@article{Dhaubhadel2007,
abstract = {We have used cDNA microarray analysis to examine changes in gene expression during embryo development in soybean (Glycine max) and to compare gene expression profiles of two soybean cultivars that differ in seed isoflavonoid content. The analysis identified 5,910 genes that were differentially expressed in both soybean cultivars grown at two different locations for two consecutive years in one of the five different stages of embryo development. An ANOVA analysis with P value {\textless} 0.05 and {\textless} 0.01 indicated that gene expression changes due to environmental factors are greater than those due to cultivar differences. Most changes in gene expression occurred at the stages when the embryos were at 30 or 70 d after pollination. A significantly larger fraction of genes (48.5{\%}) was expressed throughout the development and showed little or no change in expression. Transcript accumulation for genes related to the biosynthesis of storage components in soybean embryos showed several unique temporal expressions. Expression patterns of several genes involved in isoflavonoid biosynthesis, such as Phenylalanine Ammonia-Lyase, Chalcone Synthase (CHS)7, CHS8, and Isoflavone Synthase2, were higher at 70 d after pollination in both the cultivars. Thus, expression of these genes coincides with the onset of accumulation of isoflavonoids in the embryos. A comparative analysis of genes involved in isoflavonoid biosynthesis in RCAT Angora (high seed isoflavonoid cultivar) and Harovinton (low seed isoflavonoid cultivar) revealed that CHS7 and CHS8 were expressed at significantly greater level in RCAT Angora than in Harovinton. Our study provides a detailed transcriptome profiling of soybean embryos during development and indicates that differences in the level of seed isoflavonoids between these two cultivars could be as a result of differential expression of CHS7 and CHS8 during late stages of seed development. {\textcopyright} 2006 American Society of Plant Biologists.},
author = {Dhaubhadel, Sangeeta and Gijzen, Mark and Moy, Pat and Farhangkhoee, Mana},
doi = {10.1104/pp.106.086306},
issn = {0032-0889},
journal = {Plant Physiology},
month = {jan},
number = {1},
pages = {326--338},
title = {{Transcriptome Analysis Reveals a Critical Role of CHS7 and CHS8 Genes for Isoflavonoid Synthesis in Soybean Seeds}},
volume = {143},
year = {2007}
}
@unpublished{Ramandhani2014,
address = {Bandung},
author = {Ramandhani, Mohamad Rivai},
institution = {Institut Teknologi Bandung},
title = {{Penerapan Pattern Matching dalam Penentuan Pewarisan Sifat Genetis Tetua pada Anaknya}},
url = {http://informatika.stei.itb.ac.id/{~}rinaldi.munir/Stmik/2013-2014/Makalah2013/MakalahIF2211-2013-029.pdf},
year = {2014}
}
@article{Cheng2016,
abstract = {Background Coffee is one of the most valuable commodities exported worldwide. Greater understanding of the molecular basis of coffee quality is required to meet the increasing demands of consumers. Genotype and environment (G and E) have been shown to influence coffee quality. Analysis of coffee metabolism, the genes governing the accumulation of key components and the influence of environment on their expression during seed development supports the identification of the molecular determinants of coffee quality. Scope and approach The metabolism of important biochemical components of the coffee bean: caffeine, trigonelline, chlorogenic acids sucrose and lipids in coffee was reviewed. Analysis focused on how coffee metabolism was regulated by G and E throughout seed development and evaluation of transcriptome studies as an effective tool for use in understanding this system. Key findings and conclusions An overview of metabolism of the key components of coffee identified critical metabolic steps regulating the final concentration of metabolites that determine coffee quality. Coffee metabolism is influenced by both G and E and explains the higher quality of Arabica when compared to Robusta as well as the improvement of coffee quality by shade. Interaction of G and E (G × E) also contributes to quality. However, coffee metabolism is still not fully understood and there is scope for further studies to explain the contributions of G, E and G X E.},
author = {Cheng, Bing and Furtado, Agnelo and Smyth, Heather E and Henry, Robert J},
doi = {https://doi.org/10.1016/j.tifs.2016.09.003},
issn = {0924-2244},
journal = {Trends in Food Science {\&} Technology},
keywords = {Coffee,Environment,Genotype,Quality,Transcriptome},
pages = {20--30},
title = {{Influence of genotype and environment on coffee quality}},
url = {http://www.sciencedirect.com/science/article/pii/S0924224416302035},
volume = {57},
year = {2016}
}
@article{Juenger2010,
abstract = {Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats. Of particular interest are accessions with putatively locally adapted phenotypes - that is, accessions with attributes that are likely adaptive at their sites of origin. These genotypes may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. We studied the physiology, genome content and gene expression of two physiologically extreme accessions (Tsu-1 from Tsushima, Japan and Kas-1 from Kashmir, India). Our study was conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil drying. Genomic hybridizations identified 42 503 single feature polymorphisms (SFP) between accessions, providing an initial screen for genetic differences. Transcript profiling identified a large number (5996) of genes exhibiting constitutive differences in expression including genes involved in many biological pathways. Mild soil drying resulted in only subtle physiological responses but resulted in gene expression changes in hundreds of transcripts, including 352 genes exhibiting differential responses between accessions. Our results highlight the value of genomic studies of natural accessions as well as identify a number of candidate genes underlying physiological differences between Tsu-1 and Kas-1. {\textcopyright} 2010 Blackwell Publishing Ltd.},
author = {Juenger, Thomas E. and Sen, Saunak and Bray, Elizabeth and Stahl, Eli and Wayne, Tierney and Mckay, John and Richards, James H.},
doi = {10.1111/j.1365-3040.2010.02146.x},
issn = {01407791},
journal = {Plant, Cell and Environment},
keywords = {Acclimation,Affymetrix,Drought,Expression polymorphism,Hybridization polymorphism,Soil moisture,Water-use efficiency},
title = {{Exploring genetic and expression differences between physiologically extreme ecotypes: Comparative genomic hybridization and gene expression studies of Kas-1 and Tsu-1 accessions of Arabidopsis thaliana}},
year = {2010}
}
@article{Dixon2004,
abstract = {Collectively, plants contain several different families of natural products among which are compounds with weak estrogenic or antiestrogenic activity toward mammals. These compounds, termed phytoestrogens, include certain isoflavonoids, flavonoids, stilbenes, and lignans. The best-studied dietary phytoestrogens are the soy isoflavones and the flaxseed lignans. Their perceived health beneficial properties extend beyond hormone-dependent breast and prostate cancers and osteoporosis to include cognitive function, cardiovascular disease, immunity and inflammation, and reproduction and fertility. In the future, metabolic engineering of plants could generate novel and exquisitely controlled dietary sources with which to better assess the potential health beneficial effects of phytoestrogens.},
author = {Dixon, Richard A},
doi = {10.1146/annurev.arplant.55.031903.141729},
issn = {1543-5008 (Print)},
journal = {Annual review of plant biology},
keywords = {Diet,Flavonoids,Food Analysis,Humans,Lignans,Phytoestrogens,Plant Physiological Phenomena,Plants,classification,metabolism},
pages = {225--261},
pmid = {15377220},
title = {{Phytoestrogens.}},
volume = {55},
year = {2004}
}
@article{Veyrieras2008,
abstract = {Recent studies of the HapMap lymphoblastoid cell lines have identified large numbers of quantitative trait loci for gene expression (eQTLs). Reanalyzing these data using a novel Bayesian hierarchical model, we were able to create a surprisingly high-resolution map of the typical locations of sites that affect mRNA levels in cis. Strikingly, we found a strong enrichment of eQTLs in the 250 bp just upstream of the transcription end site (TES), in addition to an enrichment around the transcription start site (TSS). Most eQTLs lie either within genes or close to genes; for example, we estimate that only 5{\%} of eQTLs lie more than 20 kb upstream of the TSS. After controlling for position effects, SNPs in exons are ∼2-fold more likely than SNPs in introns to be eQTLs. Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation. {\textcopyright} 2008 Veyrieras et al.},
author = {Veyrieras, Jean Baptiste and Kudaravalli, Sridhar and Kim, Su Yeon and Dermitzakis, Emmanouil T. and Gilad, Yoav and Stephens, Matthew and Pritchard, Jonathan K.},
doi = {10.1371/journal.pgen.1000214},
issn = {15537390},
journal = {PLoS Genetics},
title = {{High-resolution mapping of expression-QTLs yields insight into human gene regulation}},
year = {2008}
}
@article{Lam2010,
abstract = {We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and {\textgreater}90{\%} coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis. {\textcopyright} 2010 Nature America, Inc. All rights reserved.},
author = {Lam, Hon Ming and Xu, Xun and Liu, Xin and Chen, Wenbin and Yang, Guohua and Wong, Fuk Ling and Li, Man Wah and He, Weiming and Qin, Nan and Wang, Bo and Li, Jun and Jian, Min and Wang, Jian and Shao, Guihua and Wang, Jun and Sun, Samuel Sai Ming and Zhang, Gengyun},
doi = {10.1038/ng.715},
issn = {10614036},
journal = {Nature Genetics},
title = {{Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection}},
year = {2010}
}
@article{Park2006,
abstract = {The high- and low-growth lines of chickens have been developed from a single founder population by divergent selection for body weight at 56 days of age for more than 40 generations. The two lines show a ninefold difference in body weight at selection age and several interesting correlated selection responses such as altered body composition and metabolic differences. We have generated a reciprocal intercross comprising {\textgreater}800 F2 birds. In a previous study, we reported the detection of 13 quantitative trait loci (QTLs) affecting growth. Here we report QTLs for body composition (fat deposition, muscle development), weight of internal organs, and metabolic traits (plasma concentrations of glucose, insulin, cholesterol, glucagon, triglycerides, and IGF-I). Most of the QTLs with convincing statistical support mapped in the vicinity of growth QTLs. One of the most interesting observations was that the type of reciprocal cross had highly significant effects on body weight at hatch and on plasma concentrations of glucose, cholesterol, insulin, and IGF-I, but it had no significant effect on body weight at 56 days of age. The reciprocal cross explained between 15 and 35{\%} of the phenotypic variance for weight at hatch and for plasma concentrations of glucose and insulin. The observed pattern indicated that these effects were caused by maternal effects or by genetic differences in mitochondrial DNA. Copyright {\textcopyright} 2006 the American Physiological Society.},
author = {Park, Hee Bok and Jacobsson, Lina and Wahlberg, Per and Siegel, Paul B. and Andersson, Leif},
doi = {10.1152/physiolgenomics.00113.2005},
issn = {10948341},
journal = {Physiological Genomics},
keywords = {Correlated selection response,Quantitative trait locus},
title = {{QTL analysis of body composition and metabolic traits in an intercross between chicken lines divergently selected for growth}},
year = {2006}
}
@article{Chiari2006,
abstract = {We studied the genetic basis of isoflavone content inheritance in soybean seeds. The progenitors BARC-8 (low isoflavone content), IAC-100 (high isoflavone content), the F1 and F2 populations derived from reciprocal crosses, and backcross populations were analyzed for isoflavone content and composition. Six isoflavones were detected: daidzin (DZ), genistin (GT), glycitin (GC), malonyldaidzin (MDZ), malonylgenistin (MGT) and malonylglycitin (MGC). DZ, GT, MDZ and MGT contents were influenced by the cytoplasm and the nuclear genes of the maternal parent. For this reason, a genetic model was considered that included the cytoplasmic effect and epistasis between nuclear and cytoplasmic genes. Except for GT, the additive effect was the most important one. For GT content the cytoplasmic effect was the most important. Except for MDZ, the epistatic effects were significant for all the isoflavone forms. Our data indicate that genetic improvement for these traits should explore the additive genetic variances in superior lines or the cytoplasmic effect and the epistatic interactions between cytoplasmic and nuclear genes to obtain the largest selection gains. {\textcopyright} Springer 2006.},
author = {Chiari, Lucimara and {Koshy Naoe}, Lucas and Piovesan, Newton Deniz and {Chamel Jos{\'{e}}}, In{\^{e}}s and {Dami{\~{a}}o Cruz}, Cosme and {Alves Moreira}, Maurilio and {Gon{\c{c}}alves De Barros}, Everaldo},
doi = {10.1007/s10681-006-9102-y},
issn = {00142336},
journal = {Euphytica},
keywords = {Cytoplasmic effect,Daidzin,Genistin,Glycine max,Inheritance,Maternal effect},
title = {{Inheritance of isoflavone contents in soybean seeds}},
year = {2006}
}
@article{Sheffield2008,
abstract = {Extended abstract of a paper presented at Microscopy and Microanalysis 2008 in Albuquerque, New Mexico, USA, August 3 – August 7, 2008},
author = {Sheffield, J B},
doi = {DOI: 10.1017/S1431927608088752},
edition = {2008/08/03},
issn = {1431-9276},
journal = {Microscopy and Microanalysis},
number = {S2},
pages = {898--899},
publisher = {Cambridge University Press},
title = {{An Introduction to ImageJ: A Useful Tool for Biological Image Processing and Analysis}},
url = {https://www.cambridge.org/core/article/an-introduction-to-imagej-a-useful-tool-for-biological-image-processing-and-analysis/00C658C8DC4108F2CB6DF8E6D9C9C12E},
volume = {14},
year = {2008}
}
@incollection{Dhaubhadel2011,
abstract = {Abstract Long-haul travel does not constitute an obstacle for tourists to travel and is fast gaining the attention of tourists in new and unique experiences. This study was conducted to identify the long-haul travel motivation by international tourists to Penang. A total of 400 respondents participated in this survey, conducted around the tourist attractions in Penang, using cluster random sampling. However, only 370 questionnaires were only used for this research. Data were analysed using SPSS software 22 version. The findings, ‘knowledge and novelty seeking' were the main push factors that drove long-haul travel by international tourists to Penang. Meanwhile, the main pull factor that attracts long- haul travel by international tourists to Penang was its ‘culture and history'. Additionally, there were partly direct and significant relationships between socio-demographic, trip characteristics and travel motivation (push factors and pull factors). Overall, this study identified the long-haul travel motivations by international tourists to Penang based on socio-demographic, trip characteristics and travel motivation and has indirectly helped in understanding the long-haul travel market particularly for Penang and Southeast Asia. This research also suggested for an effective marketing and promotion strategy in pro- viding useful information that is the key to attract international tourists to travel long distances. Keywords:},
author = {Dhaubhadel, Sangeeta},
booktitle = {Soybean - Biochemistry, Chemistry and Physiology},
doi = {10.5772/15120},
title = {{Regulation of Isoflavonoid Biosynthesis in Soybean Seeds}},
year = {2011}
}
@article{Marioni2008,
abstract = {Ultra-high-throughput sequencing is emerging as an attractive alternative to microarrays for genotyping, analysis of methylation patterns, and identification of transcription factor binding sites. Here, we describe an application of the Illumina sequencing (formerly Solexa sequencing) platform to study mRNA expression levels. Our goals were to estimate technical variance associated with Illumina sequencing in this context and to compare its ability to identify differentially expressed genes with existing array technologies. To do so, we estimated gene expression differences between liver and kidney RNA samples using multiple sequencing replicates, and compared the sequencing data to results obtained from Affymetrix arrays using the same RNA samples. We find that the Illumina sequencing data are highly replicable, with relatively little technical variation, and thus, for many purposes, it may suffice to sequence each mRNA sample only once (i.e., using one lane). The information in a single lane of Illumina sequencing data appears comparable to that in a single array in enabling identification of differentially expressed genes, while allowing for additional analyses such as detection of low-expressed genes, alternative splice variants, and novel transcripts. Based on our observations, we propose an empirical protocol and a statistical framework for the analysis of gene expression using ultra-high-throughput sequencing technology. {\textcopyright}2008 by Cold Spring Harbor Laboratory Press.},
author = {Marioni, John C. and Mason, Christopher E. and Mane, Shrikant M. and Stephens, Matthew and Gilad, Yoav},
doi = {10.1101/gr.079558.108},
issn = {10889051},
journal = {Genome Research},
pmid = {18550803},
title = {{RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays}},
year = {2008}
}
@article{Akada1993,
author = {Akada, S. and Kung, S. D. and Dube, S. K.},
doi = {10.1104/pp.102.1.321},
issn = {00320889},
journal = {Plant physiology},
title = {{Nucleotide sequence and putative regulatory elements of a nodule-development-specific member of the soybean (Glycine max) chalcone synthase multigene family, Gmchs 7.}},
year = {1993}
}
@phdthesis{vionnet:tel-00781279,
author = {Vionnet, Vincent},
keywords = {Terrestrial laser ; Numerical modeling ; Mountain},
month = {nov},
number = {2012PEST1167},
school = {Universit{\'{e}} Paris-Est},
title = {{Blowing and drifting snow in alpine terrain : observations and modeling using a snowpack-atmosphere coupled system}},
type = {Theses},
url = {https://pastel.archives-ouvertes.fr/tel-00781279},
year = {2012}
}
@article{Maston2006,
abstract = {The faithful execution of biological processes requires a precise and carefully orchestrated set of steps that depend on the proper spatial and temporal expression of genes. Here we review the various classes of transcriptional regulatory elements (core promoters, proximal promoters, distal enhancers, silencers, insulators/boundary elements, and locus control regions) and the molecular machinery (general transcription factors, activators, and coactivators) that interacts with the regulatory elements to mediate precisely controlled patterns of gene expression. The biological importance of transcriptional regulation is highlighted by examples of how alterations in these transcriptional components can lead to disease. Finally, we discuss the methods currently used to identify transcriptional regulatory elements, and the ability of these methods to be scaled up for the purpose of annotating the entire human genome.},
author = {Maston, Glenn A. and Evans, Sara K. and Green, Michael R.},
doi = {10.1146/annurev.genom.7.080505.115623},
isbn = {0824337077},
issn = {1527-8204},
journal = {Annual Review of Genomics and Human Genetics},
title = {{Transcriptional Regulatory Elements in the Human Genome}},
year = {2006}
}
@article{McKay2003,
abstract = {We examined patterns of genetic variance and covariance in two traits (i) carbon stable isotope ratio $\delta$ 13 C (dehydration avoidance) and (ii) time to flowering (drought escape), both of which are putative adaptations to local water availability. Greenhouse screening of 39 genotypes of Arabidopsis thaliana native to habitats spanning a wide range of climatic conditions, revealed a highly significant positive genetic correlation between $\delta$ 13 C and flowering time. Studies in a range of C 3 annuals have also reported large positive correlations, suggesting the presence of a genetically based trade-off between mechanisms of dehydration avoidance ($\delta$ 13 C) and drought escape (early flowering). We examined the contribution of pleiotropy by using a combination of mutant and near-isogenic lines to test for positive mutational covariance between $\delta$ 13 C and flowering time. Ecophysiological mutants generally showed variation in $\delta$ 13 C but not flowering time. However, flowering time mutants generally demonstrated pleiotropic effects consistent with natural variation. Mutations that caused later flowering also typically resulted in less negative $\delta$ 13 C and thus probably higher water use efficiency. We found strong evidence for pleiotropy using near-isogenic lines of Frigida and Flowering Locus C, cloned loci known to be responsible for natural variation in flowering time. These data suggest the correlated evolution of $\delta$ 13 C and flowering time is explained in part by the fixation of pleiotropic alleles that alter both $\delta$ 13 C and time to flowering.},
author = {McKay, John K. and Richards, Jim H. and Mitchell-Olds, Thomas},
doi = {10.1046/j.1365-294X.2003.01833.x},
issn = {09621083},
journal = {Molecular Ecology},
keywords = {Carbon isotope ratio,Correlated traits,Flowering locus c,Flowering time,Frigida,Pleiotropy},
title = {{Genetics of drought adaptation in Arabidopsis thaliana: I. Pleiotropy contributes to genetic correlations among ecological traits}},
year = {2003}
}
@article{Xu2008,
abstract = {Black soybeans have been used as an excellent dietary source for disease prevention and health promotion in China for hundreds of years. However, information about the distribution of healthpromoting phenolic compositions in different physical parts of black soybean and the contribution of phenolic compositions to overall antioxidant capacity is limited. To elucidate the distribution of phenolic composition and their contribution to antioxidant activities in black soybean, the total and individual phenolic profiles, and antioxidant capacities of seed coat, dehulled and whole black soybean were systematically investigated. The seed coat exhibited much higher total phenolic indexes and antioxidant activities than whole and dehulled black soybean. Dehulled black soybean possessed similar levels of total phenolic content, total flavonoid content, 2-diphenyl-1-picryhydrazyl (DPPH) radical scavenging activity, ferric reducing antioxidant power (FRAP), and oxygen radical absorbance capacity (ORAC) activities as compared to whole yellow soybean. Cyanidin-3-glucoside, petunidin-3-glucoside, and peonidin-3-glucoside were detected in the seed coat but not in dehulled black soybean and yellow soybean. Among benzoic acid detected, caffeic and chlorogenic acid were the predominant phenolic acids. Whole black soybean and dehulled black soybean exhibited similar isoflavone contents in 7-O-$\beta$-glucosides and malonylglucosides of daidzein and genistein. The seed coat possessed significantly (p {\textless} 0.05) lower 7-O-$\beta$-glucosides and malonylglucosides of daidzein and genistein, acetylglycitin, and total isoflavones than whole and dehulled black soybean. The contribution of phenolics in the seed coat to the antioxidant activity of black soybean parts depends on the assay methods. When measured with the DPPH and FRAP methods, the seed coat contributed 90{\%} of the total antioxidant capacity of black soybean. However, when measured with the ORAC method, the seed coat and dehulled portion contributed approximately equally the total antioxidant capacity of black soybeans. The information generated from this study on the distribution and content of their active components is useful for the effective use of black soybeans as an ingredient for promoting health. {\textcopyright} 2008 American Chemical Society.},
author = {Xu, Baojun and Chang, Sam K.C.},
doi = {10.1021/jf801196d},
issn = {00218561},
journal = {Journal of Agricultural and Food Chemistry},
keywords = {Anthocyanins,Antioxidants,Black soybean,DPPH,Dehulled bean,FRAP,HPLC,Isoflavones,ORAC,Phenolic acids,Seed coat},
title = {{Antioxidant capacity of seed coat, dehulled bean, and whole black soybeans in relation to their distributions of total phenolics, phenolic acids, anthocyanins, and isoflavones}},
year = {2008}
}
@article{Yu2003,
abstract = {Isoflavone levels in Glycine max (soybean) were increased via metabolic engineering of the complex phenylpropanoid biosynthetic pathway. Phenylpropanoid pathway genes were activated by expression of the maize Cl and R transcription factors in soybean seed, which decreased genistein and increased the daidzein levels with a small overall increase in total isoflavone levels. Cosuppression of flavanone 3-hydroxylase to block the anthocyanin branch of the pathway, in conjunction with Cl/R expression, resulted in higher levels of isoflavones. The combination of transcription factor-driven gene activation and suppression of a competing pathway provided a successful means of enhancing accumulation of isoflavones in soybean seed. {\textcopyright} 2003 Elsevier Ltd. All rights reserved.},
author = {Yu, Oliver and Shi, June and Hession, Aideen O. and Maxwell, Carl A. and McGonigle, Brian and Odell, Joan T.},
doi = {10.1016/S0031-9422(03)00345-5},
issn = {00319422},
journal = {Phytochemistry},
keywords = {Fabaceae,Flavanone 3-hydroxylase,Glycine max,Isoflavone,Transcription Factor},
title = {{Metabolic engineering to increase isoflavone biosynthesis in soybean seed}},
year = {2003}
}
@article{Gutierrez-Gonzalez2010,
abstract = {Numerous environmental factors influence isoflavone accumulation and have long hampered their genetic dissection. Temperature and water regimes are two of the most significant abiotic factors. However, while the effects of temperature have been widely studied, little is known about how water scarcity might affect isoflavone concentration in seeds. Studies have shown that accumulation of isoflavones is promoted by well-watered conditions, but the molecular basis remains elusive. The length and severity of the water stress required to induce changes are also still unknown. In the present work, several intensities of water stress were evaluated at various critical stages for soybean [Glycine max (L.) Merr.] seed development, in both field and controlled environments. The results suggested that only long-term progressive drought, spanning most of the seed developmental stages, significantly decreased isoflavone content in seeds. The reduction is proportional to the intensity of the stress and appears to occur in a genotype-dependent manner. However, regardless of water regime, isoflavone compounds were mainly accumulated in the later seed developmental stages. Transcripts of the most important genes for isoflavone biosynthesis were also quantified from samples collected at key seed developmental stages under well-watered and long-term water deficit conditions. Expression of CHS7, CHS8 and IFS2 correlated with isoflavone accumulation under well-watered conditions. Interestingly, we found that the two isoflavone synthase genes in soybean (IFS1 and IFS2) showed different patterns of expression. The abundance of IFS1 transcripts was maintained at a constant rate, whereas IFS2 was down-regulated and highly correlated with isoflavone accumulation under both water deficit and well-watered conditions, suggesting IFS2 as a main contributor to isoflavone diminution under drought. {\textcopyright} 2010 The Author.},
author = {Gutierrez-Gonzalez, Juan J. and Guttikonda, Satish K. and Tran, Lam Son Phan and Aldrich, Donavan L. and Zhong, Rui and Yu, Oliver and Nguyen, Henry T. and Sleper, David A.},
doi = {10.1093/pcp/pcq065},
issn = {00320781},
journal = {Plant and Cell Physiology},
keywords = {Daidzein,Drought,Genistein,Isoflavone,Isoflavone synthase,Phenylpropanoid transcripts},
title = {{Differential expression of isoflavone biosynthetic genes in soybean during water deficits}},
year = {2010}
}
@article{Zeyl2005,
abstract = {Abstract In addition to the familiar possibility of epistasis between nuclear loci, interactions may evolve between the mitochondrial and nuclear genomes in eukaryotic cells. We looked for such interactions in Saccharomyces cerevisiae genotypes evolved independently and asexually in the laboratory for 2000 generations, and in an ecologically distinct pathogenic S. cerevisiae strain. From these strains we constructed derivatives entirely lacking mitochondrial DNA and then used crosses to construct matched and unmatched pairings of nuclear and mitochondrial genomes. We detected fitness effects of such interactions in an evolved laboratory strain and in crosses between the laboratory and pathogen strains. In both cases, there were significant contributions to progeny fitness of both nuclear and mitochondrial genomes and of their interaction. A second evolved genotype showed incompatibility with the first evolved genotype, but the nuclear and mitochondrial contributions to this incompatibility could not be resolved. These results indicate that cytonuclear interactions analogous to those already known from plants and animals can evolve rapidly on an evolutionary timescale.},
annote = {doi: 10.1111/j.0014-3820.2005.tb01764.x},
author = {Zeyl, Clifford and Andreson, Bethany and Weninck, Emily},
doi = {10.1111/j.0014-3820.2005.tb01764.x},
issn = {0014-3820},
journal = {Evolution},
keywords = {Co-evolution,epistasis,fitness,nuclear-mitochondrial interaction,yeast},
month = {apr},
number = {4},
pages = {910--914},
publisher = {John Wiley {\&} Sons, Ltd (10.1111)},
title = {{NUCLEAR-MITOCHONDRIAL EPISTASIS FOR FITNESS IN SACCHAROMYCES CEREVISIAE}},
url = {https://doi.org/10.1111/j.0014-3820.2005.tb01764.x},
volume = {59},
year = {2005}
}
@article{Christie1996,
author = {Christie, John M and Jenkins, Gareth I and Christie, John M and Jenkins, Gareth I},
doi = {doi:10.2307/3870250.},
journal = {American Society of Plant Biologists},
number = {9},
pages = {1555--1567},
title = {{Distinct UV-B and UV-A / Blue Light Signal Transduction Pathways Induce Chalcone Synthase Gene Expression in Arabidopsis Cells}},
volume = {8},
year = {1996}
}
@article{Fritze1991,
abstract = {Expression directed by the 1.1-kb snapdragon chalcone synthase (CHS) promoter linked to the ??-glucuronidase reporter gene has been studied in transgenic tobacco. The pattern of expression of the chimeric gene was compared with the expression of the endogenous CHS genes in tobacco and snapdragon. We demonstrate that expression of the CHS promoter is controlled in both an organ-specific and tissue-specific manner. The highest level of expression was observed in immature seeds. Deletions were used to define regions of the promoter required for expression in roots, stems, leaves, seeds, and flower petals of transgenic plants. We have defined the minimal sequences required for expression in different organs and mapped regions of the promoter that influence expression in either a positive or negative manner. A promoter fragment truncated to -39 activates transcription in roots of 4-week-old seedlings, whereas a fragment extending to -197 bp directs expression in petals and seeds. A positive regulatory element located between -661 and -566 and comprising a 47-bp direct repeat is active in all tissues investigated except petals. UV light-regulated expression in leaves of transgenic tobacco seedlings is dependent on the presence of sequences also required for leaf-specific expression. Within the intact promoter, sequences that individually confer different patterns of expression interact to produce the highly regulated expression pattern of CHS.},
author = {Fritze, Klaus and Staiger, Dorothee and Czaja, Inge and Walden, Richard and Schell, Jeff and Wing, David},
doi = {10.2307/3869153},
issn = {10404651},
journal = {Plant Cell},
title = {{Developmental and UV light regulation of the snapdragon chalcone synthase promoter}},
year = {1991}
}
@article{Jung2000,
abstract = {Isoflavones have drawn much attention because of their benefits to human health. These compounds which are produced almost exclusively in legumes, have natural roles in plant defense and root nodulation Isoflavone synthase catalyzes the first committed step of isoflavone biosynthesis, a branch of the phenylpropanoid pathway. To identify the gene encoding this enzyme, we used a yeast expression assay to screen soybean ESTs encoding cytochrome P450 proteins. We identified two soybean genes encoding isoflavone synthase, and used them to isolate homologous genes from other leguminous species including red clover, white clover, hairy vetch, mung bean, alfalfa, lentil, snow pea, and lupine, as well as from the nonleguminous sugarbeet. We expressed soybean isoflavone synthase in Arabidopsis thaliana, which led to production of the isoflavone genistein in this nonlegume plant. Identification of the isoflavone synthase gene should allow manipulation of the phenylpropanoid pathway for agronomic and nutritional purposes.},
author = {Jung, Woosuk and Yu, Oliver and Lau, Sze Mei Cindy and O'Keefe, Daniel P. and Odell, Joan and Fader, Gary and McGonigle, Brian},
doi = {10.1038/72671},
issn = {10870156},
journal = {Nature Biotechnology},
keywords = {Cytochrome P450,Isoflavone,Phenylpropanoid},
title = {{Identification and expression of isoflavone synthase, the key enzyme for biosynthesis of isoflavones in legumes}},
year = {2000}
}
@article{Stranger2007,
abstract = {Genetic variation influences gene expression, and this variation in gene expression can be efficiently mapped to specific genomic regions and variants. Here we have used gene expression profiling of Epstein-Barr virus-transformed lymphoblastoid cell lines of all 270 individuals genotyped in the HapMap Consortium to elucidate the detailed features of genetic variation underlying gene expression variation. We find that gene expression is heritable and that differentiation between populations is in agreement with earlier small-scale studies. A detailed association analysis of over 2.2 million common SNPs per population (5{\%} frequency in HapMap) with gene expression identified at least 1,348 genes with association signals in cis and at least 180 in trans. Replication in at least one independent population was achieved for 37{\%} of cis signals and 15{\%} of trans signals, respectively. Our results strongly support an abundance of cis-regulatory variation in the human genome. Detection of trans effects is limited but suggests that regulatory variation may be the key primary effect contributing to phenotypic variation in humans. We also explore several methodologies that improve the current state of analysis of gene expression variation. {\textcopyright} 2007 Nature Publishing Group.},
author = {Stranger, Barbara E. and Nica, Alexandra C. and Forrest, Matthew S. and Dimas, Antigone and Bird, Christine P. and Beazley, Claude and Ingle, Catherine E. and Dunning, Mark and Flicek, Paul and Koller, Daphne and Montgomery, Stephen and Tavar{\'{e}}, Simon and Deloukas, Panos and Dermitzakis, Emmanouil T.},
doi = {10.1038/ng2142},
issn = {10614036},
journal = {Nature Genetics},
title = {{Population genomics of human gene expression}},
year = {2007}
}
@article{Dajanta2013,
abstract = {B. subtilis TN51 was inoculated in cooked black and yellow soybeans, after incubating at 42??C and 4??C for 48 h, the fermented thua nao were produced. The antioxidant capacities, total pehenolics and flavonoids of the fermented black (TN-BS) and yellow (TN-YS) soybeans were then examined as compared to their cooked non-fermented (CNF) soybeans. It was found that fermentation enhanced the increase of total phenolic and flavonoid contents (except yellow soybean fermentation) as well as antioxidant activities of anti-DPPH radicals and ferric reducing antioxidant power (FRAP) of the soybean extracts. The extracts of CNF black soybean and TN-BS, showed higher total phenolic content, total flavonoids, anti-DPPH radicals and lipid peroxidation inhibition than those of yellow soybean extracts. While, FRAP value was found higher in the extract of TN-YS than that in TN-BS extract. Correlation studies indicated significant (P ??? 0.01) positive correlation between the total phenolic contents and the values of FRAP in soybean extracts (r = 0.889). Whereas, the contents of total phenolics (r = -0.731) and flavonoids (r = -0.709) were negatively correlated (P ??? 0.01) with IC50 of DPPH radical-scavenging activity. Also, a significant negative correlation (P ??? 0.01, r = -7.39) was demonstrated between the total flavonoid contents and IC50 of lipid peroxidation inhibition. These results show that black soybean thua nao produced by powder culture B. subtilis TN51 could be used for possible commercial production of functional food to alleviate oxidative stress.},
author = {Dajanta, K. and Janpum, P. and Leksing, W.},
issn = {19854668},
journal = {International Food Research Journal},
keywords = {Antioxidant quality,Bacillus subtilis,Fermented soybean,Soybean,Thua nao},
title = {{Antioxidant capacities, total phenolics and flavonoids in black and yellow soybeans fermented by Bacillus subtilis: A comparative study of Thai fermented soybeans (thua nao)}},
year = {2013}
}