Kontribusi Genomika dalam Penemuan Gen Toleran Salinitas pada Tanaman Padi

https://doi.org/10.22146/veg.54889

Bagus Herwibawa(1*), Florentina Kusmiyati(2)

(1) Laboratorium Fisiologi dan Pemuliaan Tanaman, Fakultas Peternakan dan Pertanian, Universitas Diponegoro
(2) Laboratorium Fisiologi dan Pemuliaan Tanaman, Fakultas Peternakan dan Pertanian, Universitas Diponegoro
(*) Corresponding Author

Abstract


Kendala abiotik seperti salinitas, merupakan tantangan utama yang menjadi pembatas produktivitas tanaman padi. Sifat toleran salinitas sangat kompleks dan melibatkan banyak gen. Oleh sebab itu sangat sulit menyimpulkan bagaimana tanaman padi merespon cekaman salinitas. Artikel ini bertujuan untuk menjelaskan kontribusi genomika dalam penemuan gen toleran salinitas tanaman padi. Saat ini, genomika telah berkontribusi dalam penemuan gen toleran salinitas tanaman padi, khususnya melalui genomika komparatif dan kajian asosiasi lintas genom. Pengembangan pangkalan data genom juga bermanfaat untuk mengidentifikasi famili gen yang berkaitan dengan toleransi salinitas antar spesies berdasarkan homologi dan sintaksis. Gen-gen toleran salinitas yang ditemukan dapat dimanfaatkan melalui silang balik berbantuan penanda, seleksi berbantuan penanda, dan seleksi genomik, namun hingga saat ini gen-gen tersebut belum secara optimal dimanfaatkan. Penggunaan teknik baru, seperti rekayasa genetika dan pengeditan genom juga menjadi metode baru dan cepat untuk menghasilkan tanaman padi toleran salinitas. Meskipun demikian, kedua pendekatan tersebut juga belum banyak memanfaatkan gen-gen toleran salinitas yang telah ditemukan. Tren penelitian pangkalan data berbasis web diperkirakan akan terus meningkat karena murah, relatif mudah, dan mampu menghasilkan data prediktif. Pangkalan data yang akan terus berkembang, tentu harus dapat dimanfaatkan oleh peneliti dan pemulia tanaman di Indonesia.


Keywords


Cekaman abiotik, identifikasi gen, kajian asosiasi lintas genom, pengurutan genom lengkap, perbaikan tanaman padi

Full Text:

PDF


References

Abhayawickrama, B., D. Gimhani, N. Kottearachchi, V. Herath, D. Liyanage dan P. Senadheera. 2020. In silico identification of QTL-based polymorphic genes as salt-responsive potential candidates through mapping with two reference genomes in rice. Plants. 9: 233. DOI: 10.3390/plants9020233

Balai Besar Penelitian Tanaman Padi (BB Padi). 2010. Deskripsi Varietas Unggul Baru Padi 2010. Subang: Badan Penelitian dan Pengembangan Pertanian, Kementerian Pertanian.

Balai Besar Penelitian Tanaman Padi (BB Padi). 2018. Deskripsi Varietas Unggul Baru Padi 2018. Subang: Badan Penelitian dan Pengembangan Pertanian, Kementerian Pertanian.

Bindusree, G., P. Natarajan, S. Kalva dan P. Madasamy. 2017. Whole genome sequencing of Oryza sativa L. cv. Seeragasamba identifies a new fragrance allele in rice. PloS ONE. 12(11): e0188920. DOI: 10.1371/journal.pone.0188920

Carvalho, U. 2019. How CRISPR/Cas9 can help unravel salt stress responses in rice. <http://www.global-engage.com/agricultural-biotechnology/how-crispr-cas9-can-help-unravel-salt-stress-responses-in-rice/>. Diakses pada 26 Agustus 2020.

Chutimanukul, P., B. Kositsup, K. Plaimas, T. Buaboocha, M. Siangliw, T. Toojinda, L. Comai dan S. Chadchawan. 2018. Photosynthetic responses and identification of salt tolerance genes in a chromosome segment substitution line of ‘Khao dawk Mali 105’ rice. Environmental and Experimental Botany. 155: 497 – 508. DOI: 10.1016/j.envexpbot.2018.07.019

Cubero, M.J.A., M. Saiz, B. M. García, S. M. Sayalero, C. Entrala, J. A. Lorente, dan L. J. M. Gonzalez. 2017. Next generation sequencing: an application in forensic sciences? Annals of Human Biology. 44 (7): 581-592. DOI: 10.1080/03014460.2017.1375155

Fu, Y.B. 2017. The vulnerability of plant genetic resources conserved ex situ. Crop Science. 57 (5): 2314-2328. DOI: 10.2135/cropsci2017.01.0014

Goff, S.A., D. Ricke, T. H. Lan, G. Presting, R. Wang, M. Dunn, J. Glazebrook, A. Sessions, P. Oeller, H. Varma, D. Hadley, D. Hutchison, C. Martin, F. Katagiri, B. M. Lange, T. Moughamer, Y. Xia, P. Budworth, J. Zhong, T. Miguel, U. Paszkowski, S. Zhang, M. Colbert, W. Sun, L. Chen, B. Cooper, S. Park, T. C. Wood, L. Mao, P. Quail, R. Wing, R. Dean, Y. Yu, A. Zharkikh, R. Shen, S. Sahasrabudhe, A. Thomas, R. Cannings, A. Gutin, D. Pruss, J. Reid, S. Tavtigian, J. Mitchell, G. Eldredge, T. Scholl, R. M. Miller, S. Bhatnagar, N. Adey, T. Rubano, N. Tusneem, R. Robinson, J. Feldhaus, T. Macalma, A. Oliphant dan S. Briggs. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science. 296 (5565): 92 – 100. DOI: 10.1126/science.1068275

Gupta B. dan B. Huang. 2014. Mechanism of salinity tolerance in plants: physiological, biochemical and molecular characterization. International Journal of Genomics. 2014: 701596. DOI: 10.1155/2014/701596

Hao, W. dan H.X. Lin. 2010. Toward understanding genetic mechanisms of complex traits in rice. Journal of Genetics and Genomics. 37(10): 653–666. DOI: 10.1016/S1673-8527(09)60084-9

Horie, T., I. Karahara dan M. Katsuhara. 2012. Salinity tolerance mechanisms in glycophytes: An overview with the central focus on rice plants. Rice. 5: 11. DOI: 10.1186/1939-8433-5-11

Huang, X. dan B. Han. 2014. Natural variations and genome-wide association studies in crop plants. Annual Review of Plant Biology. 65: 531 - 51. DOI: 10.1146/annurev-arplant-050213-035715

Jain, M, K.C. Moharana, R. Shankar, R. Kumari dan R. Garg. 2014. Genome-wide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance. Plant Biotechnology Journal. 12(2): 253–264. DOI: 10.1111/pbi.12133

Jain, R., J. Jenkins, S. Shu, M. Chern, J. A. Martin, D. Copetti, P. Q. Duong, N. T. Pham, D. A. Kudrna, J. Talag, W. S. Schackwitz, A. M. Lipzen, D. Dilworth, D. Bauer, J. Grimwood, C. R. Nelson, F. Xing, W. Xie, K. W. Barry, R. A. Wing, J. Schmutz, G. Li dan P. C. Ronald. 2019. Genome sequence of the model rice variety KitaakeX. BMC Genomis. 20: 905. DOI: 10.1186/s12864-019-6262-4

Kaewneramit, T., T. Buaboocha, P. Sangchai dan N. Wutipraditkul. 2019. Oscam1-1 overexpression in the transgenic rice mitigated salt-induced oxidative damage. Biologia Plantarum. 63: 335-342, 2019. DOI: 10.32615/bp.2019.039

Khrueasan, N., P. Chutimanukul, K. Plaimas, T. Buaboocha, M. Siangliw, T. Toojinda, L. Comai dan S. Chadchawan. 2019. Comparison between the transcriptomes of ‘KDML105’ rice and a salt-tolerant chromosome segment substitution line. Genes. 10 (10): 742. DOI: 10.3390/genes10100742

Kusmiyati, F., Sutarno, M.G.A. Sas dan B. Herwibawa. 2018. Mutagenic effects of gamma rays on sobean (Glycine max L.) germination and seedlings. IOP Conference Series: Earth and Environmental Science. 102: 012059. DOI: 10.1088/1755-1315/102/1/012959

Lekklar, C., M. Pongpanich, D. Suriya-arunroj, A. Chinpongpanich, H. Tsai, L. Comai, S. Chadchawan dan T. Buaboocha. 2019a. Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand. BMC Genomics. 20 (1): 76. DOI: 10.1186/s12864-018-5317-2

Lekklar, C., D. Suriya-arunroj, M. Pongpanich, L. Comai, B. Kositsup, S. Chadchawan dan T. Buaboocha. 2019b. Comparative genomic analysis of rice with contrasting photosynthesis and grain production under salt stress. Genes. 10: 562. DOI: 10.3390/genes10080562

Li, Y.F., Y. Zheng, L. R. Vemireddy, S. K. Panda, S. Jose, A. Ranjan, P. Panda, G. Govindan, J. Cui, K. Wei, M. W. Yaish, G. C. Naidoo dan R. Sunkar. 2018. Comparative transcriptome and translatome analysis in contrasting rice genotypes reveals differential mRNA translation in salt-tolerant Pokkali under salt stress. BMC Genomics. 19: 935. DOI: 10.1186/s12864-018-5279-4

Linh, L. H., T. H. Linh, T. D. Xuan, L. H. Ham, A. M. Ismail dan T. D. Khanh. 2012. Molecular breeding to improve salt tolerance of rice (Oryza sativa L.) in the red river delta of Vietnam. International Journal of Plant Genomics. 2012: 949038. DOI: 10.1155/2012/949038

Liu, C., K. Chen, X. Zhao, X. Wang, C. Shen, Y. Zhu, M. Dai, X. Qiu, R. Yang, D. Xing, Y. Pang dan J. Xu. 2019. Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study. Rice. 12: 88. DOI: 10.1186/s12284-019-0349-z

Liu, L., Y. Li, S. Li, N. Hu, Y. He, R. Pong, D. Lin, L. Lu dan M. Law. 2012. Comparison of next-generation sequencing systems. Journal of Biomedicine and Biotechnology. 2012: 251364. DOI: 10.1155/2012/251364

Mansuri, R. M., Z. S. Shobbar, N. B. Jelodar, M. R. Ghaffari, G. A. Nematzadeh dan S. Asari. 2019. Dissecting molecular mechanisms underlying salt tolerance in rice: a comparative transcriptional profiling of the contrasting genotypes. Rice. 12: 13. DOI: 10.1186/s12284-019-0273-2

Pereira, R., J. Oliveira dan M. Sousa. 2020. Bioinformatics and computational tools for next generation sequencing analysis in clinical genetics. Journal of Clinical Medicine. 9: (1): 132. DOI: 10.3390/jcm9010132

Rad, H.E., F. Aref dan M. Rezaei. 2012. Response of rice to different salinity levels during different growth stage. Research Journal of Applied Sciences, Engineering and Technology. 4(17): 3040 - 3047.

Rana, M.M., T. Takamatsu, M. Baslam, K. Kaneko, K. Itoh, N. Harada, T. Sugiyama, T. Ohnishi, T. Kinoshita, H. Takagi dan T. Mitsui. 2019. Salt tolerance improvement in rice through efficient SNP marker-assisted selection coupled with speed-breeding. International Journal of Molecular Sciences. 20: 2585. DOI: 10.3390/ijms20102585

Razzaque, S., S. M. Elias, T. Haque, S. Biswas, G. M. N. A. Jewel, S. Rahman, X. Weng, A. M. Ismail, H. Walia, T. E. Juenger dan Z. I. Seraj. 2019. Gene expression analysis associated with salt stress in a reciprocally crossed rice population. Scientific Reports. 9: 8249. DOI: 10.1038/s41598-019-44757-4

Sahi, C., A. Singh, K. Kumar, E. Blumwald dan A. Grover. 2006. Salt stress response in rice: genetics, molecular biology, and comparative genomics. Functional and Integrative Genomics. 6: 263–284. DOI: 10.1007/s10142-006-0032-5

Sankar, P.D., M.A.A.M. Saleh dan C.I. Selvaraj. 2011. Rice breeding for salt tolerance. Research in Biotechnology. 2: 1-10.

Senadhira, D., F.J. Zapata-Arias, G.B. Gregorio, M.S. Alejar, H.C. de la Cruz, T.F. Padolina dan A.M. Galvez. 2002. Development of first salt-tolerant rice cultivar through indica/indica anther culture. Field Crops Research. 76(2-3): 103-110. DOI: 10.1016/S0378-4290(02)00032-1

Shi, Y., L. Gao, Z. Wu, X. Zhang, M. Wang, C. Zhang, F. Zhang, Y. Zhou dan Z. Li. 2017. Genome-wide association study of salt tolerance at the seed germination stage in rice. BMC Plant Biology. 17: 92. DOI: 10.1186/s12870-017-1044-0

Singhabahu, S., C. Wijesinghe, D. Gunawardana, M.D. Senarath-Yapa, M. Kannangara, R. Edirisinghe dan H.W.V. Dissanayake. 2017. Whole genome sequencing and analysis of Godawee, a salt tolerant indica rice variety. Rice Research: Open Access. 5: 177. DOI: 10.4172/2375-4338.1000177

Tang, Y. X. Bao, Y. Zhi, Q. Wu, Y. Guo, X. Yin, L. Zeng, J. Li, J. Zhang, W. He, W. Liu, Q. Wang, C. Jia, Z. Li dan K. Liu. 2019. Overexpression of a MYB family gene, OsMYB6, increases drought and salinity stress tolerance in transgenic rice. Frontiers in Plant Science. 10: 168. DOI: 10.3389/fpls.2019.00168

Wang, J., J. Zhu, Y. Zhang, F. Fan, W. Li, F. Wang, W. Zhong, C. Wang dan J. Yang. 2018. Comparative transcriptome analysis reveals molecular response to salinity stress of salt-tolerant and sensitive genotypes of indica rice at seedling stage. Scientific Reports. 8: 2085. DOI: 10.1038/s41598-018-19984-w

Yu, J., W. Zhao, W. Tong, Q. He, M. Y. Yoon, F. P. Li, B. Choi, E. B. Heo, K. W. Kim dan Y. J. Park. 2018. A genome-wide association study reveals candidate genes related to salt tolerance in rice (Oryza sativa) at the germination stage. International Journal of Molecular Science. 19 (10): 3145. DOI: 10.3390/ijms19103145

Yu, J., S. Hu, J. Wang, G. K. S. Wong, S. Li, B. Liu, Y. Deng, L. Dai, Y. Zhou, X. Zhang, M. Cao, J. Liu, J. Sun, J. Tang, Y. Chen, X. Huang, W. Lin, C. Ye, W. Tong, L. Cong, J. Geng, Y. Han, L. Li, W. Li, G. Hu, X. Huang, W. Li, J. Li, Z. Liu, L. Li, J. Liu, Q. Qi, J. Liu, L. Li, T. Li, X. Wang, H. Lu, T. Wu, M. Zhu, P. Ni, H. Han, W. Dong, X. Ren, X. Feng, P. Goff, X. Li, H. Wang, X. Xu, W. Zhai, Z. Xu, J. Zhang, S. He, J. Zhang, J. Xu, K. Zhang, X. Zheng, J. Dong, W. Zeng, L. Tao, J. Ye, J. Tan, X. Ren, X. Chen, J. He, D. Liu, W. Tian, C. Tian, H. Xia, Q. Bao, G. Li, H. Gao, T. Cao, J. Wang, W. Zhao, P. Li, W. Chen, X. Wang, Y. Zhang, J. Hu, J. Wang, S. Liu, J. Yang, G. Zhang, Y. Xiong, Z. Li, L. Mao, C. Zhou, Z. Zhu, R. Chen, B. Hao, W. Zheng, S. Chen, W. Guo, G. Li, S. Liu, M. Tao, J. Wang, L. Zhu, L. Yuan dan H. Yang. 2002. A draft sequence of rice genome (Oryza sativa L. ssp. indica). Science. 296 (5565): 79 - 92. DOI: 10.1126/science.1068037

Yuan, J., X. Wang, Y. Zhao, N.U. Khan, Z. Zhao, Y. Zhang, X. Wen, F. Tang, F. Wang dan Z. Li. 2020. Genetic basis and identification of candidate genes for salt tolerance in rice by GWAS. Scientific Reports. 10: 9958. DOI: 10.1038/s41498-020-66604-7

Zhang, A., Y. Liu, F. Wang, T. Li, Z. Chen, D. Kong, J. Bi, F. Zhang, X. Luo, J. Wang, J. Tang, X. Yu, G. Liu dan L. Luo. 2019. Enhanced rice salinity tolerance via CRISPR/Cas9-targeted mutagenesis of the OsRR22 gene. Molecular Breeding. 39: 47. DOI: 10.1007/s11032-019-0954-y

Zhu, M., H. Xie, X. Wei, K. Dossa, Y. Yu, S. Hui, G. Tang, X. Zeng, Y. Yu, P. Hu dan J. Wang. 2019. WGCNA analysis of salt-responsive core transcriptome identifies novel hub genes in rice. Genes. 10(9): 719. DOI: 10.3390/genes10090719



DOI: https://doi.org/10.22146/veg.54889

Article Metrics

Abstract views : 4104 | views : 3186

Refbacks

  • There are currently no refbacks.


Copyright (c) 2020 Vegetalika

Creative Commons License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

VEGETALIKA journal indexed by: 

 

       

  

View My Stats