechnology}, volume = {40}, issn = {0141-5492, 1573-6776}, shorttitle = {{BABY} {BOOM} ({BBM})}, url = {http://link.springer.com/10.1007/s10529-018-2613-5}, doi = {10.1007/s10529-018-2613-5}, abstract = {Plants have evolved a number of transcription factors, many of which are implicated in signaling pathways as well as regulating diverse cellular functions. BABY BOOM (BBM), transcription factors of the AP2/ERF family are key regulators of plant cell totipotency. Ectopic expression of the BBM gene, originally identified in Brassica napus, has diverse functions in plant cell proliferation, growth and development without exogenous growth regulators. The BBM gene has been implicated to play an important role as a gene marker in multiple signaling developmental pathways in plant development. This review focuses on recent advances in our understanding of a member of the AP2 family of transcription factor BBM in plant biotechnology including plant embryogenesis, cell proliferation, regeneration, plant transformation and apogamy. Recent discoveries about the BBM gene will inevitably help to unlock the long-standing mysteries of different biological mechanisms of plant cells.}, language = {en}, number = {11-12}, urldate = {2021-05-26}, journal = {Biotechnol Lett}, author = {Jha, Priyanka and Kumar, Vijay}, month = dec, year = {2018}, pages = {1467--1475}, file = {Jha and Kumar - 2018 - BABY BOOM (BBM) a candidate transcription factor .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\YIGZQ223\\Jha and Kumar - 2018 - BABY BOOM (BBM) a candidate transcription factor .pdf:application/pdf}, } @article{duan_strigolactone_2019-2, title = {Strigolactone promotes cytokinin degradation through transcriptional activation of \textit{{CYTOKININ}} {OXIDASE}/{DEHYDROGENASE} 9 in rice}, volume = {116}, issn = {0027-8424, 1091-6490}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1810980116}, doi = {10.1073/pnas.1810980116}, abstract = {Strigolactones (SLs), a group of terpenoid lactones derived from carotenoids, are plant hormones that control numerous aspects of plant development. Although the framework of SL signaling that the repressor DWARF 53 (D53) could be SL-dependently degraded via the SL receptor D14 and F-box protein D3 has been established, the downstream response genes to SLs remain to be elucidated. Here we show that the cytokinin (CK) content is dramatically increased in shoot bases of the rice SL signaling mutant d53 . By examining transcript levels of all the CK metabolism-related genes after treatment with SL analog GR24, we identified CYTOKININ OXIDASE/DEHYDROGENASE 9 ( OsCKX9 ) as a primary response gene significantly up-regulated within 1 h of treatment in the wild type but not in d53 . We also found that OsCKX9 functions as a cytosolic and nuclear dual-localized CK catabolic enzyme, and that the overexpression of OsCKX9 suppresses the browning of d53 calli. Both the CRISPR/Cas9-generated OsCKX9 mutants and OsCKX9 -overexpressing transgenic plants showed significant increases in tiller number and decreases in plant height and panicle size, suggesting that the homeostasis of OsCKX9 plays a critical role in regulating rice shoot architecture. Moreover, we identified the CK-inducible rice type-A response regulator OsRR5 as the secondary SL-responsive gene, whose expression is significantly repressed after 4 h of GR24 treatment in the wild type but not in osckx9 . These findings reveal a comprehensive plant hormone cross-talk in which SL can induce the expression of OsCKX9 to down-regulate CK content, which in turn triggers the response of downstream genes.}, language = {en}, number = {28}, urldate = {2021-05-26}, journal = {Proc Natl Acad Sci USA}, author = {Duan, Jingbo and Yu, Hong and Yuan, Kun and Liao, Zhigang and Meng, Xiangbing and Jing, Yanhui and Liu, Guifu and Chu, Jinfang and Li, Jiayang}, month = jul, year = {2019}, pages = {14319--14324}, file = {Duan et al. - 2019 - Strigolactone promotes cytokinin degradation throu.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\7HYBKEAF\\Duan et al. - 2019 - Strigolactone promotes cytokinin degradation throu.pdf:application/pdf}, } @article{lee_regulation_nodate-1, title = {Regulation of {Ethylene} {Biosynthesis} by {Phytohormones} in {Etiolated} {Rice} ({Oryza} sativa {L}.) {Seedlings}}, abstract = {The gaseous hormone ethylene influences many aspects of plant growth, development, and responses to a variety of stresses. The biosynthesis of ethylene is tightly regulated by various internal and external stimuli, and the primary target of the regulation is the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS), which catalyzes the rate-limiting step of ethylene biosynthesis. We have previously demonstrated that the regulation of ethylene biosynthesis is a common feature of most of the phytohormones in etiolated Arabidopsis seedlings via the modulation of the protein stability of ACS. Here, we show that various phytohormones also regulate ethylene biosynthesis from etiolated rice seedlings in a similar manner to those in Arabidopsis. Cytokinin, brassinosteroids, and gibberellic acid increase ethylene biosynthesis without changing the transcript levels of neither OsACS nor ACC oxidases (OsACO), a family of enzymes catalyzing the final step of the ethylene biosynthetic pathway. Likewise, salicylic acid and abscisic acid do not alter the gene expression of OsACS, but both hormones downregulate the transcript levels of a subset of ACO genes, resulting in a decrease in ethylene biosynthesis. In addition, we show that the treatment of the phytohormones results in distinct etiolated seedling phenotypes, some of which resemble ethylene-responsive phenotypes, while others display ethylene-independent morphologies, indicating a complicated hormone crosstalk in rice. Together, our study brings a new insight into crosstalk between ethylene biosynthesis and other phytohormones, and provides evidence that rice ethylene biosynthesis could be regulated by the post-transcriptional regulation of ACS proteins.}, language = {en}, author = {Lee, Han Yong and Yoon, Gyeong Mee}, pages = {9}, file = {Lee and Yoon - Regulation of Ethylene Biosynthesis by Phytohormon.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\GSNIBSGR\\Lee and Yoon - Regulation of Ethylene Biosynthesis by Phytohormon.pdf:application/pdf}, } @article{binder_ethylene_2020-2, title = {Ethylene signaling in plants}, volume = {295}, issn = {00219258}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925817494610}, doi = {10.1074/jbc.REV120.010854}, language = {en}, number = {22}, urldate = {2021-05-29}, journal = {Journal of Biological Chemistry}, author = {Binder, Brad M.}, month = may, year = {2020}, pages = {7710--7725}, file = {Binder - 2020 - Ethylene signaling in plants.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\ZHK3HFTC\\Binder - 2020 - Ethylene signaling in plants.pdf:application/pdf}, } @article{jiang_correlation_2017-1, title = {A correlation analysis on chlorophyll content and {SPAD} value in tomato leaves}, volume = {71}, url = {https://doi.org/10.20776/S18808824-71-P37}, abstract = {To investigate relationship between tomato（Solanum lycopersicum）leaf chlorophyll content and Minolta SPAD-502 plus chlorophyll meter, we studied leaves at plant vegetative growth stage and reproductive growth stage, and conducted correlation analysis to establish most optimal function model. The results showed that the correlation of SPAD value and the content of chlorophyll a, chlorophyll b and total chlorophyll content were significantly correlated in tomato leaves. At plant vegetative growth stage, the optimal mathematic function for SPAD value and chlorophyll a, chlorophyll b and total chlorophyll were y = 0.0006x1.924（r = 0.785）, y = 0.0006x1.8009（r = 0.756）and y = 0.2317e0.0406x（r = 0.869）respectively. At reproductive growth stage, the optimal function models were y = 0.0236x － 0.0705（r = 0.856）for chlorophyll a, y = 0.2975e0.0127x（r = 0.793）for chlorophyll b and y = 0.0306x + 0.1443（r = 0.869）for total chlorophyll. All these data proved SPAD-502 can be an effective tool used for rapid and nondestructive estimation of leaf chlorophyll content in tomato.}, language = {en}, urldate = {2021-06-05}, journal = {Hort Research}, author = {Jiang, Chengyao and Johkan, Masahumi and Hohjo, Masaaki and Tsukagoshi, Satoru and Maturo, Toru}, month = mar, year = {2017}, pages = {37--42}, file = {JIANG et al. - 2017 - A correlation analysis on chlorophyll content and .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\XUTKSGEK\\JIANG et al. - 2017 - A correlation analysis on chlorophyll content and .pdf:application/pdf}, } @article{sweeney_complex_2007-1, title = {The {Complex} {History} of the {Domestication} of {Rice}}, volume = {100}, issn = {0305-7364, 1095-8290}, url = {https://academic.oup.com/aob/article-lookup/doi/10.1093/aob/mcm128}, doi = {10.1093/aob/mcm128}, language = {en}, number = {5}, urldate = {2021-06-19}, journal = {Annals of Botany}, author = {Sweeney, M. and McCouch, S.}, month = jul, year = {2007}, pages = {951--957}, file = {Sweeney and McCouch - 2007 - The Complex History of the Domestication of Rice.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\YFK7YZYG\\Sweeney and McCouch - 2007 - The Complex History of the Domestication of Rice.pdf:application/pdf}, } @book{dunna_rice_2018-1, address = {India}, title = {Rice ({Oryza} sativa {L}.)}, url = {https://www.researchgate.net/publication/281152980}, language = {english}, publisher = {Research Gate}, author = {Dunna, Vijay and Roy, Bidhan}, year = {2018}, annote = {ICAR: India Agricultural Research Institute. India : New India Publishing Agency}, } @article{ali_improved_2021-2, title = {Improved {Anther} {Culture} {Media} for {Enhanced} {Callus} {Formation} and {Plant} {Regeneration} in {Rice} ({Oryza} sativa {L}.)}, volume = {10}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/10/5/839}, doi = {10.3390/plants10050839}, abstract = {Anther culture technique is the most viable and efficient method of producing homozygous doubled haploid plants within a short period. However, the practical application of this technology in rice improvement is still limited by various factors that influence culture efficiency. The present study was conducted to determine the effects of two improved anther culture media, Ali-1 (A1) and Ali-2 (A2), a modified N6 medium, to enhance the callus formation and plant regeneration of japonica, indica, and hybrids of indica and japonica cross. The current study demonstrated that genotype and media had a significant impact (p {\textbackslash}textless 0.001) on both callus induction frequency and green plantlet regeneration efficiency. The use of the A1 and A2 medium significantly enhanced callus induction frequency of japonica rice type, Nipponbare, and the hybrids of indica × japonica cross (CXY6, CXY24, and Y2) but not the indica rice type, NSIC Rc480. However, the A1 medium is found superior to the N6 medium as it significantly improved the green plantlet regeneration efficiency of CXY6, CXY24, and Y2 by almost 36\%, 118\%, and 277\%, respectively. Furthermore, it substantially reduced the albino plantlet regeneration of the induced callus in two hybrids (CXY6 and Y2). Therefore, the improved anther culture medium A1 can produce doubled haploid rice plants for indica × japonica, which can be useful in different breeding programs that will enable the speedy development of rice varieties for resource-poor farmers.}, language = {en}, number = {5}, urldate = {2021-06-29}, journal = {Plants}, author = {Ali, Jauhar and Nicolas, Katrina Leslie C. and Akther, Shahana and Torabi, Azerkhsh and Ebadi, Ali Akbar and Marfori-Nazarea, Corinne M. and Mahender, Anumalla}, month = apr, year = {2021}, pages = {839}, file = {Ali et al. - 2021 - Improved Anther Culture Media for Enhanced Callus .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\7QKR7M54\\Ali et al. - 2021 - Improved Anther Culture Media for Enhanced Callus .pdf:application/pdf}, } @article{lardon_natural_2020-1, title = {Natural {Variation} in {Plant} {Pluripotency} and {Regeneration}}, volume = {9}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/9/10/1261}, doi = {10.3390/plants9101261}, abstract = {Plant regeneration is essential for survival upon wounding and is, hence, considered to be a strong natural selective trait. The capacity of plant tissues to regenerate in vitro, however, varies substantially between and within species and depends on the applied incubation conditions. Insight into the genetic factors underlying this variation may help to improve numerous biotechnological applications that exploit in vitro regeneration. Here, we review the state of the art on the molecular framework of de novo shoot organogenesis from root explants in Arabidopsis, which is a complex process controlled by multiple quantitative trait loci of various effect sizes. Two types of factors are distinguished that contribute to natural regenerative variation: master regulators that are conserved in all experimental systems (e.g., WUSCHEL and related homeobox genes) and conditional regulators whose relative role depends on the explant and the incubation settings. We further elaborate on epigenetic variation and protocol variables that likely contribute to differential explant responsivity within species and conclude that in vitro shoot organogenesis occurs at the intersection between (epi) genetics, endogenous hormone levels, and environmental influences.}, language = {en}, number = {10}, urldate = {2021-06-29}, journal = {Plants}, author = {Lardon, Robin and Geelen, Danny}, month = sep, year = {2020}, pages = {1261}, file = {Lardon and Geelen - 2020 - Natural Variation in Plant Pluripotency and Regene.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\SJ5VRYHK\\Lardon and Geelen - 2020 - Natural Variation in Plant Pluripotency and Regene.pdf:application/pdf}, } @article{yang_response_2020-1, title = {Response of {Photosynthesis} to {High} {Growth} {Temperature} {Was} {Not} {Related} to {Leaf} {Anatomy} {Plasticity} in {Rice} ({Oryza} sativa {L}.)}, volume = {11}, issn = {1664-462X}, url = {https://www.frontiersin.org/article/10.3389/fpls.2020.00026/full}, doi = {10.3389/fpls.2020.00026}, abstract = {Photosynthesis is highly sensitive to high temperature stress, and with the rising global temperature, it is meaningful to investigate the response of photosynthesis to growth temperature and its relationship with leaf anatomy plasticity. We planted 21 cultivars including eight indica cultivars, eight japonica cultivars, and five javanica cultivars in pot experiments under high growth temperature (HT, 38/28°C, day/night) and control treatment (CK, 30/28°C, day/night). Photosynthetic rate (A), stomatal conductance (gs), transpiration rate (E), stomatal density (SD), vein density (VD), minor vein area (SVA), and major vein area (LVA) were measured after 30 treatment days. Results showed HT significantly increased A, gs, and E, while significantly decreased SD and LVA. There was no significant difference in A among the three subspecies both under CK and HT, while the javanica subspecies had higher gs, E, SVA, and LVA under HT, and the indica cultivars had higher VD and SD both under CK and HT. The javanica subspecies had higher relative value (HT/CK) of A, gs, and E, while difference was not observed in the relative value of SD, VD, and LVA among the three subspecies. The relative value of A was positively related to that of gs, while the latter was not correlated with the relative value of SD, VD, SVA, and LVA. Overall, the results suggested the increase of A and gs at HT was not attributed to leaf anatomy plasticity in respect of stomata and vein under HT.}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Yang, Desheng and Peng, Shaobing and Wang, Fei}, month = feb, year = {2020}, pages = {26}, file = {Yang et al. - 2020 - Response of Photosynthesis to High Growth Temperat.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\QMMINERU\\Yang et al. - 2020 - Response of Photosynthesis to High Growth Temperat.pdf:application/pdf}, } @article{han_highly_2021-1, title = {Highly efficient and genotype-independent barley gene editing based on anther culture}, volume = {2}, issn = {25903462}, url = {https://linkinghub.elsevier.com/retrieve/pii/S259034622030105X}, doi = {10.1016/j.xplc.2020.100082}, abstract = {Recalcitrance to tissue culture and genetic transformation is the major bottleneck for gene manipulation in crops. In barley, immature embryos of Golden Promise have typically been used as explants for transformation. However, the genotype dependence of this approach limits the genetic modification of commercial varieties. Here, we developed an anther culture-based system that permits the effective creation of transgenic and gene-edited plants from commercial barley varieties. The protocol was tested in Golden Promise and four Australian varieties, which differed in phenology, callus induction, and green plant regeneration responses. Agrobacterium-mediated transformation was performed on microspore-derived callus to target the HvPDS gene, and T0 albinos with targeted mutations were successfully obtained from commercial varieties. Further editing of three targets was achieved with an average mutation rate of 53\% in the five varieties. In 51 analyzed T0 individuals, Cas9 induced a large proportion (69\%) of single-base indels and two-base deletions in the target sites, with variable mutation rates among targets and varieties. Both ontarget and off-target activities were detected in T1 progenies. Compared with immature embryo protocols, this genotype-independent platform can deliver a high editing efficiency and more regenerant plants within a similar time frame. It shows promise for functional genomics and the application of CRISPR technologies for the precise improvement of commercial varieties.}, language = {en}, number = {2}, urldate = {2021-06-29}, journal = {Plant Communications}, author = {Han, Yong and Broughton, Sue and Liu, Li and Zhang, Xiao-Qi and Zeng, Jianbin and He, Xiaoyan and Li, Chengdao}, month = mar, year = {2021}, pages = {100082}, file = {Han et al. - 2021 - Highly efficient and genotype-independent barley g.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\9FB4Y9YN\\Han et al. - 2021 - Highly efficient and genotype-independent barley g.pdf:application/pdf}, } @article{indoliya_decoding_2016-1, title = {Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies}, volume = {6}, issn = {2045-2322}, url = {http://www.nature.com/articles/srep23050}, doi = {10.1038/srep23050}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Sci Rep}, author = {Indoliya, Yuvraj and Tiwari, Poonam and Chauhan, Abhisekh Singh and Goel, Ridhi and Shri, Manju and Bag, Sumit Kumar and Chakrabarty, Debasis}, month = sep, year = {2016}, pages = {23050}, file = {Indoliya et al. - 2016 - Decoding regulatory landscape of somatic embryogen.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\QYIXRDYA\\Indoliya et al. - 2016 - Decoding regulatory landscape of somatic embryogen.pdf:application/pdf}, } @article{tran_effect_2015-1, title = {Effect of antibiotics on callus regeneration during transformation of {IR} 64 rice}, volume = {7}, issn = {2215017X}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2215017X15000399}, doi = {10.1016/j.btre.2015.06.004}, language = {en}, urldate = {2021-06-29}, journal = {Biotechnology Reports}, author = {Tran, Thanh Ngoc and Sanan-Mishra, Neeti}, month = sep, year = {2015}, pages = {143--149}, file = {Tran and Sanan-Mishra - 2015 - Effect of antibiotics on callus regeneration durin.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\LIZIP6UF\\Tran and Sanan-Mishra - 2015 - Effect of antibiotics on callus regeneration durin.pdf:application/pdf}, } @article{tian_breeding_2019-1, title = {Breeding {Rice} lines for physio-functional food through indica ‘{Zhaxima}’ × japonica ‘{Nanjing} 46’ haploid technique}, volume = {1}, issn = {2661-8974}, url = {https://fppn.biomedcentral.com/articles/10.1186/s43014-019-0010-7}, doi = {10.1186/s43014-019-0010-7}, abstract = {Resistant starch (RS) encompasses those forms of starch which are not accessible to human digestive enzymes and are fermented in the colons producing short chain fatty acids. The plant materials containing RS are few in the world. In this contribution, the culture ability of callus from anthers of F1 plants from, landraces, ‘Zhaxima’(Oryza sativa var. indica, high-RS rice line with 7.705 ± 0.142, g/100 g) × ‘Nanjing 46’ (Oryza sativa var. japonica, rice variety with RS content (g/100 g) of 0.200 ± 0.001 crosses were studied for obtaining high RS rice plants. The results showed that when M8 basic induction medium was added with 1.5 mg /L 2,4-D、2 mg /LNAA and 0.3 mg /L KT, the inductivity of callus was high as 32.14\% for 21 d after pretreatment at 4 °C for 3 d; When MS differentiation basic medium was added with 2 mg /LKT and 3 mg /L ABA, the frequency of regeneration for callus was 50.3\% with only a regeneration frequency of 4.55\% grown into green seedlings. The RS content in the seeds was between those of the two parents and was partially normally distributed, the highest RS contents of the regenerated plants was as high as 7.66 ± 1.197\%. This produced an efficient technology for regenerating stable rice lines with high RS and good eating quality using anthers culture.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Food Prod Process and Nutr}, author = {Tian, Q. Q. and Li, X. and Lu, C. M. and Fang, X. W.}, month = dec, year = {2019}, pages = {12}, file = {Tian et al. - 2019 - Breeding Rice lines for physio-functional food thr.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\IGN57C9J\\Tian et al. - 2019 - Breeding Rice lines for physio-functional food thr.pdf:application/pdf}, } @article{solanki_optimization_2019-1, title = {Optimization of in vitro culture media for improvement in yield of {Navara} ancient {Indian} medicinal rice}, volume = {9}, issn = {2190-572X, 2190-5738}, url = {http://link.springer.com/10.1007/s13205-019-1797-2}, doi = {10.1007/s13205-019-1797-2}, abstract = {Medicinally important ancient Navara rice (GI Kerala, India 2007) is a very short duration (60–70 days) variety with a yield of only 0.5 tonnes/hectare costing {\textbackslash}textasciitilde Rs. 400/kg. It is used for indigenous treatment for chronic diseases by local and oral consumption. In this study, scutellum-derived calli were generated from mature Navara seeds and these were inoculated on different CIM-1 to CIM-5 media supplemented with 2.5 mg/l 2,4-dichlorophenoxyacetic acid. Regeneration of calli on different regeneration media RI, RII and RIII media were performed. Regeneration of 30-day-old calli on RI media showed 30\%, for RII it showed no regeneration and on RIII media only 12\% regeneration was obtained. The addition of glutamine and proline showed a 30–40\% improvement in somatic embryogenesis. The 74–88\% callus induction frequency was obtained on CIM-1 to CIM-5. The fresh weight (mg) of 30-day-old calli is CIM-2 {\textbackslash}textless CIM-3 {\textbackslash}textless CIM-4 {\textbackslash}textless CIM-1 {\textbackslash}textless{\textbackslash}textless CIM-5 and corresponding size shows CIM-2–CIM-3 {\textbackslash}textless CIM-5 {\textbackslash}textless CIM-1 {\textbackslash}textless CIM-4. A negative correlation between the callus fresh weight and the regeneration efficiency was observed. In CIM-5, 20–25 days 3.4-fold increase and 25–30 days a 1.7-fold increase in fresh weight of calli is noted. The 20-day-old calli transfer to RI media shows 80\% regeneration frequency and 6–7 plantlets/callus, which are twofold higher as compared with 30-day-old calli. The somatic embryogenesis and its regeneration on synthetic media provide an alternative for biotechnological intervention for yield improvement, in turn cost reduction for Navara rice.}, language = {en}, number = {7}, urldate = {2021-06-29}, journal = {3 Biotech}, author = {Solanki, Manish and Sinha, Anshika and Shukla, Lata I.}, month = jul, year = {2019}, pages = {270}, file = {Solanki et al. - 2019 - Optimization of in vitro culture media for improve.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\XWZ86N8Y\\Solanki et al. - 2019 - Optimization of in vitro culture media for improve.pdf:application/pdf}, } @article{juarez-gonzalez_explant_2019-1, title = {The explant developmental stage profoundly impacts small {RNA}-mediated regulation at the dedifferentiation step of maize somatic embryogenesis}, volume = {9}, issn = {2045-2322}, url = {http://www.nature.com/articles/s41598-019-50962-y}, doi = {10.1038/s41598-019-50962-y}, abstract = {Abstract Maize somatic embryogenesis (SE) requires the induction of embryogenic callus and establishment of proliferation before plant regeneration. The molecular mechanisms underlying callus embryogenic potential are not well understood. Here we explored the role of small RNAs (sRNAs) and the accumulation of their target transcripts in maize SE at the dedifferentiation step using VS-535 zygotic embryos collected at distinct developmental stages and displaying contrasting in vitro embryogenic potential and morphology. MicroRNAs (miRNAs), trans -acting siRNAs (tasiRNAs), heterochromatic siRNAs (hc-siRNAs) populations and their RNA targets were analyzed by high-throughput sequencing. Abundances of specific miRNAs, tasiRNAs and targets were validated by qRT-PCR. Unique accumulation patterns were found for immature embryo at 15 Days After Pollination (DAP) and for the callus induction from this explant, as compared to 23 DAP and mature embryos. miR156, miR164, miR166, tasiARFs and the 24 nt hc-siRNAs displayed the most strikingly different patterns between explants and during dedifferentiation. According to their role in auxin responses and developmental cues, we conclude that sRNA-target regulation operating within the 15 DAP immature embryo explant provides key molecular hints as to why this stage is relevant for callus induction with successful proliferation and plant regeneration.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Sci Rep}, author = {Juárez-González, Vasti T. and López-Ruiz, Brenda A. and Baldrich, Patricia and Luján-Soto, Eduardo and Meyers, Blake C. and Dinkova, Tzvetanka D.}, month = dec, year = {2019}, pages = {14511}, file = {Juárez-González et al. - 2019 - The explant developmental stage profoundly impacts.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\AAEI6KCT\\Juárez-González et al. - 2019 - The explant developmental stage profoundly impacts.pdf:application/pdf}, } @article{xu_atacing_2020-1, title = {{ATACing} {Somatic} {Embryogenesis}}, volume = {54}, issn = {15345807}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580720307103}, doi = {10.1016/j.devcel.2020.09.008}, language = {en}, number = {6}, urldate = {2021-06-29}, journal = {Developmental Cell}, author = {Xu, Jian}, month = sep, year = {2020}, pages = {689--690}, file = {Xu - 2020 - ATACing Somatic Embryogenesis.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\AZQMWXQC\\Xu - 2020 - ATACing Somatic Embryogenesis.pdf:application/pdf}, } @article{gulzar_genes_2020-1, title = {Genes, proteins and other networks regulating somatic embryogenesis in plants}, volume = {18}, issn = {2090-5920}, url = {https://jgeb.springeropen.com/articles/10.1186/s43141-020-00047-5}, doi = {10.1186/s43141-020-00047-5}, abstract = {Background: Somatic embryogenesis (SE) is an intricate molecular and biochemical process principally based on cellular totipotency and a model in studying plant development. In this unique embryo-forming process, the vegetative cells acquire embryogenic competence under cellular stress conditions. The stress caused by plant growth regulators (PGRs), nutrient, oxygenic, or other signaling elements makes cellular reprogramming and transforms vegetative cells into embryos through activation/deactivation of a myriad of genes and transcriptional networks. Hundreds of genes have been directly linked to zygotic and somatic embryogeneses; some of them like SOMATIC EMBRYOGENESIS LIKE RECEPTOR KINASE (SERK), LEAFY COTYLEDON (LEC), BABYBOOM (BBM), and AGAMOUSLIKE 15 (AGL15) are very important and are part of molecular network. Main text (observation): This article reviews various genes/orthologs isolated from different plants; encoded proteins and their possible role in regulating somatic embryogenesis of plants have been discussed. The role of SERK in regulating embryogenesis is also summarized. Different SE-related proteins identified through LC–MS at various stages of embryogenesis are also described; a few proteins like 14-3-3, chitinase, and LEA are used as potential SE markers. These networks are interconnected in a complicated manner, posing challenges for their complete elucidation. Conclusions: The various gene networks and factors controlling somatic embryogenesis have been discussed and presented. The roles of stress, PGRs, and other signaling elements have been discussed. In the last two-to-three decades’ progress, the challenges ahead and its future applications in various fields of research have been highlighted. The review also presents the need of high throughput, innovative techniques, and sensitive instruments in unraveling the mystery of SE.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {J Genet Eng Biotechnol}, author = {Gulzar, Basit and Mujib, A. and Malik, Moien Qadir and Sayeed, Rukaya and Mamgain, Jyoti and Ejaz, Bushra}, month = dec, year = {2020}, pages = {31}, file = {Gulzar et al. - 2020 - Genes, proteins and other networks regulating soma.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\4W8FX5V5\\Gulzar et al. - 2020 - Genes, proteins and other networks regulating soma.pdf:application/pdf}, } @article{vercruyssen_growth_2015-1, title = {{GROWTH} {REGULATING} {FACTOR5} {Stimulates} {Arabidopsis} {Chloroplast} {Division}, {Photosynthesis}, and {Leaf} {Longevity}}, volume = {167}, issn = {1532-2548}, url = {https://academic.oup.com/plphys/article/167/3/817/6113750}, doi = {10.1104/pp.114.256180}, abstract = {Abstract Arabidopsis (Arabidopsis thaliana) leaf development relies on subsequent phases of cell proliferation and cell expansion. During the proliferation phase, chloroplasts need to divide extensively, and during the transition from cell proliferation to expansion, they differentiate into photosynthetically active chloroplasts, providing the plant with energy. The transcription factor GROWTH REGULATING FACTOR5 (GRF5) promotes the duration of the cell proliferation period during leaf development. Here, it is shown that GRF5 also stimulates chloroplast division, resulting in a higher chloroplast number per cell with a concomitant increase in chlorophyll levels in 35S:GRF5 leaves, which can sustain higher rates of photosynthesis. Moreover, 35S:GRF5 plants show delayed leaf senescence and are more tolerant for growth on nitrogen-depleted medium. Cytokinins also stimulate leaf growth in part by extending the cell proliferation phase, simultaneously delaying the onset of the cell expansion phase. In addition, cytokinins are known to be involved in chloroplast development, nitrogen signaling, and senescence. Evidence is provided that GRF5 and cytokinins synergistically enhance cell division and chlorophyll retention after dark-induced senescence, which suggests that they also cooperate to stimulate chloroplast division and nitrogen assimilation. Taken together with the increased leaf size, ectopic expression of GRF5 has great potential to improve plant productivity.}, language = {en}, number = {3}, urldate = {2021-06-29}, journal = {Plant Physiology}, author = {Vercruyssen, Liesbeth and Tognetti, Vanesa B. and Gonzalez, Nathalie and Van Dingenen, Judith and De Milde, Liesbeth and Bielach, Agnieszka and De Rycke, Riet and Van Breusegem, Frank and Inzé, Dirk}, month = feb, year = {2015}, pages = {817--832}, file = {Vercruyssen et al. - 2015 - GROWTH REGULATING FACTOR5 Stimulates Arabidopsis C.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\3WL535NS\\Vercruyssen et al. - 2015 - GROWTH REGULATING FACTOR5 Stimulates Arabidopsis C.pdf:application/pdf}, } @article{yasmin_ethylene_2014-1, title = {Ethylene influences in vitro regeneration frequency in the {FR13A} rice harbouring the {SUB1A} gene}, volume = {72}, issn = {0167-6903, 1573-5087}, url = {http://link.springer.com/10.1007/s10725-013-9840-5}, doi = {10.1007/s10725-013-9840-5}, abstract = {Many studies have examined the effects of ethylene on in vitro plant growth and development, often with controversial results. Ethylene accumulates in culture vessels due to both the release from the tissues and the physical entrapment due to the need for closed containers. This hormone has several effects on plant regeneration, depending on the plant species and even the cultivar. A prerequisite for ethylene use for in vitro culture is thus to formulate a specific protocol for the genotype of interest. In rice, ethylene is a key regulator of adaptation strategies to low oxygen environments. In particular, the SUBMERGENCE1A (SUB1A) gene, when present, drives the acclimation response which when activated by ethylene produced by submerged plants leads to adaptation through reduced plant growth and ethanolic fermentation enhancement. This gene is restricted to a limited number of rice for which a very specific response to ethylene is expected, whatever the source. This paper reports the regeneration differences between a SUB1A rice landrace (indica-aus, FR13A) and a non-SUB1A variety (japonica, Nipponbare). Our results suggest that regeneration protocols with exogenous ethylene precursors supply are required for the FR13A rice harbouring the SUB1A gene to overcome the problem of low regeneration efficiency.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Plant Growth Regul}, author = {Yasmin, Sabina and Mensuali-Sodi, Anna and Perata, Pierdomenico and Pucciariello, Chiara}, month = jan, year = {2014}, pages = {97--103}, file = {Yasmin et al. - 2014 - Ethylene influences in vitro regeneration frequenc.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\9TP5JDR3\\Yasmin et al. - 2014 - Ethylene influences in vitro regeneration frequenc.pdf:application/pdf}, } @article{neves_modulation_2021-1, title = {Modulation of {Organogenesis} and {Somatic} {Embryogenesis} by {Ethylene}: {An} {Overview}}, volume = {10}, issn = {2223-7747}, shorttitle = {Modulation of {Organogenesis} and {Somatic} {Embryogenesis} by {Ethylene}}, url = {https://www.mdpi.com/2223-7747/10/6/1208}, doi = {10.3390/plants10061208}, abstract = {Ethylene is a plant hormone controlling physiological and developmental processes such as fruit maturation, hairy root formation, and leaf abscission. Its effect on regeneration systems, such as organogenesis and somatic embryogenesis (SE), has been studied, and progress in molecular biology techniques have contributed to unveiling the mechanisms behind its effects. The influence of ethylene on regeneration should not be overlooked. This compound affects regeneration differently, depending on the species, genotype, and explant. In some species, ethylene seems to revert recalcitrance in genotypes with low regeneration capacity. However, its effect is not additive, since in genotypes with high regeneration capacity this ability decreases in the presence of ethylene precursors, suggesting that regeneration is modulated by ethylene. Several lines of evidence have shown that the role of ethylene in regeneration is markedly connected to biotic and abiotic stresses as well as to hormonalcrosstalk, in particular with key regeneration hormones and growth regulators of the auxin and cytokinin families. Transcriptional factors of the ethylene response factor (ERF) family are regulated by ethylene and strongly connected to SE induction. Thus, an evident connection between ethylene, stress responses, and regeneration capacity is markedly established. In this review the effect of ethylene and the way it interacts with other players during organogenesis and somatic embryogenesis is discussed. Further studies on the regulation of ERF gene expression induced by ethylene during regeneration can contribute to new insights on the exact role of ethylene in these processes. A possible role in epigenetic modifications should be considered, since some ethylene signaling components are directly related to histone acetylation.}, language = {en}, number = {6}, urldate = {2021-06-29}, journal = {Plants}, author = {Neves, Mariana and Correia, Sandra and Cavaleiro, Carlos and Canhoto, Jorge}, month = jun, year = {2021}, pages = {1208}, file = {Neves et al. - 2021 - Modulation of Organogenesis and Somatic Embryogene.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\7RJQJPZQ\\Neves et al. - 2021 - Modulation of Organogenesis and Somatic Embryogene.pdf:application/pdf}, } @article{gao_transcriptome_2020-1, title = {Transcriptome sequencing and identification of key callus browning-related genes from petiole callus of tree peony ({Paeonia} suffruticosa cv. {Kao}) cultured on media with three browning inhibitors}, volume = {149}, issn = {09819428}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0981942820300371}, doi = {10.1016/j.plaphy.2020.01.029}, abstract = {Abstract: Tree peony (Paeonia suffruticosa Andrews) has ornamental, oil, and medicinal values, and demand in the markets for uniform tree peony seedlings is increasing. Micropropagation could quickly propagate uniform seedlings. However, the heavy browning phenomenon hinders large-scale development of uniform tree peony seedlings. In this paper, we measured the total phenolic compounds content, and sequenced the transcriptomes of tree peony ‘Kao’ petiole calluses cultured on media with three browning antagonist treatments and fresh petioles to identify the key genes involved in callus browning. Polyvinylpyrrolidone (PVP) treatment can reduce production of phenolic compounds and promote callus regeneration. A total of 218,957 unigenes were obtained from fresh petiole and three kinds of browning petiole calluses by transcriptome sequencing. The average sequence length of unigenes was 446 bp with an N50 of 493 bp. Functional annotation analysis revealed that 43,428, 45,357, 31,194, 30,019, and 21,357 unigenes were annotated using the NCBI-NR database, Swiss-Prot, KOG, GO, and KEGG, respectively. In total, 33 differentially expressed genes (DEGs) were identified as potentially associated with callus browning. Among these DEGs, 12 genes were predicted to participate in phenolic compounds biosynthesis, three genes were predicted to be involved in phenolic compounds oxidation, and six genes were predicted to participate in callus regeneration. Moreover, six transcription factors were observed to be differentially expressed in the fresh petiole and three treated petioles in tree peony. This study comprehensively identifies browning-related gene resources and will possibly help in deciphering the molecular mechanisms of callus browning of tree peony in the future.}, language = {en}, urldate = {2021-06-29}, journal = {Plant Physiology and Biochemistry}, author = {Gao, Jie and Xue, Jingqi and Xue, Yuqian and Liu, Rong and Ren, Xiuxia and Wang, Shunli and Zhang, Xiuxin}, month = apr, year = {2020}, pages = {36--49}, file = {Gao et al. - 2020 - Transcriptome sequencing and identification of key.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\AY2CJHZI\\Gao et al. - 2020 - Transcriptome sequencing and identification of key.pdf:application/pdf}, } @article{jones_inhibition_2013-1, title = {Inhibition of {Phenylpropanoid} {Biosynthesis} in {Artemisia} annua {L}.: {A} {Novel} {Approach} to {Reduce} {Oxidative} {Browning} in {Plant} {Tissue} {Culture}}, volume = {8}, issn = {1932-6203}, shorttitle = {Inhibition of {Phenylpropanoid} {Biosynthesis} in {Artemisia} annua {L}.}, url = {https://dx.plos.org/10.1371/journal.pone.0076802}, doi = {10.1371/journal.pone.0076802}, abstract = {Oxidative browning is a common and often severe problem in plant tissue culture systems caused by the accumulation and oxidation of phenolic compounds. The current study was conducted to investigate a novel preventative approach to address this problem by inhibiting the activity of the phenylalanine ammonia lyase enzyme (PAL), thereby reducing the biosynthesis of phenolic compounds. This was accomplished by incorporating 2aminoindane-2-phosphonic acid (AIP), a competitive PAL inhibitor, into culture media of Artemisia annua as a model system. Addition of AIP into culture media resulted in significant reductions in visual tissue browning, a reduction in total phenol content, as well as absorbance and autoflourescence of tissue extracts. Reduced tissue browning was accompanied with a significant increase in growth on cytokinin based medium. Microscopic observations demonstrated that phenolic compounds accumulated in discrete cells and that these cells were more prevalent in brown tissue. These cells were highly plasmolyzed and often ruptured during examination, demonstrating a mechanism in which phenolics are released into media in this system. These data indicate that inhibiting phenylpropanoid biosynthesis with AIP is an effective approach to reduce tissue browning in A. annua. Additional experiments with Ulmus americana and Acer saccharum indicate this approach is effective in many species and it could have a wide application in systems where oxidative browning restricts the development of biotechnologies.}, language = {en}, number = {10}, urldate = {2021-06-29}, journal = {PLoS ONE}, author = {Jones, Andrew Maxwell Phineas and Saxena, Praveen Kumar}, editor = {Liu, Ji-Hong}, month = oct, year = {2013}, pages = {e76802}, file = {Jones and Saxena - 2013 - Inhibition of Phenylpropanoid Biosynthesis in Arte.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\6X3TAARU\\Jones and Saxena - 2013 - Inhibition of Phenylpropanoid Biosynthesis in Arte.pdf:application/pdf}, } @article{watkins_ethylene-induced_2014-1, title = {Ethylene-{Induced} {Flavonol} {Accumulation} in {Guard} {Cells} {Suppresses} {Reactive} {Oxygen} {Species} and {Moderates} {Stomatal} {Aperture}}, volume = {164}, issn = {0032-0889, 1532-2548}, url = {https://academic.oup.com/plphys/article/164/4/1707-1717/6112792}, doi = {10.1104/pp.113.233528}, language = {en}, number = {4}, urldate = {2021-06-29}, journal = {Plant Physiol.}, author = {Watkins, Justin M. and Hechler, Paul J. and Muday, Gloria K.}, month = apr, year = {2014}, pages = {1707--1717}, file = {Watkins et al. - 2014 - Ethylene-Induced Flavonol Accumulation in Guard Ce.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\BVVRHTX7\\Watkins et al. - 2014 - Ethylene-Induced Flavonol Accumulation in Guard Ce.pdf:application/pdf}, } @article{ikeuchi_wounding_2017-1, title = {Wounding {Triggers} {Callus} {Formation} via {Dynamic} {Hormonal} and {Transcriptional} {Changes}}, volume = {175}, issn = {0032-0889, 1532-2548}, url = {https://academic.oup.com/plphys/article/175/3/1158-1174/6116893}, doi = {10.1104/pp.17.01035}, language = {en}, number = {3}, urldate = {2021-06-29}, journal = {Plant Physiol.}, author = {Ikeuchi, Momoko and Iwase, Akira and Rymen, Bart and Lambolez, Alice and Kojima, Mikiko and Takebayashi, Yumiko and Heyman, Jefri and Watanabe, Shunsuke and Seo, Mitsunori and De Veylder, Lieven and Sakakibara, Hitoshi and Sugimoto, Keiko}, month = nov, year = {2017}, pages = {1158--1174}, file = {Ikeuchi et al. - 2017 - Wounding Triggers Callus Formation via Dynamic Hor.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\7DCN35VL\\Ikeuchi et al. - 2017 - Wounding Triggers Callus Formation via Dynamic Hor.pdf:application/pdf}, } @article{zhang_common_2020-4, title = {A common wild rice-derived {BOC1} allele reduces callus browning in indica rice transformation}, volume = {11}, issn = {2041-1723}, url = {http://www.nature.com/articles/s41467-019-14265-0}, doi = {10.1038/s41467-019-14265-0}, abstract = {Abstract Callus browning, a common trait derived from the indica rice cultivar ( Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 ( BOC1 ) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession ( Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1 , which consequently improves the genetic transformation efficiency. The presence of a Tourist -like miniature inverted-repeat transposable element ( Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Nat Commun}, author = {Zhang, Kun and Su, Jingjing and Xu, Min and Zhou, Zhihui and Zhu, Xiaoyang and Ma, Xin and Hou, Jingjing and Tan, Lubin and Zhu, Zuofeng and Cai, Hongwei and Liu, Fengxia and Sun, Hongying and Gu, Ping and Li, Chen and Liang, Yuntao and Zhao, Wensheng and Sun, Chuanqing and Fu, Yongcai}, month = dec, year = {2020}, pages = {443}, file = {Zhang et al. - 2020 - A common wild rice-derived BOC1 allele reduces cal.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\L73WQV57\\Zhang et al. - 2020 - A common wild rice-derived BOC1 allele reduces cal.pdf:application/pdf}, } @article{binder_ethylene_2020-3, title = {Ethylene signaling in plants}, volume = {295}, issn = {00219258}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925817494610}, doi = {10.1074/jbc.REV120.010854}, language = {en}, number = {22}, urldate = {2021-06-29}, journal = {Journal of Biological Chemistry}, author = {Binder, Brad M.}, month = may, year = {2020}, pages = {7710--7725}, file = {Binder - 2020 - Ethylene signaling in plants.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\S6EG7ZKY\\Binder - 2020 - Ethylene signaling in plants.pdf:application/pdf;3. Dunna, 2013.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\GRKFHYRI\\3. Dunna, 2013.pdf:application/pdf}, } @article{cunha_ethylene-induced_2017-1, title = {Ethylene-induced transcriptional and hormonal responses at the onset of sugarcane ripening}, volume = {7}, issn = {2045-2322}, url = {http://www.nature.com/articles/srep43364}, doi = {10.1038/srep43364}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Sci Rep}, author = {Cunha, Camila P. and Roberto, Guilherme G. and Vicentini, Renato and Lembke, Carolina G. and Souza, Glaucia M. and Ribeiro, Rafael V. and Machado, Eduardo C. and Lagôa, Ana M. M. A. and Menossi, Marcelo}, month = mar, year = {2017}, pages = {43364}, file = {Cunha et al. - 2017 - Ethylene-induced transcriptional and hormonal resp.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\47CUAQDQ\\Cunha et al. - 2017 - Ethylene-induced transcriptional and hormonal resp.pdf:application/pdf}, } @article{wang_tree1-ein3mediated_2020-1, title = {{TREE1}-{EIN3}–mediated transcriptional repression inhibits shoot growth in response to ethylene}, volume = {117}, issn = {0027-8424, 1091-6490}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2018735117}, doi = {10.1073/pnas.2018735117}, abstract = {Ethylene is an important plant hormone that regulates plant growth, in which the master transcriptionactivator EIN3 (Ethylene Insensitive 3)-mediated transcriptional activation plays vital roles. However, the EIN3-mediated transcriptional repression in ethylene response is unknown. We report here that a Transcriptional Repressor of EIN3-dependent Ethylene-response 1 (TREE1) interacts with EIN3 to regulate transcriptional repression that leads to an inhibition of shoot growth in response to ethylene. Tissue-specific transcriptome analysis showed that most of the genes are down-regulated by ethylene in shoots, and a DNA binding motif was identified that is important for this transcriptional repression. TREE1 binds to the DNA motif to repress gene expression in an EIN3-dependent manner. Genetic validation demonstrated that repression of TREE1-targeted genes leads to an inhibition of shoot growth. Overall, this work establishes a mechanism by which transcriptional repressor TREE1 interacts with EIN3 to inhibit shoot growth via transcriptional repression in response to ethylene.}, language = {en}, number = {46}, urldate = {2021-06-29}, journal = {Proc Natl Acad Sci USA}, author = {Wang, Likai and Ko, Eun Esther and Tran, Jaclyn and Qiao, Hong}, month = nov, year = {2020}, pages = {29178--29189}, file = {Wang et al. - 2020 - TREE1-EIN3–mediated transcriptional repression inh.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\4TPBWLVW\\Wang et al. - 2020 - TREE1-EIN3–mediated transcriptional repression inh.pdf:application/pdf}, } @article{sharma_modulatory_2017-1, title = {Modulatory {Effects} of {Exogenously} {Applied} {Polyamines} on {Postharvest} {Physiology}, {Antioxidant} {System} and {Shelf} {Life} of {Fruits}: {A} {Review}}, volume = {18}, issn = {1422-0067}, shorttitle = {Modulatory {Effects} of {Exogenously} {Applied} {Polyamines} on {Postharvest} {Physiology}, {Antioxidant} {System} and {Shelf} {Life} of {Fruits}}, url = {http://www.mdpi.com/1422-0067/18/8/1789}, doi = {10.3390/ijms18081789}, abstract = {Polyamines (PAs) are natural compounds involved in many growth and developmental processes in plants, and, specifically in fruits, play a vital role regulating its development, ripening and senescence processes. Putrescine (PUT), spermine (SPE), and spermidine (SPD) are prominent PAs applied exogenously to extend shelf life of fruits. They also originate endogenously during developmental phases of horticultural crops and simultaneously affect the quality attributes and shelf life. Their anti-ethylene nature is being exploited to enhance the shelf life when exogenously applied on fruits. In growth and development of fruits, PA levels generally fall, which marks the beginning of senescence at postharvest phase. PUT, SPE and SPD treatments are being applied during postharvest phase to prolong the shelf life. They enhance the shelf life of fruits by reducing respiration rate, ethylene release and enhance firmness and quality attributes in fruits. PAs have a mitigating impact on biotic and abiotic stresses including chilling injury (CI) in tropical and sub-tropical fruits. PAs are environment friendly in nature and are biodegradable without showing any negative effect on environment. Biotechnological interventions by using chimeric gene constructs of PA encoding genes has boosted the research to develop transgenic fruits and vegetables which would possess inherent or in situ mechanism of enhanced biosynthesis of PAs at different stages of development and thereby will enhance the shelf life and quality in fruits. Internal and external quality attributes of fruits are improved by modulation of antioxidant system and by strengthening biophysical morphology of fruits by electrostatic interaction between PAs and phospholipids in the cell wall.}, language = {en}, number = {8}, urldate = {2021-06-29}, journal = {IJMS}, author = {Sharma, Sunil and Pareek, Sunil and Sagar, Narashans and Valero, Daniel and Serrano, Maria}, month = aug, year = {2017}, pages = {1789}, file = {Sharma et al. - 2017 - Modulatory Effects of Exogenously Applied Polyamin.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\X56SU2EQ\\Sharma et al. - 2017 - Modulatory Effects of Exogenously Applied Polyamin.pdf:application/pdf}, } @article{sgamma_ethylene_2015-1, title = {Ethylene inhibitor silver nitrate enhances regeneration and genetic transformation of {Prunus} avium ({L}.) cv {Stella}}, volume = {120}, issn = {0167-6857, 1573-5044}, url = {http://link.springer.com/10.1007/s11240-014-0581-6}, doi = {10.1007/s11240-014-0581-6}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Plant Cell Tiss Organ Cult}, author = {Sgamma, Tiziana and Thomas, Brian and Muleo, Rosario}, month = jan, year = {2015}, pages = {79--88}, file = {Sgamma et al. - 2015 - Ethylene inhibitor silver nitrate enhances regener.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\ZZSGLJVA\\Sgamma et al. - 2015 - Ethylene inhibitor silver nitrate enhances regener.pdf:application/pdf}, } @incollection{schaller_inhibitors_2017, address = {New York, NY}, title = {Inhibitors of {Ethylene} {Biosynthesis} and {Signaling}}, volume = {1573}, isbn = {978-1-4939-6852-7 978-1-4939-6854-1}, url = {http://link.springer.com/10.1007/978-1-4939-6854-1_15}, abstract = {Ethylene is a gas biosynthesized by plants which has many physiological and developmental effects on their growth. Ethylene affects agriculturally and horticulturally important traits such as fruit ripening, postharvest physiology, senescence, and abscission, and so ethylene action is often inhibited to improve the shelf life of fruits, vegetables, and cut flowers. Chemical inhibitors of ethylene action are also useful for research to characterize the mechanisms of ethylene biosynthesis and signal transduction, and the role that ethylene plays in various physiological processes. Here, we describe the use of three inhibitors commonly used for the study of ethylene action in plants: 2-a­ minoethoxyvinyl glycine (AVG), silver ions (Ag), and the gaseous compound 1-methylcyclopropene (1-MCP). AVG is an inhibitor of 1-aminocyclopropane-1-carboxylic acid (ACC) synthase, a key enzyme involved in ethylene biosynthesis. Silver and 1-MCP are both inhibitors of the ethylene receptors. Inhibitor use as well as off-target effects are described with a focus on ethylene responses in dark-grown Arabidopsis seedlings. Methods for the use of these inhibitors can be applied to other plant growth assays.}, language = {en}, urldate = {2021-06-29}, booktitle = {Ethylene {Signaling}}, publisher = {Springer New York}, author = {Schaller, G. Eric and Binder, Brad M.}, editor = {Binder, Brad M. and Eric Schaller, G.}, year = {2017}, doi = {10.1007/978-1-4939-6854-1_15}, pages = {223--235}, annote = {Series Title: Methods in Molecular Biology}, file = {Schaller and Binder - 2017 - Inhibitors of Ethylene Biosynthesis and Signaling.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\77WDLCAD\\Schaller and Binder - 2017 - Inhibitors of Ethylene Biosynthesis and Signaling.pdf:application/pdf}, } @article{barros_detection_2013-1, title = {Detection of 1-aminocyclopropane-1-carboxylate oxidase activity in seeds of {Stylosanthes} humilis {H}.{B}.{K}}, issn = {21970025}, url = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S2197-00252013000300008&lng=en&nrm=iso&tlng=en}, doi = {10.1590/S2197-00252013000300008}, abstract = {The activity of 1-aminocyclopropane-1-carboxylate oxidase (ACO) was characterized in seeds of the tropical legume Townsville stylo (Stylosanthes humilis) both in vitro (desalted extract of non-dormant seeds) and in vivo (entire dormant seeds). Optimum conditions for maximum in vitro ACO activity in a Trizma-HCl 100 mM buffered medium were: pH 7.0, temperature 32ºC and cofactors and co-substrate at the following concentrations: NaHCO3 30 mM, sodium ascorbate 30 mM and FeSO4 50 μM. Rates of in vitro reaction catalyzed by ACO were shown to be constant within the interval 15-150 minutes from the onset of the reaction. The apparent Km for in vitro ACO, as determined from the non-linear curve fitting to the Michaelis-Menten equation, was 156±8.3 μM ACC with a Vmax 5.4±0.08 mmol (ET) g-1 h-1 on a fresh matter (FM) basis. In vivo (control basal medium: HCl-KOH 10 mM pH 7.0, 30ºC, reaction time 15 hours) apparent Km was 230±27 μM ACC and Vmax 11.9±0.38 mmol (ET) g-1.h-1 on a FM basis. These data suggest that the enzyme exhibits a relatively low affinity for the substrate. The well-known inhibitors of ACO activity, α-aminoisobutyric acid, salicylic and acetylsalicylic acids, n-propylgallate and cobaltous ions, were highly effective in inhibiting ACO activity of Townsville stylo seeds.}, language = {en}, urldate = {2021-06-29}, journal = {Theor. Exp. Plant Physiol.}, author = {Barros, Raimundo Santos and Araújo Pinheiro, Frank James and Müller, Caroline and Pires, Marcel Viana and Silva, Alexei Gresta Vieira da and Ribeiro, Dimas Mendes}, year = {2013}, file = {Barros et al. - 2013 - Detection of 1-aminocyclopropane-1-carboxylate oxi.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\HPRJUUP3\\Barros et al. - 2013 - Detection of 1-aminocyclopropane-1-carboxylate oxi.pdf:application/pdf}, } @article{suekawa_exogenous_2019-1, title = {Exogenous proline has favorable effects on growth and browning suppression in rice but not in tobacco}, volume = {142}, issn = {09819428}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0981942819302670}, doi = {10.1016/j.plaphy.2019.06.032}, abstract = {Proline is one of the amino acids that compose proteins and has various roles under non-stress and stress conditions. In this study, we investigated the effect of proline on the growth and browning of two plants, tobacco and rice, by exogenous application and endogenous increase of proline. Exogenous proline had a different effect on the growth and browning between tobacco and rice: proline affected negatively the growth of tobacco seedlings and favorably that of rice seedlings. In addition, proline prevented browning only in rice cultured cells, consistent with the increase of proline contents, but not in tobacco BY-2 cells. These results might be due to the difference of exogenous proline uptake activity in these cells. From the Lineweaver-Burk plots, proline inhibited polyphenol oxidase activity in vitro, which is a major factor of enzymatic browning in plants, by affecting the enzyme-substrate complex. Proline could suppress the browning of the plant callus by inhibition of PPO activity.}, language = {en}, urldate = {2021-06-29}, journal = {Plant Physiology and Biochemistry}, author = {Suekawa, Marina and Fujikawa, Yukichi and Esaka, Muneharu}, month = sep, year = {2019}, pages = {1--7}, file = {Suekawa et al. - 2019 - Exogenous proline has favorable effects on growth .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\RSC357FG\\Suekawa et al. - 2019 - Exogenous proline has favorable effects on growth .pdf:application/pdf}, } @article{sun_pyrazinamide_2017-1, title = {Pyrazinamide and derivatives block ethylene biosynthesis by inhibiting {ACC} oxidase}, volume = {8}, issn = {2041-1723}, url = {http://www.nature.com/articles/ncomms15758}, doi = {10.1038/ncomms15758}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Nat Commun}, author = {Sun, Xiangzhong and Li, Yaxin and He, Wenrong and Ji, Chenggong and Xia, Peixue and Wang, Yichuan and Du, Shuo and Li, Hongjiang and Raikhel, Natasha and Xiao, Junyu and Guo, Hongwei}, month = aug, year = {2017}, pages = {15758}, file = {Sun et al. - 2017 - Pyrazinamide and derivatives block ethylene biosyn.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\HM3PJ72I\\Sun et al. - 2017 - Pyrazinamide and derivatives block ethylene biosyn.pdf:application/pdf}, } @article{kuklin_ethylene_1995-1, title = {Ethylene {Impact} on {Somatic} {Embryogenesis}: {Biotechnological} {Considerations}}, volume = {9}, issn = {1310-2818, 1314-3530}, shorttitle = {Ethylene {Impact} on {Somatic} {Embryogenesis}}, url = {http://www.tandfonline.com/doi/abs/10.1080/13102818.1995.10818856}, doi = {10.1080/13102818.1995.10818856}, abstract = {The gaseous plant hormone ethylene affects somatic emb1yogenesis in various ways depending on the species or explants used. Inclusion of ethylene action inhibitors, name{\textbackslash}textasciitildev silver ions in culture media increased somatic embryogenesis in some species. Large scale (bioreactor) yields of somatic emb1yos were less than these ji·01n flask cultures. Ethylene depletion from the bioreactors due to aeration is considered as a possible reason for the decrease in somatic emb1yogenesis. Ethylene is discussed as a physiological marker related to emb1yogenic potential. {\textbackslash}textasciitildeVound ethylene evolved after transformation experiments might have some inhibit01:v role on transformation but results are contradictory. Ethylene plays different roles in long term storage (low and ambient temperatures) of emb1yogenic cultures. Use of transgenic technology in ethylene biosynthesis reduction is discussed as a way to understanding ethylene role in somatic emb(vogenesis.}, language = {en}, number = {4}, urldate = {2021-06-29}, journal = {Biotechnology \& Biotechnological Equipment}, author = {Kuklin, A.}, month = jan, year = {1995}, pages = {12--19}, file = {Kuklin - 1995 - Ethylene Impact on Somatic Embryogenesis Biotechn.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\J5EGXEN7\\Kuklin - 1995 - Ethylene Impact on Somatic Embryogenesis Biotechn.pdf:application/pdf}, } @article{wang_transcriptomes_2021-1, title = {Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in {Hevea} brasiliensis}, volume = {22}, issn = {1471-2164}, url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07501-9}, doi = {10.1186/s12864-021-07501-9}, abstract = {Background: Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE are still not well understood. Results: In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92\% of them were mapped to the rubber tree genome. The de novo assembly generated 36,937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions: This study provides important information to elucidate the molecular regulation during rubber tree late SE.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {BMC Genomics}, author = {Wang, Ying and Li, Hui-Liang and Zhou, Yong-Kai and Guo, Dong and Zhu, Jia-Hong and Peng, Shi-Qing}, month = dec, year = {2021}, pages = {183}, file = {Wang et al. - 2021 - Transcriptomes analysis reveals novel insight into.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\K4ANRUSU\\Wang et al. - 2021 - Transcriptomes analysis reveals novel insight into.pdf:application/pdf}, } @article{wojcik_current_2020-1, title = {Current {Perspectives} on the {Auxin}-{Mediated} {Genetic} {Network} that {Controls} the {Induction} of {Somatic} {Embryogenesis} in {Plants}}, volume = {21}, issn = {1422-0067}, url = {https://www.mdpi.com/1422-0067/21/4/1333}, doi = {10.3390/ijms21041333}, abstract = {Auxin contributes to almost every aspect of plant development and metabolism as well as the transport and signalling of auxin-shaped plant growth and morphogenesis in response to endo- and exogenous signals including stress conditions. Consistently with the common belief that auxin is a central trigger of developmental changes in plants, the auxin treatment of explants was reported to be an indispensable inducer of somatic embryogenesis (SE) in a large number of plant species. Treating in vitro-cultured tissue with auxins (primarily 2,4-dichlorophenoxyacetic acid, which is a synthetic auxin-like plant growth regulator) results in the extensive reprogramming of the somatic cell transcriptome, which involves the modulation of numerous SE-associated transcription factor genes (TFs). A number of SE-modulated TFs that control auxin metabolism and signalling have been identified, and conversely, the regulators of the auxin-signalling pathway seem to control the SE-involved TFs. In turn, the different expression of the genes encoding the core components of the auxin-signalling pathway, the AUXIN/INDOLE-3-ACETIC ACIDs (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs), was demonstrated to accompany SE induction. Thus, the extensive crosstalk between the hormones, in particular, auxin and the TFs, was revealed to play a central role in the SE-regulatory network. Accordingly, LEAFY COTYLEDON (LEC1 and LEC2), BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15) and WUSCHEL (WUS) were found to constitute the central part of the complex regulatory network that directs the somatic plant cell towards embryogenic development in response to auxin. The revealing picture shows a high degree of complexity of the regulatory relationships between the TFs of the SE-regulatory network, which involve direct and indirect interactions and regulatory feedback loops. This review examines the recent advances in studies on the auxin-controlled genetic network, which is involved in the mechanism of SE induction and focuses on the complex regulatory relationships between the down- and up-stream targets of the SE-regulatory TFs. In particular, the outcomes from investigations on Arabidopsis, which became a model plant in research on genetic control of SE, are presented.}, language = {en}, number = {4}, urldate = {2021-06-29}, journal = {IJMS}, author = {Wójcik, Anna M. and Wójcikowska, Barbara and Gaj, Małgorzata D.}, month = feb, year = {2020}, pages = {1333}, file = {Wójcik et al. - 2020 - Current Perspectives on the Auxin-Mediated Genetic.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\FR2IKD9W\\Wójcik et al. - 2020 - Current Perspectives on the Auxin-Mediated Genetic.pdf:application/pdf}, } @article{abiri_enhancing_2017-3, title = {Enhancing somatic embryogenesis of {Malaysian} rice cultivar {MR219} using adjuvant materials in a high-efficiency protocol}, volume = {14}, issn = {1735-1472, 1735-2630}, url = {http://link.springer.com/10.1007/s13762-016-1221-y}, doi = {10.1007/s13762-016-1221-y}, language = {en}, number = {5}, urldate = {2021-06-29}, journal = {Int. J. Environ. Sci. Technol.}, author = {Abiri, R. and Maziah, M. and Shaharuddin, N. A. and Yusof, Z. N. B. and Atabaki, N. and Hanafi, M. M. and Sahebi, M. and Azizi, P. and Kalhori, N. and Valdiani, A.}, month = may, year = {2017}, pages = {1091--1108}, file = {Abiri et al. - 2017 - Enhancing somatic embryogenesis of Malaysian rice .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\IYA496E6\\Abiri et al. - 2017 - Enhancing somatic embryogenesis of Malaysian rice .pdf:application/pdf}, } @article{wojcikowska_epigenetic_2020-1, title = {Epigenetic {Regulation} of {Auxin}-{Induced} {Somatic} {Embryogenesis} in {Plants}}, volume = {21}, issn = {1422-0067}, url = {https://www.mdpi.com/1422-0067/21/7/2307}, doi = {10.3390/ijms21072307}, abstract = {Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.}, language = {en}, number = {7}, urldate = {2021-06-29}, journal = {IJMS}, author = {Wójcikowska, Barbara and Wójcik, Anna M. and Gaj, Małgorzata D.}, month = mar, year = {2020}, pages = {2307}, file = {Wójcikowska et al. - 2020 - Epigenetic Regulation of Auxin-Induced Somatic Emb.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\DTGEDUUT\\Wójcikowska et al. - 2020 - Epigenetic Regulation of Auxin-Induced Somatic Emb.pdf:application/pdf}, } @article{ma_auxin_2018-3, title = {Auxin signaling: a big question to be addressed by small molecules}, volume = {69}, issn = {0022-0957, 1460-2431}, shorttitle = {Auxin signaling}, url = {https://academic.oup.com/jxb/article/69/2/313/4641657}, doi = {10.1093/jxb/erx375}, abstract = {Providing a mechanistic understanding of the crucial roles of the phytohormone auxin has been an important and coherent aspect of plant biology research. Since its discovery more than a century ago, prominent advances have been made in the understanding of auxin action, ranging from metabolism and transport to cellular and transcriptional responses. However, there is a long road ahead before a thorough understanding of its complex effects is achieved, because a lot of key information is still missing. The availability of an increasing number of technically advanced scientific tools has boosted the basic discoveries in auxin biology. A plethora of bioactive small molecules, consisting of the synthetic auxin-like herbicides and the more specific auxin-related compounds, developed as a result of the exploration of chemical space by chemical biology, have made the tool box for auxin research more comprehensive. This review mainly focuses on the compounds targeting the auxin co-receptor complex, demonstrates the various ways to use them, and shows clear examples of important basic knowledge obtained by their usage. Application of these precise chemical tools, together with an increasing amount of structural information for the major components in auxin action, will certainly aid in strengthening our insights into the complexity and diversity of auxin response.}, language = {en}, number = {2}, urldate = {2021-06-29}, journal = {Journal of Experimental Botany}, author = {Ma, Qian and Grones, Peter and Robert, Stéphanie}, month = jan, year = {2018}, pages = {313--328}, file = {Ma et al. - 2018 - Auxin signaling a big question to be addressed by.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\QP7T72ME\\Ma et al. - 2018 - Auxin signaling a big question to be addressed by.pdf:application/pdf}, } @article{a_libin_callus_2012-3, title = {Callus induction and plant regeneration of {Sarawak} rice ({Oryza} sativa {L}.) variety {Biris}}, volume = {7}, issn = {1991637X}, url = {http://www.academicjournals.org/ajar/abstracts/abstracts/Abstracts%202012/7Aug/Libin%20et%20al.htm}, doi = {10.5897/AJAR12.587}, abstract = {Sarawak Biris rice is a strong aromatic rice variety which can thrive well in rice fields prone to flood, drought and other soil constraints. Tissue culture of Biris rice is important in producing planting materials and conducting genetic improvement work. The present study was conducted to induce callus from Biris rice seed and assess its regeneration ability. Dehusked mature seeds were used as starting materials for callus induction. Sterilized seeds were cultured onto Murashige and Skoog medium containing various concentrations of 2, 4-dichlorophenoxyacetic acid (2, 4-D). The optimum 2, 4-D concentration for callus induction was 2.0 mg/L with a frequency as high as 97\%. The calli produced were of desired features (creamy in colour, globular) and relatively bigger in size as compared to other treatments. The calli produced were further tested with plant growth regulator, naphthaleneacetic acid (NAA) in combination with kinetin (Kn) for plant regeneration ability. All uncontaminated calli were found to regenerate. Up to nine shoots were induced by a callus treated with 0.5 mg/L NAA in combination with 1.0 mg/L Kn. The present study should be noted as the first attempt to induce callus and regenerate plants from seeds of Biris rice.}, language = {en}, number = {30}, urldate = {2021-06-29}, journal = {Afr. J. Agric. Res.}, author = {{A. Libin,}}, month = aug, year = {2012}, file = {A. Libin, - 2012 - Callus induction and plant regeneration of Sarawak.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\LRV23RUH\\A. Libin, - 2012 - Callus induction and plant regeneration of Sarawak.pdf:application/pdf}, } @article{sun_genome-wide_2019-1, title = {Genome-{Wide} {Analysis} of {Cotton} {Auxin} {Early} {Response} {Gene} {Families} and {Their} {Roles} in {Somatic} {Embryogenesis}}, volume = {10}, issn = {2073-4425}, url = {https://www.mdpi.com/2073-4425/10/10/730}, doi = {10.3390/genes10100730}, abstract = {Auxin is well known to regulate growth and development processes. Auxin early response genes serve as a critical component of auxin signaling and mediate auxin regulation of diverse physiological processes. In the present study, a genome-wide identification and comprehensive analysis of auxin early response genes were conducted in upland cotton. A total of 71 auxin response factor (ARF), 86 Auxin/Indole-3-Acetic Acid (Aux/IAA), 63 Gretchen Hagen3 (GH3), and 194 small auxin upregulated RNA (SAUR) genes were identified in upland cotton, respectively. Phylogenetic analysis revealed that the ARF, GH3, and SAUR families were likely subject to extensive evolutionary divergence between Arabidopsis and upland cotton, while the Aux/IAA family was evolutionary conserved. Expression profiles showed that the ARF, Aux/IAA, GH3, and SAUR family genes were extensively involved in embryogenic competence acquisition of upland cotton callus. The Aux/IAA family genes generally showed a higher expression level in the non-embryogenic callus (NEC) of highly embryogenic cultivar CCRI24 than that of recalcitrant cultivar CCRI12, which may be conducive to initializing the embryogenic transformation. Auxin early response genes were tightly co-expressed with most of the known somatic embryogenesis (SE) related genes, indicating that these genes may regulate upland cotton SE by interacting with auxin early response genes.}, language = {en}, number = {10}, urldate = {2021-06-29}, journal = {Genes}, author = {{Sun} and {Wang} and {Ma} and {Li} and {Liu}}, month = sep, year = {2019}, pages = {730}, file = {Sun et al. - 2019 - Genome-Wide Analysis of Cotton Auxin Early Respons.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\ECXF8UCL\\Sun et al. - 2019 - Genome-Wide Analysis of Cotton Auxin Early Respons.pdf:application/pdf}, } @article{antoniadi_cell-surface_2020-1, title = {Cell-surface receptors enable perception of extracellular cytokinins}, volume = {11}, issn = {2041-1723}, url = {http://www.nature.com/articles/s41467-020-17700-9}, doi = {10.1038/s41467-020-17700-9}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Nat Commun}, author = {Antoniadi, Ioanna and Novák, Ondřej and Gelová, Zuzana and Johnson, Alexander and Plíhal, Ondřej and Simerský, Radim and Mik, Václav and Vain, Thomas and Mateo-Bonmatí, Eduardo and Karady, Michal and Pernisová, Markéta and Plačková, Lenka and Opassathian, Korawit and Hejátko, Jan and Robert, Stéphanie and Friml, Jiří and Doležal, Karel and Ljung, Karin and Turnbull, Colin}, month = dec, year = {2020}, pages = {4284}, file = {Antoniadi et al. - 2020 - Cell-surface receptors enable perception of extrac.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\Y9DJW6W8\\Antoniadi et al. - 2020 - Cell-surface receptors enable perception of extrac.pdf:application/pdf}, } @article{li_cytokinins_2021-1, title = {Cytokinins as central regulators during plant growth and stress response}, volume = {40}, issn = {0721-7714, 1432-203X}, url = {http://link.springer.com/10.1007/s00299-020-02612-1}, doi = {10.1007/s00299-020-02612-1}, abstract = {Key message Cytokinins are a class of phytohormone that participate in the regulation of the plant growth, development, and stress response. In this review, the potential regulating mechanism during plant growth and stress response are discussed.}, language = {en}, number = {2}, urldate = {2021-06-29}, journal = {Plant Cell Rep}, author = {Li, Si-Min and Zheng, Hong-Xiang and Zhang, Xian-Sheng and Sui, Na}, month = feb, year = {2021}, pages = {271--282}, file = {Li et al. - 2021 - Cytokinins as central regulators during plant grow.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\RR48A3JK\\Li et al. - 2021 - Cytokinins as central regulators during plant grow.pdf:application/pdf}, } @article{kieber_cytokinins_2014-4, title = {Cytokinins}, volume = {e0168}, issn = {1543-8120}, url = {http://www.bioone.org/doi/10.1199/tab.0168}, doi = {10.1199/tab.0168}, language = {en}, urldate = {2021-06-29}, journal = {The Arabidopsis Book}, author = {Kieber, Joseph J. and Schaller, G. Eric}, month = jan, year = {2014}, pages = {1--35}, file = {Kieber and Schaller - 2014 - Cytokinins.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\Q6IEE6MQ\\Kieber and Schaller - 2014 - Cytokinins.pdf:application/pdf}, } @article{kroll_cytokinin_2020-1, title = {Cytokinin {Signaling} {Downstream} of the {His}-{Asp} {Phosphorelay} {Network}: {Cytokinin}-{Regulated} {Genes} and {Their} {Functions}}, volume = {11}, issn = {1664-462X}, shorttitle = {Cytokinin {Signaling} {Downstream} of the {His}-{Asp} {Phosphorelay} {Network}}, url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.604489/full}, doi = {10.3389/fpls.2020.604489}, abstract = {The plant hormone cytokinin, existing in several molecular forms, is perceived by membrane-localized histidine kinases. The signal is transduced to transcription factors of the type-B response regulator family localized in the nucleus by a multi-step histidineaspartate phosphorelay network employing histidine phosphotransmitters as shuttle proteins across the nuclear envelope. The type-B response regulators activate a number of primary response genes, some of which trigger in turn further signaling events and the expression of secondary response genes. Most genes activated in both rounds of transcription were identified with high confidence using different transcriptomic toolkits and meta analyses of multiple individual published datasets. In this review, we attempt to summarize the existing knowledge about the primary and secondary cytokinin response genes in order to try connecting gene expression with the multitude of effects that cytokinin exerts within the plant body and throughout the lifespan of a plant.}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Kroll, Carlo K. and Brenner, Wolfram G.}, month = nov, year = {2020}, pages = {604489}, file = {Kroll and Brenner - 2020 - Cytokinin Signaling Downstream of the His-Asp Phos.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\YDGI9EVX\\Kroll and Brenner - 2020 - Cytokinin Signaling Downstream of the His-Asp Phos.pdf:application/pdf}, } @article{an_kinetin_2017-1, title = {Kinetin {Improves} {Barrier} {Function} of the {Skin} by {Modulating} {Keratinocyte} {Differentiation} {Markers}}, volume = {29}, issn = {1013-9087, 2005-3894}, url = {https://anndermatol.org/DOIx.php?id=10.5021/ad.2017.29.1.6}, doi = {10.5021/ad.2017.29.1.6}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Ann Dermatol}, author = {An, Sungkwan and Cha, Hwa Jun and Ko, Jung-Min and Han, Hyunjoo and Kim, Su Young and Kim, Kyung-Suk and Lee, Song Jeong and An, In-Sook and Kim, Sangwon and Youn, Hae Jeong and Ahn, Kyu Joong and Kim, Soo-Yeon}, year = {2017}, pages = {6}, file = {An et al. - 2017 - Kinetin Improves Barrier Function of the Skin by M.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\F8SBRDIV\\An et al. - 2017 - Kinetin Improves Barrier Function of the Skin by M.pdf:application/pdf}, } @article{rose_somatic_2019-1, title = {Somatic {Embryogenesis} in the {Medicago} truncatula {Model}: {Cellular} and {Molecular} {Mechanisms}}, volume = {10}, issn = {1664-462X}, shorttitle = {Somatic {Embryogenesis} in the {Medicago} truncatula {Model}}, url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00267/full}, doi = {10.3389/fpls.2019.00267}, abstract = {Medicago truncatula is now widely regarded as a legume model where there is an increasing range of genomic resources. Highly regenerable lines have been developed from the wildtype Jemalong cultivar, most likely due to epigenetic changes. These lines with high rates of somatic embryogenesis (SE) can be compared with wild-type where SE is rare. Much of the research has been with the high SE genotype Jemalong 2HA (2HA). SE can be induced from leaf tissue explants or isolated mesophyll protoplasts. In 2HA, the exogenous phytohormones 1-naphthaleneacetic acid (NAA) and 6-benzylaminopurine (BAP) are central to SE. However, there are interactions with ethylene, abscisic acid (ABA), and gibberellic acid (GA) which produce maximum SE. In the main, somatic embryos are derived from dedifferentiated cells, undergo organellar changes, and produce stem-like cells. There is evidence that the SE is induced as a result of a stress and hormone interaction and this is discussed. In M. truncatula, there are connections between stress and specific up-regulated genes and specific hormones and up-regulated genes during the SE induction phase. Some of the transcription factors have been knocked down using RNAi to show they are critical for SE induction (MtWUSCHEL, MtSERF1). SE research in M. truncatula has utilized high throughput transcriptomic and proteomic studies and the more detailed investigation of some individual genes. In this review, these studies are integrated to suggest a framework and timeline for some of the key events of SE induction in M. truncatula.}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Rose, Ray J.}, month = mar, year = {2019}, pages = {267}, file = {Rose - 2019 - Somatic Embryogenesis in the Medicago truncatula M.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\3S4R7GYM\\Rose - 2019 - Somatic Embryogenesis in the Medicago truncatula M.pdf:application/pdf}, } @article{li_identification_2017-1, title = {Identification of novel {miRNAs} and {miRNA} expression profiling in embryogenic tissues of {Picea} balfouriana treated by 6-benzylaminopurine}, volume = {12}, issn = {1932-6203}, url = {https://dx.plos.org/10.1371/journal.pone.0176112}, doi = {10.1371/journal.pone.0176112}, abstract = {Here, we compared miRNA expression profiles in embryonic cell cultures of the conifer Picea balfouriana following application of the synthetic cytokinin 6-benzylaminopurine (6-BAP). We used next-generation sequencing to analyze three libraries of small RNAs from the treated embryogenic cell cultures and generated 24,000,000 raw reads from each of the libraries. Over 70 differentially regulated micro RNA (miRNA) families (!2 fold change in expression) were identified between pairs of treatments. A quantitative analysis showed that miR3633 and miR1026 were upregulated in tissues with the highest embryogenic ability. These two miRNAs were predicted to target genes encoding receptor-like protein kinase and GAMYB transcription factors, respectively. In one library, miR1160, miR5638, miR1315, and miR5225 were downregulated. These four miRNAs were predicted to target genes encoding APETALA2, calmodulin-binding protein, and calciumdependent protein kinase transcription factors. The expression patterns of the miRNAs and their targets were negatively correlated. Approximately 181 potentially novel P. balfouriana miRNAs were predicted from the three libraries, and seven were validated during the quantitative analysis. This study is the first report of differential miRNA regulation in tissues treated with 6-BAP during somatic embryogenesis. The differentially expressed miRNAs will be of value for investigating the mechanisms of embryogenic processes that are responsive to 6-BAP in P. balfouriana.}, language = {en}, number = {5}, urldate = {2021-06-29}, journal = {PLoS ONE}, author = {Li, Qingfen and Deng, Cheng and Xia, Yan and Kong, Lisheng and Zhang, Hanguo and Zhang, Shougong and Wang, Junhui}, editor = {Zheng, Yun}, month = may, year = {2017}, pages = {e0176112}, file = {Li et al. - 2017 - Identification of novel miRNAs and miRNA expressio.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\5SPZH7KV\\Li et al. - 2017 - Identification of novel miRNAs and miRNA expressio.pdf:application/pdf}, } @article{ming_combination_2019-3, title = {Combination of {Plant} {Growth} {Regulators}, {Maltose}, and {Partial} {Desiccation} {Treatment} {Enhance} {Somatic} {Embryogenesis} in {Selected} {Malaysian} {Rice} {Cultivar}}, volume = {8}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/8/6/144}, doi = {10.3390/plants8060144}, abstract = {The development of efficient tissue culture protocol for somatic embryo would facilitate the genetic modification breeding program. The callus induction and regeneration were studied by using different parameters i.e., auxins, cytokinins, and desiccation treatment. Scanning electron microscopy and histological analysis were performed to identify the embryogenic callus for regeneration. The callus percentage results showed that MS (Murashige and Skoog) basal medium supplemented with 3 mg/L 2, 4-D and 30g/L maltose were the optimal callus induction medium for MR220 (80\%) and MR220-CL2 (95\%). The morphology of the embryogenic callus was confirmed by the SEM (Scanning Electron Microscopy) (presence of extracellular matrix surface network) and later by histological analysis. Finally, MS media supplemented with 0.5 mg/L NAA (Naphthalene Acetic Acid), 2 mg/L kin, and 1 mg/L BAP were selected as the optimum regeneration media treatment while callus desiccated for 48 h was proved to produce more plantlets in MR220 (60\%) and MR220-CL2 (73.33\%) compared to control treatment (without desiccation). The protocol presented here showed the necessity for the inclusion of partial desiccation as an important step in the tissue culture protocol of Malaysian indica rice genotypes in order to enhance their regeneration potential.}, language = {en}, number = {6}, urldate = {2021-06-29}, journal = {Plants}, author = {Ming, NG Ja and Binte Mostafiz, Suraiya and Johon, Nur Syafiqoh and Abdullah Zulkifli, Nur Saliha and Wagiran, Alina}, month = may, year = {2019}, pages = {144}, file = {Ming et al. - 2019 - Combination of Plant Growth Regulators, Maltose, a.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\6HLTTG3R\\Ming et al. - 2019 - Combination of Plant Growth Regulators, Maltose, a.pdf:application/pdf}, } @article{yang_ethylene_2015-1, title = {Ethylene {Signaling} in {Rice} and {Arabidopsis}: {Conserved} and {Diverged} {Aspects}}, volume = {8}, issn = {16742052}, shorttitle = {Ethylene {Signaling} in {Rice} and {Arabidopsis}}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205215000908}, doi = {10.1016/j.molp.2015.01.003}, abstract = {Ethylene as a gas phytohormone plays significant roles in the whole life cycle of plants, ranging from growth and development to stress responses. A linear ethylene signaling pathway has been established in the dicotyledonous model plant Arabidopsis. However, the ethylene signaling mechanism in monocotyledonous plants such as rice is largely unclear. In this review, we compare the ethylene response phenotypes of dark-grown seedlings of Arabidopsis, rice, and other monocotyledonous plants (maize, wheat, sorghum, and Brachypodium distachyon) and pinpoint that rice has a distinct phenotype of root inhibition but coleoptile promotion in etiolated seedlings upon ethylene treatment. We further summarize the homologous genes of Arabidopsis ethylene signaling components in these monocotyledonous plants and discuss recent progress. Although conserved in most aspects, ethylene signaling in rice has evolved new features compared with that in Arabidopsis. These analyses provide novel insights into the understanding of ethylene signaling in the dicotyledonous Arabidopsis and monocotyledonous plants, particularly rice. Further characterization of rice ethylene-responsive mutants and their corresponding genes will help us better understand the whole picture of ethylene signaling mechanisms in plants.}, language = {en}, number = {4}, urldate = {2021-06-29}, journal = {Molecular Plant}, author = {Yang, Chao and Lu, Xiang and Ma, Biao and Chen, Shou-Yi and Zhang, Jin-Song}, month = apr, year = {2015}, pages = {495--505}, file = {Yang et al. - 2015 - Ethylene Signaling in Rice and Arabidopsis Conser.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\V68HKA57\\Yang et al. - 2015 - Ethylene Signaling in Rice and Arabidopsis Conser.pdf:application/pdf}, } @article{khanday_male-expressed_2019-1, title = {A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds}, volume = {565}, issn = {0028-0836, 1476-4687}, url = {http://www.nature.com/articles/s41586-018-0785-8}, doi = {10.1038/s41586-018-0785-8}, language = {en}, number = {7737}, urldate = {2021-06-29}, journal = {Nature}, author = {Khanday, Imtiyaz and Skinner, Debra and Yang, Bing and Mercier, Raphael and Sundaresan, Venkatesan}, month = jan, year = {2019}, pages = {91--95}, file = {Khanday et al. - 2019 - A male-expressed rice embryogenic trigger redirect.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\MY2JXSCG\\Khanday et al. - 2019 - A male-expressed rice embryogenic trigger redirect.pdf:application/pdf}, } @article{lowe_morphogenic_2016-2, title = {Morphogenic {Regulators} \textit{{Baby}} boom and \textit{{Wuschel}} {Improve} {Monocot} {Transformation}}, volume = {28}, issn = {1040-4651, 1532-298X}, url = {https://academic.oup.com/plcell/article/28/9/1998-2015/6098336}, doi = {10.1105/tpc.16.00124}, language = {en}, number = {9}, urldate = {2021-06-29}, journal = {Plant Cell}, author = {Lowe, Keith and Wu, Emily and Wang, Ning and Hoerster, George and Hastings, Craig and Cho, Myeong-Je and Scelonge, Chris and Lenderts, Brian and Chamberlin, Mark and Cushatt, Josh and Wang, Lijuan and Ryan, Larisa and Khan, Tanveer and Chow-Yiu, Julia and Hua, Wei and Yu, Maryanne and Banh, Jenny and Bao, Zhongmeng and Brink, Kent and Igo, Elizabeth and Rudrappa, Bhojaraja and Shamseer, Pm and Bruce, Wes and Newman, Lisa and Shen, Bo and Zheng, Peizhong and Bidney, Dennis and Falco, Carl and Register, Jim and Zhao, Zuo-Yu and Xu, Deping and Jones, Todd and Gordon-Kamm, William}, month = sep, year = {2016}, pages = {1998--2015}, file = {Lowe et al. - 2016 - Morphogenic Regulators Baby boom and Wus.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\L3AEZ6CG\\Lowe et al. - 2016 - Morphogenic Regulators Baby boom and Wus.pdf:application/pdf}, } @article{nic-can_new_2013-1, title = {New {Insights} into {Somatic} {Embryogenesis}: {LEAFY} {COTYLEDON1}, {BABY} {BOOM1} and {WUSCHEL}-{RELATED} {HOMEOBOX4} {Are} {Epigenetically} {Regulated} in {Coffea} canephora}, volume = {8}, issn = {1932-6203}, shorttitle = {New {Insights} into {Somatic} {Embryogenesis}}, url = {https://dx.plos.org/10.1371/journal.pone.0072160}, doi = {10.1371/journal.pone.0072160}, abstract = {Plant cells have the capacity to generate a new plant without egg fertilization by a process known as somatic embryogenesis (SE), in which differentiated somatic cells can form somatic embryos able to generate a functional plant. Although there have been advances in understanding the genetic basis of SE, the epigenetic mechanism that regulates this process is still unknown. Here, we show that the embryogenic development of Coffea canephora proceeds through a crosstalk between DNA methylation and histone modifications during the earliest embryogenic stages of SE. We found that low levels of DNA methylation, histone H3 lysine 9 dimethylation (H3K9me2) and H3K27me3 change according to embryo development. Moreover, the expression of LEAFY COTYLEDON1 (LEC1) and BABY BOOM1 (BBM1) are only observed after SE induction, whereas WUSCHEL-RELATED HOMEOBOX4 (WOX4) decreases its expression during embryo maturation. Using a pharmacological approach, it was found that 5-Azacytidine strongly inhibits the embryogenic response by decreasing both DNA methylation and gene expression of LEC1 and BBM1. Therefore, in order to know whether these genes were epigenetically regulated, we used Chromatin Immunoprecipitation (ChIP) assays. It was found that WOX4 is regulated by the repressive mark H3K9me2, while LEC1 and BBM1 are epigenetically regulated by H3K27me3. We conclude that epigenetic regulation plays an important role during somatic embryogenic development, and a molecular mechanism for SE is proposed.}, language = {en}, number = {8}, urldate = {2021-06-29}, journal = {PLoS ONE}, author = {Nic-Can, Geovanny I. and López-Torres, Adolfo and Barredo-Pool, Felipe and Wrobel, Kazimierz and Loyola-Vargas, Víctor M. and Rojas-Herrera, Rafael and De-la-Peña, Clelia}, editor = {Candela, Hector}, month = aug, year = {2013}, pages = {e72160}, file = {Nic-Can et al. - 2013 - New Insights into Somatic Embryogenesis LEAFY COT.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\AFSHLG5N\\Nic-Can et al. - 2013 - New Insights into Somatic Embryogenesis LEAFY COT.pdf:application/pdf}, } @article{duan_strigolactone_2019-3, title = {Strigolactone promotes cytokinin degradation through transcriptional activation of \textit{{CYTOKININ}} {OXIDASE}/{DEHYDROGENASE} 9 in rice}, volume = {116}, issn = {0027-8424, 1091-6490}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1810980116}, doi = {10.1073/pnas.1810980116}, abstract = {Strigolactones (SLs), a group of terpenoid lactones derived from carotenoids, are plant hormones that control numerous aspects of plant development. Although the framework of SL signaling that the repressor DWARF 53 (D53) could be SL-dependently degraded via the SL receptor D14 and F-box protein D3 has been established, the downstream response genes to SLs remain to be elucidated. Here we show that the cytokinin (CK) content is dramatically increased in shoot bases of the rice SL signaling mutant d53 . By examining transcript levels of all the CK metabolism-related genes after treatment with SL analog GR24, we identified CYTOKININ OXIDASE/DEHYDROGENASE 9 ( OsCKX9 ) as a primary response gene significantly up-regulated within 1 h of treatment in the wild type but not in d53 . We also found that OsCKX9 functions as a cytosolic and nuclear dual-localized CK catabolic enzyme, and that the overexpression of OsCKX9 suppresses the browning of d53 calli. Both the CRISPR/Cas9-generated OsCKX9 mutants and OsCKX9 -overexpressing transgenic plants showed significant increases in tiller number and decreases in plant height and panicle size, suggesting that the homeostasis of OsCKX9 plays a critical role in regulating rice shoot architecture. Moreover, we identified the CK-inducible rice type-A response regulator OsRR5 as the secondary SL-responsive gene, whose expression is significantly repressed after 4 h of GR24 treatment in the wild type but not in osckx9 . These findings reveal a comprehensive plant hormone cross-talk in which SL can induce the expression of OsCKX9 to down-regulate CK content, which in turn triggers the response of downstream genes.}, language = {en}, number = {28}, urldate = {2021-06-29}, journal = {Proc Natl Acad Sci USA}, author = {Duan, Jingbo and Yu, Hong and Yuan, Kun and Liao, Zhigang and Meng, Xiangbing and Jing, Yanhui and Liu, Guifu and Chu, Jinfang and Li, Jiayang}, month = jul, year = {2019}, pages = {14319--14324}, file = {Duan et al. - 2019 - Strigolactone promotes cytokinin degradation throu.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\5IHG45YF\\Duan et al. - 2019 - Strigolactone promotes cytokinin degradation throu.pdf:application/pdf}, } @article{mou_ethylene-independent_2020-1, title = {Ethylene-independent signaling by the ethylene precursor {ACC} in {Arabidopsis} ovular pollen tube attraction}, volume = {11}, issn = {2041-1723}, url = {http://www.nature.com/articles/s41467-020-17819-9}, doi = {10.1038/s41467-020-17819-9}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Nat Commun}, author = {Mou, Wangshu and Kao, Yun-Ting and Michard, Erwan and Simon, Alexander A. and Li, Dongdong and Wudick, Michael M. and Lizzio, Michael A. and Feijó, José A. and Chang, Caren}, month = dec, year = {2020}, pages = {4082}, file = {Mou et al. - 2020 - Ethylene-independent signaling by the ethylene pre.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\J2WUHWVI\\Mou et al. - 2020 - Ethylene-independent signaling by the ethylene pre.pdf:application/pdf}, } @article{zhang_common_2020-5, title = {A common wild rice-derived {BOC1} allele reduces callus browning in indica rice transformation}, volume = {11}, issn = {2041-1723}, url = {http://www.nature.com/articles/s41467-019-14265-0}, doi = {10.1038/s41467-019-14265-0}, abstract = {Abstract Callus browning, a common trait derived from the indica rice cultivar ( Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 ( BOC1 ) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession ( Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1 , which consequently improves the genetic transformation efficiency. The presence of a Tourist -like miniature inverted-repeat transposable element ( Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Nat Commun}, author = {Zhang, Kun and Su, Jingjing and Xu, Min and Zhou, Zhihui and Zhu, Xiaoyang and Ma, Xin and Hou, Jingjing and Tan, Lubin and Zhu, Zuofeng and Cai, Hongwei and Liu, Fengxia and Sun, Hongying and Gu, Ping and Li, Chen and Liang, Yuntao and Zhao, Wensheng and Sun, Chuanqing and Fu, Yongcai}, month = dec, year = {2020}, pages = {443}, file = {Zhang et al. - 2020 - A common wild rice-derived BOC1 allele reduces cal.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\B2H4YQM5\\Zhang et al. - 2020 - A common wild rice-derived BOC1 allele reduces cal.pdf:application/pdf}, } @article{wambugu_genetics_2021-1, title = {Genetics and {Genomics} of {African} {Rice} ({Oryza} glaberrima {Steud}) {Domestication}}, volume = {14}, issn = {1939-8425, 1939-8433}, url = {https://thericejournal.springeropen.com/articles/10.1186/s12284-020-00449-6}, doi = {10.1186/s12284-020-00449-6}, abstract = {African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Rice}, author = {Wambugu, Peterson W. and Ndjiondjop, Marie-Noelle and Henry, Robert}, month = dec, year = {2021}, pages = {6}, file = {Wambugu et al. - 2021 - Genetics and Genomics of African Rice (Oryza glabe.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\4GTYBZYS\\Wambugu et al. - 2021 - Genetics and Genomics of African Rice (Oryza glabe.pdf:application/pdf}, } @article{rodrigo_risk_2021-1, title = {Risk of {Bacillus} cereus in {Relation} to {Rice} and {Derivatives}}, volume = {10}, issn = {2304-8158}, url = {https://www.mdpi.com/2304-8158/10/2/302}, doi = {10.3390/foods10020302}, abstract = {Rice is a very popular food throughout the world and the basis of the diet of the citizens of many countries. It is used as a raw material for the preparation of many complex dishes in which different ingredients are involved. Rice, as a consequence of their cultivation, harvesting, and handling, is often contaminated with spores of Bacillus cereus, a ubiquitous microorganism found mainly in the soil. B. cereus can multiply under temperature conditions as low as 4 ◦C in foods that contain rice and have been cooked or subjected to treatments that do not produce commercial sterility. B. cereus produces diarrhoeal or emetic foodborne toxin when the consumer eats food in which a sufficient number of cells have grown. These circumstances mean that every year many outbreaks of intoxication or intestinal problems related to this microorganism are reported. This work is a review from the perspective of risk assessment of the risk posed by B. cereus to the health of consumers and of some control measures that can be used to mitigate such a risk.}, language = {en}, number = {2}, urldate = {2021-06-29}, journal = {Foods}, author = {Rodrigo, Dolores and Rosell, Cristina M. and Martinez, Antonio}, month = feb, year = {2021}, pages = {302}, file = {Rodrigo et al. - 2021 - Risk of Bacillus cereus in Relation to Rice and De.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\YXV2X4T8\\Rodrigo et al. - 2021 - Risk of Bacillus cereus in Relation to Rice and De.pdf:application/pdf}, } @article{ciulu_extraction_2018-1, title = {Extraction and {Analysis} of {Phenolic} {Compounds} in {Rice}: {A} {Review}}, volume = {23}, issn = {1420-3049}, shorttitle = {Extraction and {Analysis} of {Phenolic} {Compounds} in {Rice}}, url = {http://www.mdpi.com/1420-3049/23/11/2890}, doi = {10.3390/molecules23112890}, abstract = {Rice represents the main source of calorie intake in many world countries and about 60\% of the world population include rice in their staple diet. Whole grain rice, also called brown rice, represent the unpolished version of the more common white rice including bran, germ, and endosperm. Many health-promoting properties have been associated to the consumption of whole grain rice and, for this reason, great attention has been paid by the scientific community towards the identification and the quantification of bioactive compounds in this food item. In this contribution, the last five years progresses in the quali-quantitative determination of phenolic compounds in rice have been highlighted. Special attention has been devoted to the most recent strategies for the extraction of the target compounds from rice along with the analytical approaches adopted for the separation, identification and quantification of phenolic acids, flavonoids, anthocyanins, and proanthocyanidins. More specifically, the main features of the “traditional” extraction methods (i.e., maceration, ultrasound-assisted extraction) have been described, as well as the more innovative protocols involving advanced extraction techniques, such as MAE (microwave-assisted extraction). The predominant role of HPLC in the definition of the phenolic profile has been examined also presenting the most recent results obtained by using mass spectrometry-based detection systems. In addition, the most common procedures aimed to the quantification of the total amount of the cited classes of phenolic compounds have been described together with the spectrophotometric protocols aimed to the evaluation of the antioxidant properties of rice phenolic extracts (i.e., FRAP, DPPH, ABTS and ORAC).}, language = {en}, number = {11}, urldate = {2021-06-29}, journal = {Molecules}, author = {Ciulu, Marco and Cádiz-Gurrea, Maria and Segura-Carretero, Antonio}, month = nov, year = {2018}, pages = {2890}, file = {Ciulu et al. - 2018 - Extraction and Analysis of Phenolic Compounds in R.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\NKLRZ526\\Ciulu et al. - 2018 - Extraction and Analysis of Phenolic Compounds in R.pdf:application/pdf}, } @article{efferth_biotechnology_2019-1, title = {Biotechnology {Applications} of {Plant} {Callus} {Cultures}}, volume = {5}, issn = {20958099}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2095809918306131}, doi = {10.1016/j.eng.2018.11.006}, abstract = {In ethnopharmacology, and especially in traditional Chinese medicine, medicinal plants have been used for thousands of years. Similarly, agricultural plants have been used throughout the history of mankind. The recent development of the genetic engineering of plants to produce plants with desirable features adds a new and growing dimension to humanity’s usage of plants. The biotechnology of plants has come of age and a plethora of bioengineering applications in this context have been delineated during the past few decades. Callus cultures and suspension cell cultures offer a wide range of usages in pharmacology and pharmacy (including Chinese medicine), as well as in agriculture and horticulture. This review provides a timely overview of the advancements that have been made with callus cultures in these scientific fields. Genetically modified callus cultures by gene technological techniques can be used for the synthesis of bioactive secondary metabolites and for the generation of plants with improved resistance against salt, draft, diseases, and pests. Although the full potential of callus plant culture technology has not yet been exploited, the time has come to develop and market more callus culture-based products.}, language = {en}, number = {1}, urldate = {2021-06-29}, journal = {Engineering}, author = {Efferth, Thomas}, month = feb, year = {2019}, pages = {50--59}, file = {Efferth - 2019 - Biotechnology Applications of Plant Callus Culture.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\YI9RZSR4\\Efferth - 2019 - Biotechnology Applications of Plant Callus Culture.pdf:application/pdf}, } @article{mendez-hernandez_signaling_2019-2, title = {Signaling {Overview} of {Plant} {Somatic} {Embryogenesis}}, volume = {10}, issn = {1664-462X}, url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00077/full}, doi = {10.3389/fpls.2019.00077}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Méndez-Hernández, Hugo A. and Ledezma-Rodríguez, Maharshi and Avilez-Montalvo, Randy N. and Juárez-Gómez, Yary L. and Skeete, Analesa and Avilez-Montalvo, Johny and De-la-Peña, Clelia and Loyola-Vargas, Víctor M.}, month = feb, year = {2019}, pages = {77}, file = {Méndez-Hernández et al. - 2019 - Signaling Overview of Plant Somatic Embryogenesis.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\VKV2LC8X\\Méndez-Hernández et al. - 2019 - Signaling Overview of Plant Somatic Embryogenesis.pdf:application/pdf}, } @article{martinez_holm_2019-1, title = {Holm {Oak} {Somatic} {Embryogenesis}: {Current} {Status} and {Future} {Perspectives}}, volume = {10}, issn = {1664-462X}, shorttitle = {Holm {Oak} {Somatic} {Embryogenesis}}, url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00239/full}, doi = {10.3389/fpls.2019.00239}, abstract = {Quercus ilex (holm oak) is one of the most representative trees in the Mediterranean basin, but now the sustainability of its ecosystems is at serious risk due to the lack of natural regeneration and to the presence of a severe disease called oak decline that has caused the death of thousands of trees. The application of biotechnological tools, such as somatic embryogenesis, allows programs of genetic improvement of the species to be speeded up and helps in the conservation of its ecosystems. Somatic embryogenesis is currently considered one of the main biotechnological techniques that has demonstrated significant benefits when has applied to forest tree species, providing significant advantages such as mass propagation, genetic transformation, application of synthetic seed, and cryopreservation of elite genotypes. In this report, the state of the art of somatic embryogenesis in holm oak is reviewed. Factors affecting the induction (plant donor age, type of explant, or plant growth regulators) and maintenance and proliferation of the embryogenic cultures are summarized. Advances on the conversion of somatic embryos into plants and on the acclimatization of these plantlets, as well as the results obtained on the application of the genetic transformation and the cryopreservation procedures to holm oak embryogenic cultures, are also presented.}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Martínez, María Teresa and San-José, María del Carmen and Arrillaga, Isabel and Cano, Vanesa and Morcillo, Marián and Cernadas, María José and Corredoira, Elena}, month = mar, year = {2019}, pages = {239}, file = {Martínez et al. - 2019 - Holm Oak Somatic Embryogenesis Current Status and.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\HIZD7NNE\\Martínez et al. - 2019 - Holm Oak Somatic Embryogenesis Current Status and.pdf:application/pdf}, } @article{nic-can_somatic_2015-1, title = {Somatic {Embryogenesis}: {Identified} {Factors} that {Lead} to {Embryogenic} {Repression}. {A} {Case} of {Species} of the {Same} {Genus}}, volume = {10}, issn = {1932-6203}, shorttitle = {Somatic {Embryogenesis}}, url = {https://dx.plos.org/10.1371/journal.pone.0126414}, doi = {10.1371/journal.pone.0126414}, abstract = {Somatic embryogenesis is a powerful biotechnological tool for the mass production of economically important cultivars. Due to the cellular totipotency of plants, somatic cells under appropriate conditions are able to develop a complete functional embryo. During the induction of somatic embryogenesis, there are different factors involved in the success or failure of the somatic embryogenesis response. Among these factors, the origin of the explant, the culture medium and the in vitro environmental conditions have been the most studied. However, the secretion of molecules into the media has not been fully addressed. We found that the somatic embryogenesis of Coffea canephora, a highly direct embryogenic species, is disrupted by the metabolites secreted from C. arabica, a poorly direct embryogenic species. These metabolites also affect DNA methylation. Our results show that the abundance of two major phenolic compounds, caffeine and chlorogenic acid, are responsible for inhibiting somatic embryogenesis in C. canephora.}, language = {en}, number = {6}, urldate = {2021-06-29}, journal = {PLoS ONE}, author = {Nic-Can, Geovanny I. and Galaz-Ávalos, Rosa M. and De-la-Peña, Clelia and Alcazar-Magaña, Armando and Wrobel, Kazimierz and Loyola-Vargas, Víctor M.}, editor = {Candela, Hector}, month = jun, year = {2015}, pages = {e0126414}, file = {Nic-Can et al. - 2015 - Somatic Embryogenesis Identified Factors that Lea.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\GCSZRBTW\\Nic-Can et al. - 2015 - Somatic Embryogenesis Identified Factors that Lea.pdf:application/pdf}, } @article{berenguer_inhibition_2017-1, title = {Inhibition of {Histone} {H3K9} {Methylation} by {BIX}-01294 {Promotes} {Stress}-{Induced} {Microspore} {Totipotency} and {Enhances} {Embryogenesis} {Initiation}}, volume = {8}, issn = {1664-462X}, url = {http://journal.frontiersin.org/article/10.3389/fpls.2017.01161/full}, doi = {10.3389/fpls.2017.01161}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Berenguer, Eduardo and Bárány, Ivett and Solís, María-Teresa and Pérez-Pérez, Yolanda and Risueño, María C. and Testillano, Pilar S.}, month = jun, year = {2017}, pages = {1161}, file = {Berenguer et al. - 2017 - Inhibition of Histone H3K9 Methylation by BIX-0129.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\W53S67ZJ\\Berenguer et al. - 2017 - Inhibition of Histone H3K9 Methylation by BIX-0129.pdf:application/pdf}, } @article{pais_somatic_2019-1, title = {Somatic {Embryogenesis} {Induction} in {Woody} {Species}: {The} {Future} {After} {OMICs} {Data} {Assessment}}, volume = {10}, issn = {1664-462X}, shorttitle = {Somatic {Embryogenesis} {Induction} in {Woody} {Species}}, url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00240/full}, doi = {10.3389/fpls.2019.00240}, abstract = {Very early somatic embryogenesis has been recognized as a powerful method to propagate plants in vitro. For some woody species and in particular for some coniferous trees, somatic embryogenesis induction has become a routine procedure. For the majority, the application of this technology presents yet many limitations especially due to the genotype, the induction conditions, the number of embryos produced, maturation, and conversion, among other factors that compromise the systematic use of somatic embryogenesis for commercial purposes especially of woody species and forest trees in particular. The advancements obtained on somatic embryogenesis in Arabidopsis and the development of OMIC technologies allowed the characterization of genes and the corresponding proteins that are conserved in woody species. This knowledge will help in understanding the molecular mechanisms underlying the complex regulatory networks that control somatic embryogenesis in woody plants. In this revision, we report on developments of OMICs (genomics, transcriptomics, metabolomics, and proteomics) applied to somatic embryogenesis induction and its contribution for understanding the change of fate giving rise to the expression of somatic embryogenesis competence.}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Pais, Maria Salomé}, month = mar, year = {2019}, pages = {240}, file = {Pais - 2019 - Somatic Embryogenesis Induction in Woody Species .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\APD36PUD\\Pais - 2019 - Somatic Embryogenesis Induction in Woody Species .pdf:application/pdf;leva annarita, 2012.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\NG4PWIBC\\leva annarita, 2012.pdf:application/pdf}, } @article{mendez-hernandez_signaling_2019-3, title = {Signaling {Overview} of {Plant} {Somatic} {Embryogenesis}}, volume = {10}, issn = {1664-462X}, url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00077/full}, doi = {10.3389/fpls.2019.00077}, language = {en}, urldate = {2021-06-29}, journal = {Front. Plant Sci.}, author = {Méndez-Hernández, Hugo A. and Ledezma-Rodríguez, Maharshi and Avilez-Montalvo, Randy N. and Juárez-Gómez, Yary L. and Skeete, Analesa and Avilez-Montalvo, Johny and De-la-Peña, Clelia and Loyola-Vargas, Víctor M.}, month = feb, year = {2019}, pages = {77}, file = {Méndez-Hernández et al. - 2019 - Signaling Overview of Plant Somatic Embryogenesis.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\99RB85LC\\Méndez-Hernández et al. - 2019 - Signaling Overview of Plant Somatic Embryogenesis.pdf:application/pdf}, } @incollection{yildiz_prerequisite_2012, title = {The {Prerequisite} of the {Success} in {Plant} {Tissue} {Culture}: {High} {Frequency} {Shoot} {Regeneration}}, isbn = {978-953-51-0787-3}, shorttitle = {The {Prerequisite} of the {Success} in {Plant} {Tissue} {Culture}}, url = {http://www.intechopen.com/books/recent-advances-in-plant-in-vitro-culture/the-prerequisite-of-the-success-in-plant-tissue-culture-high-frequency-shoot-regeneration}, language = {en}, urldate = {2021-06-30}, booktitle = {Recent {Advances} in {Plant} in vitro {Culture}}, publisher = {InTech}, author = {Yildiz, Mustafa}, editor = {Leva, Annarita}, month = oct, year = {2012}, doi = {10.5772/51097}, file = {Yildiz - 2012 - The Prerequisite of the Success in Plant Tissue Cu.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\H64HTKJB\\Yildiz - 2012 - The Prerequisite of the Success in Plant Tissue Cu.pdf:application/pdf}, } @book{wen_ethylene_2015-1, address = {Dordrecht}, title = {Ethylene in {Plants}}, isbn = {978-94-017-9483-1 978-94-017-9484-8}, url = {http://link.springer.com/10.1007/978-94-017-9484-8}, language = {en}, urldate = {2021-07-01}, publisher = {Springer Netherlands}, editor = {Wen, Chi-Kuang}, year = {2015}, doi = {10.1007/978-94-017-9484-8}, file = {Wen - 2015 - Ethylene in Plants.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\BC5BQKC7\\Wen - 2015 - Ethylene in Plants.pdf:application/pdf}, } @article{jha_baby_2018-3, title = {{BABY} {BOOM} ({BBM}): a candidate transcription factor gene in plant biotechnology}, volume = {40}, issn = {0141-5492, 1573-6776}, shorttitle = {{BABY} {BOOM} ({BBM})}, url = {http://link.springer.com/10.1007/s10529-018-2613-5}, doi = {10.1007/s10529-018-2613-5}, abstract = {Plants have evolved a number of transcription factors, many of which are implicated in signaling pathways as well as regulating diverse cellular functions. BABY BOOM (BBM), transcription factors of the AP2/ERF family are key regulators of plant cell totipotency. Ectopic expression of the BBM gene, originally identified in Brassica napus, has diverse functions in plant cell proliferation, growth and development without exogenous growth regulators. The BBM gene has been implicated to play an important role as a gene marker in multiple signaling developmental pathways in plant development. This review focuses on recent advances in our understanding of a member of the AP2 family of transcription factor BBM in plant biotechnology including plant embryogenesis, cell proliferation, regeneration, plant transformation and apogamy. Recent discoveries about the BBM gene will inevitably help to unlock the long-standing mysteries of different biological mechanisms of plant cells.}, language = {en}, number = {11-12}, urldate = {2021-07-04}, journal = {Biotechnol Lett}, author = {Jha, Priyanka and Kumar, Vijay}, month = dec, year = {2018}, pages = {1467--1475}, file = {Jha and Kumar - 2018 - BABY BOOM (BBM) a candidate transcription factor .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\GJHAJWPR\\Jha and Kumar - 2018 - BABY BOOM (BBM) a candidate transcription factor .pdf:application/pdf}, } @article{inoue_identifcation_2001-1, title = {Identifcation of {CRE1} as {A} {Cytokinin} {Receptor} from {Arabidopsis}}, volume = {409 (6823)}, doi = {doi:10.1038/35059117}, abstract = {Cytokinins are a class of plant hormones that are central to the regulation of cell division and differentiation in plants1,2. It has been proposed that they are detected by a two-component system, because overexpression of the histidine kinase gene CKI1 induces typical cytokinin responses3 and genes for a set of response regulators of two-component systems can be induced by cytokinins4,5. Two-component systems use a histidine kinase as an environmental sensor and rely on a phosphorelay for signal transduction. They are common in microorganisms, and are also emerging as important signal detection routes in plants6±9. Here we report the identi®cation of a cytokinin receptor. We identi®ed Arabidopsis cre1 (cytokinin response 1) mutants, which exhibited reduced responses to cytokinins. The mutated gene CRE1 encodes a histidine kinase. CRE1 expression conferred a cytokinindependent growth phenotype on a yeast mutant that lacked the endogenous histidine kinase SLN1 (ref. 10), providing direct evidence that CRE1 is a cytokinin receptor. We also provide evidence that cytokinins can activate CRE1 to initiate phosphorelay signalling.}, journal = {Nature}, author = {Inoue, Tsutomu and Higuchi, Masayuki and Hashimoto, Yukari and Seki, Motoaki and Kobayashi, Masatomo and Kato, Tomohiko and Tabata, Satoshi and Shinozak, Kazuo and Kakimoto, Tatsuo}, month = feb, year = {2001}, pages = {1060--1063}, } @article{anderson_zygotic_2017-2, title = {The {Zygotic} {Transition} {Is} {Initiated} in {Unicellular} {Plant} {Zygotes} with {Asymmetric} {Activation} of {Parental} {Genomes}}, volume = {43}, issn = {15345807}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580717308183}, doi = {10.1016/j.devcel.2017.10.005}, abstract = {The zygotic transition, from a fertilized egg to an embryo, is central to animal and plant reproduction. Animal embryos depend upon maternally provided factors until zygotic genome activation (ZGA). In plants, the timing and parental genome contributions to ZGA are unresolved. Here, we use the flowering plant Oryza sativa (rice) to characterize transcriptomes of time-staged isogenic and hybrid zygotes following fertilization. Large-scale transcriptomic changes were observed in unicellular zygotes, including upregulation of S-phase genes, a characteristic of ZGA. The parental contributions to ZGA were highly asymmetric. Zygotic transcription was primarily from the maternal genome and included genes for basic cellular processes. Transcription of the paternal genome was highly restricted but unexpectedly included genes encoding putative pluripotency factors expressed at the onset of ZGA. Thus, distinct transcriptional activities are exhibited by the parental genomes during the initiation of embryogenesis, which presumptively derive from divergent pre-zygotic transcriptional states established in the gametes.}, language = {en}, number = {3}, urldate = {2021-07-07}, journal = {Developmental Cell}, author = {Anderson, Sarah N. and Johnson, Cameron S. and Chesnut, Joshua and Jones, Daniel S. and Khanday, Imtiyaz and Woodhouse, Margaret and Li, Chenxin and Conrad, Liza J. and Russell, Scott D. and Sundaresan, Venkatesan}, month = nov, year = {2017}, pages = {349--358.e4}, file = {Anderson et al. - 2017 - The Zygotic Transition Is Initiated in Unicellular.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\V8544CWM\\Anderson et al. - 2017 - The Zygotic Transition Is Initiated in Unicellular.pdf:application/pdf}, } @article{anderson_zygotic_2017-3, title = {The {Zygotic} {Transition} {Is} {Initiated} in {Unicellular} {Plant} {Zygotes} with {Asymmetric} {Activation} of {Parental} {Genomes}}, volume = {43}, issn = {15345807}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580717308183}, doi = {10.1016/j.devcel.2017.10.005}, abstract = {The zygotic transition, from a fertilized egg to an embryo, is central to animal and plant reproduction. Animal embryos depend upon maternally provided factors until zygotic genome activation (ZGA). In plants, the timing and parental genome contributions to ZGA are unresolved. Here, we use the flowering plant Oryza sativa (rice) to characterize transcriptomes of time-staged isogenic and hybrid zygotes following fertilization. Large-scale transcriptomic changes were observed in unicellular zygotes, including upregulation of S-phase genes, a characteristic of ZGA. The parental contributions to ZGA were highly asymmetric. Zygotic transcription was primarily from the maternal genome and included genes for basic cellular processes. Transcription of the paternal genome was highly restricted but unexpectedly included genes encoding putative pluripotency factors expressed at the onset of ZGA. Thus, distinct transcriptional activities are exhibited by the parental genomes during the initiation of embryogenesis, which presumptively derive from divergent pre-zygotic transcriptional states established in the gametes.}, language = {en}, number = {3}, urldate = {2021-07-07}, journal = {Developmental Cell}, author = {Anderson, Sarah N. and Johnson, Cameron S. and Chesnut, Joshua and Jones, Daniel S. and Khanday, Imtiyaz and Woodhouse, Margaret and Li, Chenxin and Conrad, Liza J. and Russell, Scott D. and Sundaresan, Venkatesan}, month = nov, year = {2017}, pages = {349--358.e4}, file = {Anderson et al. - 2017 - The Zygotic Transition Is Initiated in Unicellular.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\XIWH8PQH\\Anderson et al. - 2017 - The Zygotic Transition Is Initiated in Unicellular.pdf:application/pdf}, } @article{panda_biochemical_2018-1, title = {Biochemical and molecular characterisation of exogenous cytokinin application on grain filling in rice}, doi = {https://doi.org/10.1186/s12870-018-1279-4}, abstract = {Abstract Background: Poor filling of grains in the basal spikelets of large size panicles bearing numerous spikelets has been a major limitation in attempts to increase the rice production to feed the world’s increasing population. Considering that biotechnological intervention could play important role in overcoming this limitation, the role of cytokinin in grain filling was investigated based on the information on cell proliferating potential of the hormone and reports of its high accumulation in immature seeds. Results: A comparative study considering two rice varieties differing in panicle compactness, lax-panicle Upahar and compact-panicle OR-1918, revealed significant difference in grain filling, cytokinin oxidase (CKX) activity and expression, and expression of cell cycle regulators and cytokinin signaling components between the basal and apical spikelets of OR-1918, but not of Upahar. Exogenous application of cytokinin (6-Benzylaminopurine, BAP) to OR-1918 improved grain filling significantly, and this was accompanied by a significant decrease in expression and activity of CKX, particularly in the basal spikelets where the activity of CKX was significantly higher than that in the apical spikelets. Cytokinin application also resulted in significant increase in expression of cell cycle regulators like cyclin dependent kinases and cyclins in the basal spikelets that might be facilitating cell division in the endosperm cells by promoting G1/S phase and G2/M phase transition leading to improvement in grain filling. Expression studies of type-A response regulator (RR) component of cytokinin signaling indicated possible role of OsRR3, OsRR4 and OsRR6 as repressors of CKX expression, much needed for an increased accumulation of CK in cells. Furthermore, the observed effect of BAP might not be solely because of it, but also because of induced synthesis of trans-zeatin (tZ) and N 6 2 -(Δ -isopentenyl)adenine (iP), as reflected from accumulation of tZR (tZ riboside) and iPR (iP riboside), and significantly enhanced expression of an isopentenyl transferase (IPT) isoform. Conclusion: The results suggested that seed-specific overexpression of OsRR4 and OsRR6, and more importantly of IPT9 could be an effective biotechnological intervention towards improving the CK level of the developing caryopses leading to enhanced grain filling in rice cultivars bearing large panicles with numerous spikelets, and thereby increasing their yield potential. Keywords: Cytokinin oxidase, Cytokinin treatment, 6-Benzylaminopurine, Cell cycle regulators, Chromosomal endoreduplication, Oryza sativa}, language = {english}, journal = {BMC Plant Biology}, author = {Panda, Binay Bhushan and {1} and {Sudhanshu Sekhar} and {2} and {, Sushant Kumar Dash} and {2} and {, Lamboder Behera} and {and Birendra Prasad Shaw}}, year = {2018}, pages = {19}, } @article{shaopei_cytokinin_2014-1, title = {{CYTOKININ} {OXIDASE}/{DEHYDROGENASE4} {Integrates} {Cytokinin} and {Auxin} {Signaling} to {Control} {Rice} {Crown} {Root} {Formation}}, volume = {165}, url = {www.plantphyshiol.com}, abstract = {Crown roots constitute the majority of the rice (Oryza sativa) root system and play an important role in rice growth and development. However, the molecular mechanism of crown root formation in rice is not well understood. Here, we characterized a rice dominant mutant, root enhancer1 (ren1-D), which was observed to exhibit a more robust root system, increased crown root number, and reduced plant height. Molecular and genetic analyses revealed that these phenotypes are caused by the activation of a cytokinin oxidase/dehydrogenase (CKX) family gene, OsCKX4. Subcellular localization demonstrated that OsCKX4 is a cytosolic isoform of CKX. OsCKX4 is predominantly expressed in leaf blades and roots. It is the dominant CKX, preferentially expressed in the shoot base where crown root primordia are produced, underlining its role in root initiation. OsCKX4 is induced by exogenous auxin and cytokinin in the roots. Furthermore, one-hybrid assays revealed that OsCKX4 is a direct binding target of both the auxin response factor OsARF25 and the cytokinin response regulators OsRR2 and OsRR3. Overexpression and RNA interference of OsCKX4 confi rmed that OsCKX4 plays a positive role in crown root formation. Moreover, expression analysis revealed a signifi cant alteration in the expression of auxin-related genes in the ren1-D mutants, indicating that the OsCKX4 mediates crown root development by integrating the interaction between cytokinin and auxin. Transgenic plants harboring OsCKX4 under the control of the root-specifi c promoter RCc3 displayed enhanced root development without affecting their shoot parts, suggesting that this strategy could be a powerful tool in rice root engineering}, journal = {Plant Physiology}, author = {Shaopei, Gao and {, FanXu, WeiWang, Xiaohong Sun, JinfangChu,BaodongCai,} and {Yuqi Feng, and Chengcai Chu}}, month = jul, year = {2014}, pages = {1035--1046}, } @article{noauthor_notitle_nodate-3, } @article{fraiture_biotech_2016-1, title = {Biotech rice: {Current} developments and future detection challenges in food and feed chain}, volume = {52}, issn = {09242244}, shorttitle = {Biotech rice}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0924224415302028}, doi = {10.1016/j.tifs.2016.03.011}, abstract = {Background: To improve agricultural practices and the food/feed security, plant breeding techniques were developed, including transgenesis commonly using Agrobacterium tumefaciens or biolistic technologies. To guarantee the traceability of GMO in food/feed chain and the consumer's freedom of choice, regulatory frameworks were established in many countries around the world, such as in Europe. Their implementations, including detection systems usually based on qPCR, are becoming complex and expensive regarding the number of analysis to perform. Moreover, the dispersion of publicly available information about developed GMO prevents to accurately estimate the efficiency of the standard detection system applied to unauthorized GMO.}, language = {en}, urldate = {2021-10-15}, journal = {Trends in Food Science \& Technology}, author = {Fraiture, Marie-Alice and Roosens, Nancy H.C. and Taverniers, Isabel and De Loose, Marc and Deforce, Dieter and Herman, Philippe}, month = jun, year = {2016}, pages = {66--79}, file = {Fraiture et al. - 2016 - Biotech rice Current developments and future dete.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\GW27DGSH\\Fraiture et al. - 2016 - Biotech rice Current developments and future dete.pdf:application/pdf}, } @article{kieber_cytokinins_2014-5, title = {Cytokinins}, volume = {e0168}, issn = {1543-8120}, url = {http://www.bioone.org/doi/10.1199/tab.0168}, doi = {10.1199/tab.0168}, language = {en}, urldate = {2021-10-15}, journal = {The Arabidopsis Book}, author = {Kieber, Joseph J. and Schaller, G. Eric}, month = jan, year = {2014}, pages = {1--35}, file = {Kieber and Schaller - 2014 - Cytokinins.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\KDSDHY2G\\Kieber and Schaller - 2014 - Cytokinins.pdf:application/pdf}, } @article{yamburenko_functional_2020-1, title = {Functional {Analysis} of the {Rice} {Type}-{B} {Response} {Regulator} {RR22}}, volume = {11}, issn = {1664-462X}, url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.577676/full}, doi = {10.3389/fpls.2020.577676}, language = {en}, urldate = {2021-10-15}, journal = {Front. Plant Sci.}, author = {Yamburenko, Maria V. and Worthen, Jennifer M. and Zeenat, Asyia and Azhar, Beenish J. and Swain, Swadhin and Couitt, Adam R. and Shakeel, Samina N. and Kieber, Joseph J. and Schaller, G. Eric}, month = nov, year = {2020}, pages = {577676}, file = {Yamburenko et al. - 2020 - Functional Analysis of the Rice Type-B Response Re.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\AJBUHDIG\\Yamburenko et al. - 2020 - Functional Analysis of the Rice Type-B Response Re.pdf:application/pdf}, } @article{fanata_n-glycan_2013-1, title = {N-glycan maturation is crucial for cytokinin-mediated development and cellulose synthesis in \textit{{Oryza}} sativa}, volume = {73}, issn = {09607412}, url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.12087}, doi = {10.1111/tpj.12087}, abstract = {To explore the physiological significance of N-glycan maturation in the plant Golgi apparatus, gnt1, a mutant with loss of N-acetylglucosaminyltransferase I (GnTI) function, was isolated in Oryza sativa. gnt1 exhibited complete inhibition of N-glycan maturation and accumulated high-mannose N-glycans. Phenotypic analyses revealed that gnt1 shows defective post-seedling development and incomplete cell wall biosynthesis, leading to symptoms such as failure in tiller formation, brittle leaves, reduced cell wall thickness, and decreased cellulose content. The developmental defects of gnt1 ultimately resulted in early lethality without transition to the reproductive stage. However, callus induced from gnt1 seeds could be maintained for periods, although it exhibited a low proliferation rate, small size, and hypersensitivity to salt stress. Shoot regeneration and dark-induced leaf senescence assays indicated that the loss of GnTI function results in reduced sensitivity to cytokinin in rice. Reduced expression of A-type O. sativa response regulators that are rapidly induced by cytokinins in gnt1 confirmed that cytokinin signaling is impaired in the mutant. These results strongly support the proposed involvement of N-glycan maturation in transport as well as in the function of membrane proteins that are synthesized via the endomembrane system.}, language = {en}, number = {6}, urldate = {2021-10-15}, journal = {Plant J}, author = {Fanata, Wahyu Indra Duwi and Lee, Kyoung Hwan and Son, Bo Hwa and Yoo, Jae Yong and Harmoko, Rikno and Ko, Ki Seong and Ramasamy, Nirmal Kumar and Kim, Kyung Hwa and Oh, Doo-Byoung and Jung, Hyun Suk and Kim, Jae-Yean and Lee, Sang Yeol and Lee, Kyun Oh}, month = mar, year = {2013}, pages = {966--979}, file = {Fanata et al. - 2013 - N-glycan maturation is crucial for cytokinin-media.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\NCJPQX5D\\Fanata et al. - 2013 - N-glycan maturation is crucial for cytokinin-media.pdf:application/pdf}, } @article{arisandi_effect_2020-1, title = {Effect of ethylene inhibitor, type of auxin, and type of sugar on anther culture of local {East} {Java} aromatic rice varieties}, volume = {23}, issn = {1975-9479, 2005-8276}, url = {https://link.springer.com/10.1007/s12892-020-00045-6}, doi = {10.1007/s12892-020-00045-6}, abstract = {Breeding using the double haploid approach has been used in accelerating the rice breeding process. However, the main obstacle in the application of this technique in rice is the low level of callus formation and their regeneration into haploid plants. Based on these issues, this research is aimed at developing the best method for obtaining double haploid plants through anther culture using three kinds of aromatic rice of Indonesian local varieties. Anthers of Pendok, Genjah Arum, and Merah Wangi varieties were cultured in callus induction media which were either supplemented with different types of carbon sources, or auxins and ethylene inhibitors. However, the application of different sugar types did not significantly affect callus formation of Pendok and Genjah Arum. However, auxin treatment showed NAA to be more efficient for the callus induction of Pendok, while 2,4-D had no effect on callus induction in all tested varieties. The addition of ethylene inhibitor successfully induced callus formation of Merah Wangi varieties, while the rates of Pendok and Genjah Arum were not significantly affected. Callus of three plant lines were then regenerated into plantlet in regeneration media. Of the three callus varieties used, only Pendok could regenerate into plantlets and grow into adult haploid plants.}, language = {en}, number = {4}, urldate = {2021-10-15}, journal = {J. Crop Sci. Biotechnol.}, author = {Arisandi, Dewi Puspa and Paradisa, Fragaria Vesca and Sugiharto, Bambang and Avivi, Sholeh and Fanata, Wahyu Indra Duwi}, month = sep, year = {2020}, pages = {367--373}, file = {Arisandi et al. - 2020 - Effect of ethylene inhibitor, type of auxin, and t.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\S77CH2BM\\Arisandi et al. - 2020 - Effect of ethylene inhibitor, type of auxin, and t.pdf:application/pdf}, } @article{dewi_role_2008-2, title = {{ROLE} {OF} {POLYAMINES} {IN} {INHIBITION} {OF} {ETHYLENE} {BIOSYNTHESIS} {AND} {THEIR} {EFFECTS} {ON} {RICE} {ANTHER} {CULTURE} {DEVELOPMENT}}, abstract = {The polyamines such as putrescine, spermidine, and spermine were reported to increase green plant regeneration in rice anther culture. Low response of anther culture of rice sub-species indica may be improved with the addition of putrescine in the culture media. Four experiments were conducted to study the role of polyamines in inhibition of ethylene biosynthesis and their effects on rice anther culture development. Anthers of two subspecies of rice, indica (IR64, Krowal, Jatiluhur) and japonica (Taipei 309) were cultured onto media supplemented with putrescine (N6P) and without putrescine (N6). Young panicles containing the anthers at mid-to-late nucleate microspores were cold pretreated at 5 + 2°C and incubated in the dark for 8 days before the anthers were cultured. Results showed that medium without putrescine produced an earlier senescence of indica rice anther than that of japonica. The addition of 10-3 M putrescine into the culture media inhibited ethylene biosynthesis as anther senescence delayed, increased the three polyamines contents, and decreased the ACC content as well as ACC oxydase activity in anther-derived calli. In the anther and anther-derived calli of subspecies indica, the total polyamines content was lower (10.14 nM g-1 anther and 8.48 nM g-1 calli) than that of subspecies japonica (12.61 nM g-1 anther and 10.16 nM g-1 calli), whereas the ethylene production was higher (32.31 nM g-1 anther and 2.48 nM g-1 calli) than the japonica (31.68 nM g-1 anther and 1.76 nM g-1 calli). This study suggests that application of 10-3 M putrescine in anther culture of rice subspecies indica improves androgenesis by inhibiting early senescence of cultured anthers and enhancing embryo or callus formation from microspores.}, language = {en}, author = {Dewi, Iswari S and Purwoko, Bambang S}, year = {2008}, pages = {8}, file = {Dewi and Purwoko - ROLE OF POLYAMINES IN INHIBITION OF ETHYLENE BIOSY.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\5VDGEMFI\\Dewi and Purwoko - ROLE OF POLYAMINES IN INHIBITION OF ETHYLENE BIOSY.pdf:application/pdf}, } @techreport{khanday_rice_2020-1, type = {preprint}, title = {Rice embryogenic trigger {BABY} {BOOM1} promotes somatic embryogenesis by upregulation of auxin biosynthesis genes}, url = {http://biorxiv.org/lookup/doi/10.1101/2020.08.24.265025}, abstract = {ABSTRACT Somatic embryogenesis, a powerful tool for clonal propagation and for plant transformation, involves cellular reprogramming of differentiated somatic cells to acquire pluripotency. Somatic embryogenesis can be induced by treating explants with plant growth regulators. However, several plant species including agronomically important cereal crops remain recalcitrant to dedifferentiation and transformation except from embryonic tissues. Somatic embryogenesis can also be induced by ectopic expression of select embryonic factors, including in cereals by BABY BOOM (BBM) transcription factors. How BBM genes bypass the need for exogenous hormones is not well understood. Here, we investigated downstream targets during induction of somatic embryogenesis in rice by OsBBM1 (( Oryza sativa BABY BOOM1 ). Transient induction of OsBBM1 led to the upregulation of auxin biosynthesis OsYUCCA genes. Continued induction of OsBBM1 resulted in somatic embryogenesis without the need for exogenous auxins. Genetic mutant analysis of OsBBM1 downstream targets, OsYUCCA6, OsYUCCA7 and OsYUCCA9 , show that they are required for normal rice development including root and shoot development. Somatic embryogenic potential of OsYUCCA triple mutants was highly compromised despite the presence of exogenous auxin. Additionally, we show that somatic embryogenesis induction by exogenous auxin in rice requires functional BBM genes. Thus, OsBBM1 mediated cellular reprogramming and somatic embryogenesis likely involves increased localized auxin through direct upregulation of OsYUCCA genes. This study reveals mechanistic details of how somatic embryogenesis is established in differentiated tissues in rice, a monocot model and agronomically important cereal crop, with the potential utility to improve regeneration from tissue culture for recalcitrant plants in future. One-sentence summary Rice BABY BOOM1 induces somatic embryogenesis from differentiated tissues by promoting auxin biosynthesis through direct upregulation of YUCCA genes.}, language = {en}, urldate = {2021-10-15}, institution = {Developmental Biology}, author = {Khanday, Imtiyaz and Santos-Medellín, Christian and Sundaresan, Venkatesan}, month = aug, year = {2020}, doi = {10.1101/2020.08.24.265025}, file = {Khanday et al. - 2020 - Rice embryogenic trigger BABY BOOM1 promotes somat.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\TFTI6EC3\\Khanday et al. - 2020 - Rice embryogenic trigger BABY BOOM1 promotes somat.pdf:application/pdf}, } @article{fanata_daya_2020-3, title = {{DAYA} {REGENERASI} {KALUS} {DAN} {TUNAS} {IN} {VITRO} {PADI} {VARIETAS} {TARABAS} {PADA} {BERBAGAI} {KONSENTRASI} 2,4-{D}}, volume = {7}, issn = {2548-611X, 2442-2606}, url = {http://ejurnal.bppt.go.id/index.php/JBBI/article/view/4404}, doi = {10.29122/jbbi.v7i2.4404}, abstract = {The Agricultural Research and Development Agency and the West Java Provincial Government are developing new superior varieties with Japonica rice standards, namely the Tarabas variety. However, the equivalence of somatic embryogenesis ability of Tarabas rice with original Japonica variety has not been reported. In this study, the frequency of callus regeneration of Tarabas vs Hwayoung rice varieties was compared. Induction of callus from mature embryos with several concentrations of 2,4-D showed the same extent of callus formation in both rice varieties. Callus induced by 1 ppm of 2,4-D showed the higher rate of shoot formation. On the other hand, percentage of callus formation of Tarabas rice was not affected by the increase of 2,4-D concentrations and was able to show 100\% regeneration rate at the fourth week in the regeneration medium, although the shoot growth was not as fast as those from medium with 1 ppm 2,4-D. Therefore, these results suggest that Tarabas variety has a somatic embryogenesis capacity equivalent to that of japonica rice and has the potential as research objects in the field of biotechnology.}, language = {id}, number = {2}, urldate = {2021-10-15}, journal = {J Bioteknol Biosains Indones}, author = {Fanata, Wahyu Indra Duwi and Qudsiyah, Dalliyah Hadrotul}, month = dec, year = {2020}, pages = {250--258}, file = {Fanata and Qudsiyah - 2020 - DAYA REGENERASI KALUS DAN TUNAS IN VITRO PADI VARI.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\3G2V5U7D\\Fanata and Qudsiyah - 2020 - DAYA REGENERASI KALUS DAN TUNAS IN VITRO PADI VARI.pdf:application/pdf}, } @article{ali_improved_2021-3, title = {Improved {Anther} {Culture} {Media} for {Enhanced} {Callus} {Formation} and {Plant} {Regeneration} in {Rice} ({Oryza} sativa {L}.)}, volume = {10}, issn = {2223-7747}, url = {https://www.mdpi.com/2223-7747/10/5/839}, doi = {10.3390/plants10050839}, abstract = {Anther culture technique is the most viable and efficient method of producing homozygous doubled haploid plants within a short period. However, the practical application of this technology in rice improvement is still limited by various factors that influence culture efficiency. The present study was conducted to determine the effects of two improved anther culture media, Ali-1 (A1) and Ali-2 (A2), a modified N6 medium, to enhance the callus formation and plant regeneration of japonica, indica, and hybrids of indica and japonica cross. The current study demonstrated that genotype and media had a significant impact (p {\textbackslash}textless 0.001) on both callus induction frequency and green plantlet regeneration efficiency. The use of the A1 and A2 medium significantly enhanced callus induction frequency of japonica rice type, Nipponbare, and the hybrids of indica × japonica cross (CXY6, CXY24, and Y2) but not the indica rice type, NSIC Rc480. However, the A1 medium is found superior to the N6 medium as it significantly improved the green plantlet regeneration efficiency of CXY6, CXY24, and Y2 by almost 36\%, 118\%, and 277\%, respectively. Furthermore, it substantially reduced the albino plantlet regeneration of the induced callus in two hybrids (CXY6 and Y2). Therefore, the improved anther culture medium A1 can produce doubled haploid rice plants for indica × japonica, which can be useful in different breeding programs that will enable the speedy development of rice varieties for resource-poor farmers.}, language = {en}, number = {5}, urldate = {2021-10-27}, journal = {Plants}, author = {Ali, Jauhar and Nicolas, Katrina Leslie C. and Akther, Shahana and Torabi, Azerkhsh and Ebadi, Ali Akbar and Marfori-Nazarea, Corinne M. and Mahender, Anumalla}, month = apr, year = {2021}, pages = {839}, file = {Ali et al. - 2021 - Improved Anther Culture Media for Enhanced Callus .pdf:C\:\\Users\\Syafira\\Zotero\\storage\\5LJC37HW\\Ali et al. - 2021 - Improved Anther Culture Media for Enhanced Callus .pdf:application/pdf}, } @article{amer_relationship_1997-1, title = {The relationship between green spot initiation and plantlet regeneration of wheat callus grown under short-term conditions}, volume = {50}, doi = {https://doi.org/10.1023/A:1005855912655}, abstract = {Six wheat genotypes (three varieties and three whole chromosome substitution lines) were used to analyse the relationship between the initiation of green spots and plant regeneration under short-term tissue culture conditions. The highest percentage of green spot initiation was observed after one week culture on maintenance medium (M-Med.). The calluses producing green spots at the end of the first and second week on M-Med. were highest in regeneration frequency compared to late green spot producing ones. A significant positive correlation between green spot initiation and plantlet regeneration was observed for calluses showing green spots within the first two weeks on M-Med. and was decreased for calluses producing green spots afterwards. The results suggest that by selecting only calluses producing early green spots the experimental efficiency will be increased.}, language = {en}, author = {Amer, I M Ben and Borner, A}, year = {1997}, pages = {67--69}, file = {Amer and Borner - The relationship between green spot initiation and.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\PMDSMANV\\Amer and Borner - The relationship between green spot initiation and.pdf:application/pdf}, } @article{rezaei-moghadam_effect_2012-3, title = {Effect of {Turmeric} and {Carrot} {Seed} {Extracts} on {Serum} {Liver} {Biomarkers} and {Hepatic} {Lipid} {Peroxidation}, {Antioxidant} {Enzymes} and {Total} {Antioxidant} {Status} in {Rats}}, url = {http://bi.tbzmed.ac.ir/JournalIssues/AllIssues/Volume2Issue3/4201223.aspx}, doi = {10.5681/BI.2012.020}, abstract = {Introduction: Pathogenic role of free radicals are well known in various metabolic diseases. They originate from internal and external sources of body. Essential roles of antioxidant defense system for cellular redox regulation and free radical scavenging activity were described in this study. Many in vitro investigations have shown that turmeric (TE) and carrot seed extract (CSE) exhibits to possess antioxidant activities. In this study, we evaluated the antioxidant potentials of ethanolic TE and CSE based on in vivo experiment in the rats. Methods: Animals were assigned to six groups: the 1st and 2nd groups were control groups and 2nd group received 0.2 ml dimethyl sulphoxide as vehicle treated group; other four experimental groups received different doses of TE (100, 200 mg/kg b.w.) and CSE (200, 400 mg/kg b.w.) by gavages, respectively for a period of one month. The indicators of oxidative stress, lipids peroxidation, markers of hepatocyte injury and biliary function markers were measured. Results: The levels of superoxide dismutase, catalase, and glutathione peroxidase were significantly stimulated in the hepatic tissue of treatment groups. The malondialdehyde contents of liver tissue were significantly reduced in the groups fed with TE and CSE. Serum levels of alanine aminotransferase, aspartate aminotransferase and alkaline phosphatase, in treated groups were found to be significantly decreased, whereas albumin and total protein increased as compared to the control groups (P less than 0.05). Conclusion: this study showed that the regular intake of TE and CSE through the diet can improve antioxidant status and inhibit peroxidation activity in the liver tissue so that using these extracts may protect tissue oxidative stress.}, language = {en}, urldate = {2021-11-03}, journal = {BioImpacts; ISSN 2228-5660}, author = {Rezaei-Moghadam, Adel and Mohajeri, Daryoush and Rafiei, Behnam and Dizaji, Rana and Azhdari, Asghar and Yeganehzad, Mahdi and Shahidi, Maryamossadat and Mazani, Mohammad}, year = {2012}, keywords = {610 Medical sciences, Medicine}, annote = {Medium: text/html Publisher: Tabriz University of Medical Sciences}, annote = {SeriesInformation BioImpacts; ISSN 2228-5660}, file = {Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\ZLIMPDYU\\Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:application/pdf}, } @article{rezaei-moghadam_effect_2012-4, title = {Effect of {Antioxidants} and {Carbohydrates} in {Callus} {Cultures} of {Taxus} brevifolia: {Evaluation} of {Browning}, {Callus} {Growth}, {Total} {Phenolics} and {Paclitaxel} {Production}}, volume = {1}, url = {http://bi.tbzmed.ac.ir/JournalIssues/AllIssues/Volume2Issue3/4201223.aspx}, doi = {10.5681/BI.2012.020}, abstract = {Introduction: Pathogenic role of free radicals are well known in various metabolic diseases. They originate from internal and external sources of body. Essential roles of antioxidant defense system for cellular redox regulation and free radical scavenging activity were described in this study. Many in vitro investigations have shown that turmeric (TE) and carrot seed extract (CSE) exhibits to possess antioxidant activities. In this study, we evaluated the antioxidant potentials of ethanolic TE and CSE based on in vivo experiment in the rats. Methods: Animals were assigned to six groups: the 1st and 2nd groups were control groups and 2nd group received 0.2 ml dimethyl sulphoxide as vehicle treated group; other four experimental groups received different doses of TE (100, 200 mg/kg b.w.) and CSE (200, 400 mg/kg b.w.) by gavages, respectively for a period of one month. The indicators of oxidative stress, lipids peroxidation, markers of hepatocyte injury and biliary function markers were measured. Results: The levels of superoxide dismutase, catalase, and glutathione peroxidase were significantly stimulated in the hepatic tissue of treatment groups. The malondialdehyde contents of liver tissue were significantly reduced in the groups fed with TE and CSE. Serum levels of alanine aminotransferase, aspartate aminotransferase and alkaline phosphatase, in treated groups were found to be significantly decreased, whereas albumin and total protein increased as compared to the control groups (P less than 0.05). Conclusion: this study showed that the regular intake of TE and CSE through the diet can improve antioxidant status and inhibit peroxidation activity in the liver tissue so that using these extracts may protect tissue oxidative stress.}, language = {en}, urldate = {2021-11-03}, journal = {BioImpacts; ISSN 2228-5660}, author = {Rezaei-Moghadam, Adel and Mohajeri, Daryoush and Rafiei, Behnam and Dizaji, Rana and Azhdari, Asghar and Yeganehzad, Mahdi and Shahidi, Maryamossadat and Mazani, Mohammad}, year = {2012}, keywords = {610 Medical sciences, Medicine}, pages = {37--45}, annote = {Medium: text/html Publisher: Tabriz University of Medical Sciences}, annote = {SeriesInformation BioImpacts; ISSN 2228-5660}, file = {Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\BHBZEIBR\\Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:application/pdf}, } @article{rezaei-moghadam_effect_2012-5, title = {Effect of {Turmeric} and {Carrot} {Seed} {Extracts} on {Serum} {Liver} {Biomarkers} and {Hepatic} {Lipid} {Peroxidation}, {Antioxidant} {Enzymes} and {Total} {Antioxidant} {Status} in {Rats}}, url = {http://bi.tbzmed.ac.ir/JournalIssues/AllIssues/Volume2Issue3/4201223.aspx}, doi = {10.5681/BI.2012.020}, abstract = {Introduction: Pathogenic role of free radicals are well known in various metabolic diseases. They originate from internal and external sources of body. Essential roles of antioxidant defense system for cellular redox regulation and free radical scavenging activity were described in this study. Many in vitro investigations have shown that turmeric (TE) and carrot seed extract (CSE) exhibits to possess antioxidant activities. In this study, we evaluated the antioxidant potentials of ethanolic TE and CSE based on in vivo experiment in the rats. Methods: Animals were assigned to six groups: the 1st and 2nd groups were control groups and 2nd group received 0.2 ml dimethyl sulphoxide as vehicle treated group; other four experimental groups received different doses of TE (100, 200 mg/kg b.w.) and CSE (200, 400 mg/kg b.w.) by gavages, respectively for a period of one month. The indicators of oxidative stress, lipids peroxidation, markers of hepatocyte injury and biliary function markers were measured. Results: The levels of superoxide dismutase, catalase, and glutathione peroxidase were significantly stimulated in the hepatic tissue of treatment groups. The malondialdehyde contents of liver tissue were significantly reduced in the groups fed with TE and CSE. Serum levels of alanine aminotransferase, aspartate aminotransferase and alkaline phosphatase, in treated groups were found to be significantly decreased, whereas albumin and total protein increased as compared to the control groups (P less than 0.05). Conclusion: this study showed that the regular intake of TE and CSE through the diet can improve antioxidant status and inhibit peroxidation activity in the liver tissue so that using these extracts may protect tissue oxidative stress.}, language = {en}, urldate = {2021-11-03}, journal = {BioImpacts; ISSN 2228-5660}, author = {Rezaei-Moghadam, Adel and Mohajeri, Daryoush and Rafiei, Behnam and Dizaji, Rana and Azhdari, Asghar and Yeganehzad, Mahdi and Shahidi, Maryamossadat and Mazani, Mohammad}, year = {2012}, keywords = {610 Medical sciences, Medicine}, annote = {Medium: text/html Publisher: Tabriz University of Medical Sciences}, annote = {SeriesInformation BioImpacts; ISSN 2228-5660}, file = {Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\KCUP2JYH\\Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:application/pdf}, } @article{khosroushahi_effect_2011-1, title = {Effect of {Antioxidants} and {Carbohydrates} in {Callus} {Cultures} of {Taxus} brevifolia: {Evaluation} of {Browning}, {Callus} {Growth}, {Total} {Phenolics} and {Paclitaxel} {Production}}, volume = {1(1)}, url = {http://bi.tbzmed.ac.ir/JournalIssues/AllIssues/Volume2Issue3/4201223.aspx}, doi = {10.5681/BI.2012.020}, abstract = {Introduction: To control the tissue browning phenomenon, callus growth, total phenolics and paclitaxel production, in the current investigation, we evaluated the effects of citric acid and ascorbic acid (as antioxidants) and glucose, fructose and sucrose in callus cultures of Taxus brevifolia. Methods: To obtain healthy callus/cell lines of Taxus brevifolia, the effects of two antioxidants ascorbic acid (100-1000 mg/L) and citric acid (50-500 mg/L), and three carbohydrates (glucose, fructose and sucrose (5-10 g/L)) were studied evaluating activities of polyphenol oxidase (PPO) and peroxidase (PO) enzymes, callus growth/browning, total phenolics and paclitaxel production. Results: These antioxidants (ascorbic acid and citric acid) failed to show significant effects on callus growth, browning intensity or paclitaxel production. However, the carbohydrates imposed significant effects on the parameters studied. High concentrations of both glucose and sucrose increased the browning intensity, thus decreased callus growth. Glucose increased paclitaxel production, but sucrose decreased it. Conclusion: These results revealed that the browning phenomenon can be controlled through supplementation of the growth media with glucose, sucrose (5 g/L) and fructose (10 g/L), while increased paclitaxel production can be obtain by the optimized media supplemented with glucose (10 g/L), sucrose and fructose (5 g/L).}, language = {en}, urldate = {2021-11-03}, journal = {BioImpacts; ISSN 2228-5660}, author = {Khosroushahi, Ahmad Yari and Hossein, Naderi-Manesh and Henrik, Toft Simonsen}, year = {2011}, keywords = {610 Medical sciences, Medicine}, pages = {37--45}, annote = {Medium: text/html Publisher: Tabriz University of Medical Sciences}, annote = {SeriesInformation BioImpacts; ISSN 2228-5660}, file = {Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\BPT4E7BA\\Rezaei-Moghadam et al. - 2012 - Effect of Turmeric and Carrot Seed Extracts on Ser.pdf:application/pdf}, } @article{dewi_role_2008-3, title = {Role of {Polyamines} in {Inhibition} {Of} {Ethylene} {Biosynthesis} and {Their} {Effects} on {Rice} {Anther} {Culture} {Development}}, volume = {9 (2)}, doi = {DOI: 10.21082/ijas.v9n2.2008.p60-67}, abstract = {The polyamines such as putrescine, spermidine, and spermine were reported to increase green plant regeneration in rice anther culture. Low response of anther culture of rice sub-species indica may be improved with the addition of putrescine in the culture media. Four experiments were conducted to study the role of polyamines in inhibition of ethylene biosynthesis and their effects on rice anther culture development. Anthers of two subspecies of rice, indica (IR64, Krowal, Jatiluhur) and japonica (Taipei 309) were cultured onto media supplemented with putrescine (N6P) and without putrescine (N6). Young panicles containing the anthers at mid-to-late nucleate microspores were cold pretreated at 5 + 2°C and incubated in the dark for 8 days before the anthers were cultured. Results showed that medium without putrescine produced an earlier senescence of indica rice anther than that of japonica. The addition of 10-3 M putrescine into the culture media inhibited ethylene biosynthesis as anther senescence delayed, increased the three polyamines contents, and decreased the ACC content as well as ACC oxydase activity in anther-derived calli. In the anther and anther-derived calli of subspecies indica, the total polyamines content was lower (10.14 nM g-1 anther and 8.48 nM g-1 calli) than that of subspecies japonica (12.61 nM g-1 anther and 10.16 nM g-1 calli), whereas the ethylene production was higher (32.31 nM g-1 anther and 2.48 nM g-1 calli) than the japonica (31.68 nM g-1 anther and 1.76 nM g-1 calli). This study suggests that application of 10-3 M putrescine in anther culture of rice subspecies indica improves androgenesis by inhibiting early senescence of cultured anthers and enhancing embryo or callus formation from microspores.}, language = {en}, author = {Dewi, Iswari S and Bambang, S. Purwoko}, year = {2008}, pages = {60--67}, file = {Dewi and Purwoko - ROLE OF POLYAMINES IN INHIBITION OF ETHYLENE BIOSY.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\YCIS3GXW\\Dewi and Purwoko - ROLE OF POLYAMINES IN INHIBITION OF ETHYLENE BIOSY.pdf:application/pdf}, } @article{yasmin_ethylene_2013-1, title = {Ethylene influences in vitro regeneration frequency in the {FR13A} rice harbouring the {SUB1A} gene}, volume = {72}, issn = {0167-6903, 1573-5087}, url = {http://link.springer.com/10.1007/s10725-013-9840-5}, doi = {10.1007/s10725-013-9840-5}, abstract = {Many studies have examined the effects of ethylene on in vitro plant growth and development, often with controversial results. Ethylene accumulates in culture vessels due to both the release from the tissues and the physical entrapment due to the need for closed containers. This hormone has several effects on plant regeneration, depending on the plant species and even the cultivar. A prerequisite for ethylene use for in vitro culture is thus to formulate a specific protocol for the genotype of interest. In rice, ethylene is a key regulator of adaptation strategies to low oxygen environments. In particular, the SUBMERGENCE1A (SUB1A) gene, when present, drives the acclimation response which when activated by ethylene produced by submerged plants leads to adaptation through reduced plant growth and ethanolic fermentation enhancement. This gene is restricted to a limited number of rice for which a very specific response to ethylene is expected, whatever the source. This paper reports the regeneration differences between a SUB1A rice landrace (indica-aus, FR13A) and a non-SUB1A variety (japonica, Nipponbare). Our results suggest that regeneration protocols with exogenous ethylene precursors supply are required for the FR13A rice harbouring the SUB1A gene to overcome the problem of low regeneration efficiency.}, language = {en}, number = {1}, urldate = {2021-11-03}, journal = {Plant Growth Regul}, author = {Yasmin, Sabina and Mensuali-Sodi, Anna and Perata, Pierdomenico and Pucciariello, Chiara}, month = jan, year = {2013}, pages = {97--103}, file = {Yasmin et al. - 2014 - Ethylene influences in vitro regeneration frequenc.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\6LIGWLXE\\Yasmin et al. - 2014 - Ethylene influences in vitro regeneration frequenc.pdf:application/pdf}, } @article{kakimoto_ckll_1996-1, title = {{CKll}, a {Histidine} {Kinase} {Homolog} {Implicated} in {Cytokinin} {Signal} {Transduction}}, volume = {274 (5289)}, doi = {doi:10.1126/science.274.5289.982}, abstract = {Although cytokinin plays a central role in plant development, little is known about cytokinin signal transduction. Five Arabidopsis thaliana mutants that exhibit typical cytokinin responses, including rapid cell division and shoot formation in tissue culture in the absence of exogenous cytokinin, were isolated by activation transferred DNA tagging. A gene, CKI1, which was tagged in four of the five mutants and induced typical cytokinin responses after introduction and overexpression in plants, was cloned. CKll encodes a protein similar to the two-component regulators. These results suggest that CKll is involved in cytokinin signal transduction, possibly as a cytokinin receptor.}, journal = {Science}, author = {Kakimoto, Tatsuo}, year = {1996}, pages = {982--985}, } @article{hirose_overexpression_2007-1, title = {Overexpression of a {Type}-{A} {Response} {Regulator} {Alters} {Rice} {Morphology} and {Cytokinin} {Metabolism}}, volume = {48}, issn = {0032-0781, 1471-9053}, url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcm022}, doi = {10.1093/pcp/pcm022}, language = {en}, number = {3}, urldate = {2021-11-03}, journal = {Plant and Cell Physiology}, author = {Hirose, N. and Makita, N. and Kojima, M. and Kamada-Nobusada, T. and Sakakibara, H.}, month = jan, year = {2007}, pages = {523--539}, file = {Hirose et al. - 2007 - Overexpression of a Type-A Response Regulator Alte.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\MMKSGC7H\\Hirose et al. - 2007 - Overexpression of a Type-A Response Regulator Alte.pdf:application/pdf}, } @article{ren_genome-wide_2009-1, title = {Genome-{Wide} {Comparative} {Analysis} of {Type}-{A} {Arabidopsis} {Response} {Regulator} {Genes} by {Overexpression} {Studies} {Reveals} {Their} {Diverse} {Roles} and {Regulatory} {Mechanisms} in {Cytokinin} {Signaling}}, volume = {19}, issn = {1001-0602, 1748-7838}, url = {http://www.nature.com/articles/cr200988}, doi = {10.1038/cr.2009.88}, abstract = {Cytokinin is a critical growth regulator for various aspects of plant growth and development. In Arabidopsis, cytokinin signaling is mediated by a two-component system-based phosphorelay that transmits a signal from the receptors, through histidine phosphotransfer proteins, to the downstream response regulators (ARRs). Of these ARRs, type-A ARR genes, whose transcription can be rapidly induced by cytokinin, act as negative regulators of cytokinin signaling. However, because of functional redundancy, the function of type-A ARR genes in plant growth and development is not well understood by analyzing loss-of-function mutants. In this study, we performed a comparative functional study on all ten type-A ARR genes by analyzing transgenic plants overexpressing these ARR genes fused to a MYC epitope tag. Overexpression of ARR genes results in a variety of cytokinin-associated phenotypes. Notably, overexpression of different ARR transgenes causes diverse phenotypes, even between phylogenetically closely-related gene pairs, such as within the ARR3-ARR4 and ARR5-ARR6 pairs. We found that the accumulation of a subset of ARR proteins (ARR3, ARR5, ARR7, ARR16 and ARR17; possibly ARR8 and ARR15) is increased by MG132, a specific proteasomal inhibitor, indicating that stability of these proteins is regulated by proteasomal degradation. Moreover, similar to that of previously characterized ARR5, ARR6 and ARR7, stability of ARR16 and ARR17, possibly including ARR8 and ARR15, is regulated by cytokinin. These results suggest that type-A ARR proteins are regulated by a combinatorial mechanism involving both the cytokinin and proteasome pathways, thereby executing distinctive functions in plant growth and development.}, language = {en}, number = {10}, urldate = {2021-11-03}, journal = {Cell Res}, author = {Ren, Bo and Liang, Yan and Deng, Yan and Chen, Qingguo and Zhang, Jian and Yang, Xiaohui and Zuo, Jianru}, month = oct, year = {2009}, pages = {1178--1190}, file = {Ren et al. - 2009 - Genome-wide comparative analysis of type-A Arabido.pdf:C\:\\Users\\Syafira\\Zotero\\storage\\N93TL22G\\Ren et al. - 2009 - Genome-wide comparative analysis of type-A Arabido.pdf:application/pdf}, } @article{chatfield_ethylene_2008-1, title = {Ethylene and shoot regeneration: hookless1 modulates de novo shoot organogenesis in {Arabidopsis} thaliana}, volume = {27}, issn = {0721-7714, 1432-203X}, shorttitle = {Ethylene and shoot regeneration}, url = {http://link.springer.com/10.1007/s00299-007-0496-3}, doi = {10.1007/s00299-007-0496-3}, abstract = {We have investigated the role of ethylene in shoot regeneration from cotyledon explants of Arabidopsis thaliana. We examined the ethylene sensitivity of five ecotypes representing both poor and prolific shoot regenerators and identified Dijon-G, a poor regenerator, as an ecotype with dramatically enhanced ethylene sensitivity. However, inhibiting ethylene action with silver nitrate generally reduced shoot organogenesis in ecotypes capable of regeneration. In ecotype Col-0, we found that ethyleneinsensitive mutants (etr1-1, ein2-1, ein4, ein7) exhibited reduced shoot regeneration rates, whereas constitutive ethylene response mutants (ctr1-1, ctr1-12) increased the proportion of explants producing shoots. Our experiments with ethylene over-production mutants (eto1, eto2 and eto3) indicate that the ethylene biosynthesis inhibitor gene, ETO1, can act as an inhibitor of shoot regeneration. Pharmacological elevation of ethylene levels was also found to significantly increase the proportion of explants regenerating shoots. We determined that the hookless1 (hls1-1) mutant, a suppressor of the ethylene response phenotypes of ctr1 and eto1 mutants, is capable of dramatically enhancing shoot organogenesis. 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