Soybean Genome Sequence Research Articles

Next-generation sequencing in soybean breeding and genetic research

Soybean (Glycine max (L.) Merr.) is one of the most important grain legume crops whose production has been growing every year and by 2024 reached ca. 7 million tons. The objective of this review was to summarize the latest achievements in soybean breeding, including the use of high-throughput sequencing methods and genomic technologies. Soybean is one of the most studied plants. The studies of recent years showed the advantage of approaches based on the use of molecular genetic markers in breeding. The first version of the soybean genome sequence, the G. max genome “Williams 82”, was presented in 2010, and this event significantly accelerated the study and development of genetic research on the crop. The data obtained made it possible to develop resources aimed at both studying the functional organization of soybean genes and breeding new improved cultivars. The review summarizes the results of large-scale soybean sequencing projects, including pan-genome works. Methods used for high-resolution genetic mapping, such as the SNP array analysis and the GBS (genotyping-by-sequencing) technique, are described. Information is provided on soybean genes associated with valuable agronomic and breeding-oriented traits whose identification made it possible to single them out as targets for editing.

Recent advances in the improvement of soybean seed traits by genome editing

Genetic improvement of soybean seed traits is important for developing new varieties that meet the demand for soybean as a food, forage crop, and industrial products. A large number of soybean genome sequences are currently publicly available. This genome sequence information provides a significant opportunity to design genomic approaches to improve soybean traits. Genome editing represents a major advancement in biotechnology. The production of soybean mutants through genome editing is commonly achieved with either an Agrobacterium-mediated or biolistic transformation platform, which have been optimized for various soybean genotypes. Currently, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated endonuclease 9 (Cas9) system, which represents a major advance in genome editing, is used to improve soybean traits, such as fatty acid composition, protein content and composition, flavor, digestibility, size, and seed-coat color. In this review, we summarize the recent advances in the improvement of soybean seed traits through genome editing. We also discuss the characteristics of genome editing using the CRISPR/Cas9 system with transformation platforms.

Genome-Wide Identification and Characterization of the Abiotic-Stress-Responsive LACS Gene Family in Soybean (Glycine max)

Long-chain acyl-CoA synthases (LACSs) are a key factor in the formation of acyl-CoA after fatty acid hydrolysis and play an important role in plant stress resistance. This gene family has not been research in soybeans. In this study, the soybean (Glycine max (L.) Merr.) whole genome was identified, the LACS family genes of soybean were screened, and the bioinformatics, tissue expression, abiotic stress, drought stress and co-expression of transcription factors of the gene family were analyzed to preliminarily clarify the function of the LACS family of soybean. A total of 17 LACS genes were screened from soybean genome sequencing data. A bioinformatics analysis of the GmLACS gene was carried out from the aspects of phylogeny, gene structure, conserved sequence and promoter homeopathic element. The transcription spectra of GmLACSs in different organs and abiotic stresses were used by qRT-PCR. The GmLACS genes, which co-expresses the significant response of the analysis of drought stress and transcription factors. The results showed that all soybean LACS have highly conserved AMP-binding domains, and all soybean LACS genes were divided into 6 subfamilies. Transcriptome analysis indicated that the gene-encoding expression profiles under alkali, low temperature, and drought stress. The expression of GmLACS9/15/17 were significantly upregulated under alkali, low temperature and drought stress. Co-expression analysis showed that there was a close correlation between transcription factors and genes that significantly responded to LACS under drought stress. These results provide a theoretical and empirical basis for clarifying the function of LACS family genes and abiotic stress response mechanism of soybean.

Genome-wide characterization and expression analysis of TOPP-type protein phosphatases in soybean (Glycine max L.) reveal the role of GmTOPP13 in drought tolerance.

In response to various abiotic stressors such as drought, many plants engage different protein phosphatases linked to several physiological and developmental processes. However, comprehensive analysis of this gene family is lacking for soybean. This study was performed to identify the TOPP-type protein phosphatase family in soybean and investigate the gene's role under drought stress. Soybean genome sequences and transcriptome data were downloaded from the Phytozome v.12, and the microarray data were downloaded from NCBI GEO datasets GSE49537. Expression profiles of GmTOPP13 were obtained based on qRT-PCR results. GmTOPP13 gene was transformed into tobacco plants via Agrobacterium mediated method, and the drought tolerance was analyzed by water deficit assay. 15 GmTOPP genes were identified in the soybean genome database (GmTOPP1-15). GmTOPP genes were distributed on 9 of 20 chromosomes, with similar exon-intron structure and motifs arrangement. All GmTOPPs contained Metallophos and STPPase_N domains as well as the core catalytic sites. Cis-regulatory element analysis predicted that GmTOPPs were widely involved in plant development, stress and hormone response in soybean. Expression profiles showed that GmTOPPs expressed in different tissues and exhibited divergent expression patterns in leaf and root in response to drought stimulus. Moreover, GmTOPP13 gene was isolated and expression pattern analysis indicated that this gene was highly expressed in seed, root, leaf and other tissues detected, and intensively induced upon PEG6000 treatment. In addition, overexpression of GmTOPP13 gene enhanced the drought tolerance in tobacco plants. The transgenic tobacco plants showed regulation of stress-responsive genes including CAT, SOD, ERD10B and TIP during drought stress. This study provides valuable information for the study of GmTOPP gene family in soybean, and lays a foundation for further functional studies of GmTOPP13 gene under drought and other abiotic stresses.

Transcriptome-wide development and utilisation of novel intron-length polymorphic markers in common vetch (

Common vetch (Vicia sativa subsp. sativa) is one of the most economically important forage legumes, with high nutritional value and multiple uses. Although microsatellite markers have been developed and applied on a large scale for evaluation of common vetch germplasm, intron-length polymorphic (ILP) markers have not been systematically investigated and exploited. In this study, introns within the common vetch genome were located by aligning the RNA-Seq sequences of common vetch with barrel medic (Medicago truncatula), soybean (Glycine max) and Arabidopsis thaliana genome sequences, and then used for VsILP marker development. In total, 10 400 markers were generated from 44 582 common vetch unigenes. Of 300 randomly selected VsILP markers, 283 were successfully amplified in common vetch. Among these markers, 40 produced length variation in 30 accessions of common vetch, collectively yielding 166 alleles with an average of 4.0 alleles per locus. The polymorphic information content values extended from 0.06 to 0.81 with a mean of 0.49. Of the 283 VsILP markers, 84.8% exhibited transferability to other species, both leguminous (common vetch, lucerne (Medicago sativa), barrel medic, soybean, yellow sweet clover (Melilotus officinalis), Lotus corniculatus and Sophora alopecuroides) and non-leguminous (rice (Oryza sativa), Arabidopsis and tobacco (Nicotiana tabacum)). Here, we present the first large-scale development of ILP markers in common vetch and their utility in germplasm evaluation and transferability, which will be valuable for further comparative genomic studies, genetic relationship assessments, and marker-assisted breeding of leguminous and non-leguminous species.

Comprehensive Genomic Analysis and Expression Profiling of Diacylglycerol Kinase (DGK) Gene Family in Soybean (Glycine max) under Abiotic Stresses.

Diacylglycerol kinase (DGK) is an enzyme that plays a pivotal role in abiotic and biotic stress responses in plants by transforming the diacylglycerol into phosphatidic acid. However, there is no report on the characterization of soybean DGK genes in spite of the availability of the soybean genome sequence. In this study, we performed genome-wide analysis and expression profiling of the DGK gene family in the soybean genome. We identified 12 DGK genes (namely GmDGK1-12) which all contained conserved catalytic domains with protein lengths and molecular weights ranging from 436 to 727 amino acids (aa) and 48.62 to 80.93 kDa, respectively. Phylogenetic analyses grouped GmDGK genes into three clusters—cluster I, cluster II, and cluster III—which had three, four, and five genes, respectively. The qRT-PCR analysis revealed significant GmDGK gene expression levels in both leaves and roots coping with polyethylene glycol (PEG), salt, alkali, and salt/alkali treatments. This work provides the first characterization of the DGK gene family in soybean and suggests their importance in soybean response to abiotic stress. These results can serve as a guide for future studies on the understanding and functional characterization of this gene family.

Growing more with less: Breeding and developing drought resilient soybean to improve food security

Abstract Soybean (Glycine max L.) is considered an important crop, and enhancing its production under drought stress and changing climatic conditions to meet the challenges of global food security is crucial. Drought is considered one of the major abiotic factors that adversely affect soybean production. To address this challenge, we need to develop an integrative research approach that will bring together computational modelling, soil engineering, physiology, microbiology, molecular biology, genomics and plant breeding to study the underlying mechanisms of plant tolerance to drought stress. Advances in genomic technologies coupled with breeding approaches have helped scientists unravel the genes responsible for drought tolerance in crops. The success of a soybean breeding programme is largely dependent upon the extent of genetic variation in terms of drought tolerance-related traits. The availability of the whole soybean genome sequence is considered a major landmark in this process that will help design future strategies for improving soybean production. This review describes the recent advances in the study of the effect of drought stress on morpho-biochemical changes in soybean and the application of plant growth-promoting rhizobacteria, marker assisted selection, and different omics approaches to unravel the mechanism of drought tolerance. Here, in this review, we also highlight the customary knowledge on physiology, functional genomics and molecular breeding that may be significant in integrating genetic engineering and breeding approaches to improve drought tolerance in soybean crop.

GsCHX19.3, a member of cation/H+ exchanger superfamily from wild soybean contributes to high salinity and carbonate alkaline tolerance

Cation/H+ exchangers (CHX) are characterized to be involved in plant growth, development and stress responses. Although soybean genome sequencing has been completed, the CHX family hasn’t yet been systematically analyzed, especially in wild soybean. Here, through Hidden Markov Model search against Glycine soja proteome, 34 GsCHXs were identified and phylogenetically clustered into five groups. Members within each group showed high conservation in motif architecture. Interestingly, according to our previous RNA-seq data, only Group IVa members exhibited highly induced expression under carbonate alkaline stress. Among them, GsCHX19.3 displayed the greatest up-regulation in response to carbonate alkaline stress, which was further confirmed by quantitative real-time PCR analysis. We also observed the ubiquitous expression of GsCHX19.3 in different tissues and its localization on plasma membrane. Moreover, we found that GsCHX19.3 expression in AXT4K, a yeast mutant lacking four ion transporters conferred resistance to low K+ at alkali pH, as well as carbonate stress. Consistently, in Arabidopsis, GsCHX19.3 overexpression increased plant tolerance both to high salt and carbonate alkaline stresses. Furthermore, we also confirmed that GsCHX19.3 transgenic lines showed lower Na+ concentration but higher K+/Na+ values under salt-alkaline stress. Taken together, our findings indicated that GsCHX19.3 contributed to high salinity and carbonate alkaline tolerance.

Adaptive Mechanisms of Soybean Grown on Salt‐Affected Soils

AbstractSoybean (Glycine max) is an economically important pulse crop for livestock feed, human consumption and industrial use as a source for production of biodiesel. However, soybean yield is detrimentally affected by soil salinity around the world. To cope with soil salinization, in addition to soil remediation, approaches used in genetically modifying soybean genotypes to increase their productivity under saline conditions are also of importance. Thus, it is crucial to unravel the mechanisms controlling soybean responses to soil salinity in order to improve soybean performance with high salinity tolerance. Knowledge of the regulatory network for salt tolerance in model plants, includingArabidopsis, and the publically available soybean genome sequence has accelerated identification and functional analyses of genes regulating soybean responses to high salinity. This review presents an update of recent works on genetic studies of salt tolerance and the mechanisms regulating soybean responses and tolerance to soil salinity. We also discuss the effort and progress that have been made in the last decade toward developing high salt‐tolerant soybean varieties with improved productivity. Copyright © 2017 John Wiley & Sons, Ltd.

The complete chloroplast genome sequence of semi-wild soybean, Glycine gracilis (Fabales: Fabaceae)

Semi-wild soybean, Glycine gracilis, harbors unique gene resources for the soybean breeding programs, which would help to understand the process of soybean domestication. Here, we sequenced and characterized the complete chloroplast genome sequence of the semi-wild soybean. The genome of G. gracilis has 152,218 bp in length with 35.37% GC content. It contains two inverted repeats blocks of 25,574 bp, separated by the large single-copy block of 83,175 bp and small single-copy block of 17,895 bp. A total of 111 unique genes were annotated, including 77 protein coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis of the ten sequenced Glycine chloroplast genomes revealed that the semi-wild soybean G. gracilis is closer to cultivated soybean G. max than wild soybean G. soja. The newly sequenced complete chloroplast genome of G. gracilis will provide useful resources for the further genetic characterization that would enhance the conservation of this highly endangered species.

Molecular mechanisms of flowering under long days and stem growth habit in soybean.

Precise timing of flowering is critical to crop adaptation and productivity in a given environment. A number of classical E genes controlling flowering time and maturity have been identified in soybean [Glycine max (L.) Merr.]. The public availability of the soybean genome sequence has accelerated the identification of orthologues of Arabidopsis flowering genes and their functional analysis, and has allowed notable progress towards understanding the molecular mechanisms of flowering in soybean. Great progress has been made particularly in identifying genes and modules that inhibit flowering in long-day conditions, because a reduced or absent inhibition of flowering by long daylengths is an essential trait for soybean, a short-day (SD) plant, to expand its adaptability toward higher latitude environments. In contrast, the molecular mechanism of floral induction by SDs remains elusive in soybean. Here we present an update on recent work on molecular mechanisms of flowering under long days and of stem growth habit, outlining the progress in the identification of genes responsible, the interplay between photoperiod and age-dependent miRNA-mediated modules, and the conservation and divergence in photoperiodic flowering and stem growth habit in soybean relative to other legumes, Arabidopsis, and rice (Oryza sativa L.).

Genome-wide identification of soybean WRKY transcription factors in response to salt stress.

Members of the large family of WRKY transcription factors are involved in a wide range of developmental and physiological processes, most particularly in the plant response to biotic and abiotic stress. Here, an analysis of the soybean genome sequence allowed the identification of the full complement of 188 soybean WRKY genes. Phylogenetic analysis revealed that soybean WRKY genes were classified into three major groups (I, II, III), with the second group further categorized into five subgroups (IIa–IIe). The soybean WRKYs from each group shared similar gene structures and motif compositions. The location of the GmWRKYs was dispersed over all 20 soybean chromosomes. The whole genome duplication appeared to have contributed significantly to the expansion of the family. Expression analysis by RNA-seq indicated that in soybean root, 66 of the genes responded rapidly and transiently to the imposition of salt stress, all but one being up-regulated. While in aerial part, 49 GmWRKYs responded, all but two being down-regulated. RT-qPCR analysis showed that in the whole soybean plant, 66 GmWRKYs exhibited distinct expression patterns in response to salt stress, of which 12 showed no significant change, 35 were decreased, while 19 were induced. The data present here provide critical clues for further functional studies of WRKY gene in soybean salt tolerance.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-2647-x) contains supplementary material, which is available to authorized users.

Soybean Salt Tolerance 1 (GmST1) Reduces ROS Production, Enhances ABA Sensitivity, and Abiotic Stress Tolerance in Arabidopsis thaliana.

Abiotic stresses, including high soil salinity, significantly reduce crop production worldwide. Salt tolerance in plants is a complex trait and is regulated by multiple mechanisms. Understanding the mechanisms and dissecting the components on their regulatory pathways will provide new insights, leading to novel strategies for the improvement of salt tolerance in agricultural and economic crops of importance. Here we report that soybean salt tolerance 1, named GmST1, exhibited strong tolerance to salt stress in the Arabidopsis transgenic lines. The GmST1-overexpressed Arabidopsis also increased sensitivity to ABA and decreased production of reactive oxygen species under salt stress. In addition, GmST1 significantly improved drought tolerance in Arabidopsis transgenic lines. GmST1 belongs to a 3-prime part of Glyma.03g171600 gene in the current version of soybean genome sequence annotation. However, comparative reverse transcription-polymerase chain reaction analysis around Glyma.03g171600 genomic region confirmed that GmST1 might serve as an intact gene in soybean leaf tissues. Unlike Glyma.03g171600 which was not expressed in leaves, GmST1 was strongly induced by salt treatment in the leaf tissues. By promoter analysis, a TATA box was detected to be positioned close to GmST1 start codon and a putative ABRE and a DRE cis-acting elements were identified at about 1 kb upstream of GmST1 gene. The data also indicated that GmST1-transgenic lines survived under drought stress and showed a significantly lower water loss than non-transgenic lines. In summary, our results suggest that overexpression of GmST1 significantly improves Arabidopsis tolerance to both salt and drought stresses and the gene may be a potential candidate for genetic engineering of salt- and drought-tolerant crops.

Genome-wide analysis of MATE transporters and expression patterns of a subgroup of MATE genes in response to aluminum toxicity in soybean.

BackgroundMultidrug and toxic compound extrusion (MATE) family is an important group of the multidrug efflux transporters that extrude organic compounds, transporting a broad range of substrates such as organic acids, plant hormones and secondary metabolites. However, genome-wide analysis of MATE family in plant species is limited and no such studies have been reported in soybean.ResultsA total of 117 genes encoding MATE transporters were identified from the whole genome sequence of soybean (Glycine max), which were denominated as GmMATE1 - GmMATE117. These 117 GmMATE genes were unevenly localized on soybean chromosomes 1 to 20, with both tandem and segmental duplication events detected, and most genes showed tissue-specific expression patterns. Soybean MATE family could be classified into four subfamilies comprising ten smaller subgroups, with diverse potential functions such as transport and accumulation of flavonoids or alkaloids, extrusion of plant-derived or xenobiotic compounds, regulation of disease resistance, and response to abiotic stresses. Eight soybean MATE transporters clustered together with the previously reported MATE proteins related to aluminum (Al) detoxification and iron translocation were further analyzed. Seven stress-responsive cis-elements such as ABRE, ARE, HSE, LTR, MBS, as well as a cis-element of ART1 (Al resistance transcription factor 1), GGNVS, were identified in the upstream region of these eight GmMATE genes. Differential gene expression analysis of these eight GmMATE genes in response to Al stress helps us identify GmMATE75 as the candidate gene for Al tolerance in soybean, whose relative transcript abundance increased at 6, 12 and 24 h after Al treatment, with more fold changes in Al-tolerant than Al-sensitive cultivar, which is consistent with previously reported Al-tolerance related MATE genes.ConclusionsA total of 117 MATE transporters were identified in soybean and their potential functions were proposed by phylogenetic analysis with known plant MATE transporters. The cis-elements and expression patterns of eight soybean MATE genes related to Al detoxification/iron translocation were analyzed, and GmMATE75 was identified as a candidate gene for Al tolerance in soybean. This study provides a first insight on soybean MATE family and their potential roles in soybean response to abiotic stresses especially Al toxicity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2559-8) contains supplementary material, which is available to authorized users.

Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01.

BackgroundA landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines (RILs), the assembled sequence, especially in some genomic regions with sparse numbers of anchoring markers, needs to be improved. Molecular markers are being used by researchers in the soybean community, however, with the updating of the Glyma1.01 build based on the high-resolution linkage maps resulting from this research, the genome positions of these markers need to be mapped.ResultsTwo high density genetic linkage maps were constructed based on 21,478 single nucleotide polymorphism loci mapped in the Williams 82 x G. soja (Sieb. & Zucc.) PI479752 population with 1083 RILs and 11,922 loci mapped in the Essex x Williams 82 population with 922 RILs. There were 37 regions or single markers where marker order in the two populations was in agreement but was not consistent with the physical position in the Glyma1.01 build. In addition, 28 previously unanchored scaffolds were positioned. Map data were used to identify false joins in the Glyma1.01 assembly and the corresponding scaffolds were broken and reassembled to the new assembly, Wm82.a2.v1. Based upon the plots of the genetic on physical distance of the loci, the euchromatic and heterochromatic regions along each chromosome in the new assembly were delimited. Genomic positions of the commonly used markers contained in BARCSOYSSR_1.0 database and the SoySNP50K BeadChip were updated based upon the Wm82.a2.v1 assembly.ConclusionsThe information will facilitate the study of recombination hot spots in the soybean genome, identification of genes or quantitative trait loci controlling yield, seed quality and resistance to biotic or abiotic stresses as well as other genetic or genomic research.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2344-0) contains supplementary material, which is available to authorized users.

Expanding Omics Resources for Improvement of Soybean Seed Composition Traits.

Food resources of the modern world are strained due to the increasing population. There is an urgent need for innovative methods and approaches to augment food production. Legume seeds are major resources of human food and animal feed with their unique nutrient compositions including oil, protein, carbohydrates, and other beneficial nutrients. Recent advances in next-generation sequencing (NGS) together with “omics” technologies have considerably strengthened soybean research. The availability of well annotated soybean genome sequence along with hundreds of identified quantitative trait loci (QTL) associated with different seed traits can be used for gene discovery and molecular marker development for breeding applications. Despite the remarkable progress in these technologies, the analysis and mining of existing seed genomics data are still challenging due to the complexity of genetic inheritance, metabolic partitioning, and developmental regulations. Integration of “omics tools” is an effective strategy to discover key regulators of various seed traits. In this review, recent advances in “omics” approaches and their use in soybean seed trait investigations are presented along with the available databases and technological platforms and their applicability in the improvement of soybean. This article also highlights the use of modern breeding approaches, such as genome-wide association studies (GWAS), genomic selection (GS), and marker-assisted recurrent selection (MARS) for developing superior cultivars. A catalog of available important resources for major seed composition traits, such as seed oil, protein, carbohydrates, and yield traits are provided to improve the knowledge base and future utilization of this information in the soybean crop improvement programs.

Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods.

Soybean (Glycine max) is a major source of vegetable oil and protein for both animal and human consumption. The completion of soybean genome sequence led to a number of transcriptomic studies (RNA-seq), which provide a resource for gene discovery and functional analysis. Several data-driven (e.g., based on gene expression data) and knowledge-based (e.g., predictions of molecular interactions) methods have been proposed and implemented. In order to better understand gene relationships and protein interactions, we applied probabilistic graphical methods, based on Bayesian network and knowledgebase constraints using gene expression data to reconstruct soybean metabolic pathways. The results show that this method can predict new relationships between genes, improving on traditional reference pathway maps.

Le4 Is an Epicotyl Preferential Homologue of the Soybean Seed-Specific Le1 Lectin and the Vegetative Le3 Lectin Genes

Legume lectins play important roles in signaling and defense. The best known legume lectinin soybean [Glycine max (L.) Merr.] is the seed-specific soybean agglutinin (Le1). Recently, we showed that the promoters of two Le1 homologues, Le2 and Le3, drive β-glucuronidase (GUS) gene expression in transgenic Arabidopsis thaliana. In the present study, five lectin copies (Le1–Le5) were identified in the soybean genome sequence. Transcript profiles were investigated for Le1–Le4 in 2-week-old soybean seedlings using real-time qPCR and compared with public RNA-Seq-based transcript profiles. Le3 transcripts are preferentially present in leaves, flowers, and vegetative tissues, while Le4 transcripts are preferentially present in seedling nodes and epicotyls. Whereas Le2 and Le5 are likely non-expressed pseudogenes, Le3 and Le4 were further investigated for possible tertiary structure and for presence of cis-regulatory promoter motifs. Models of LE3 and LE4 tertiary structures show high similarity to the LE1 structure, although differences in the active sites allow for differences in substrates. Our results also show that several interesting cis-regulatory motifs are present. Furthermore, we show that three duplication events have led to the formation of these five lectin genes, one event of which corresponds with the most recent soybean genome duplication at 13 Mya.

A classification of basic helix-loop-helix transcription factors of soybean.

The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH) family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281) of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic selection of growth and environmental adaptation in this widely grown crop.

The Glycine max cv. Enrei Genome for Improvement of Japanese Soybean Cultivars.

We elucidated the genome sequence of Glycine max cv. Enrei to provide a reference for characterization of Japanese domestic soybean cultivars. The whole genome sequence obtained using a next-generation sequencer was used for reference mapping into the current genome assembly of G. max cv. Williams 82 obtained by the Soybean Genome Sequencing Consortium in the USA. After sequencing and assembling the whole genome shotgun reads, we obtained a data set with about 928 Mbs total bases and 60,838 gene models. Phylogenetic analysis provided glimpses into the ancestral relationships of both cultivars and their divergence from the complex that include the wild relatives of soybean. The gene models were analyzed in relation to traits associated with anthocyanin and flavonoid biosynthesis and an overall profile of the proteome. The sequence data are made available in DAIZUbase in order to provide a comprehensive informatics resource for comparative genomics of a wide range of soybean cultivars in Japan and a reference tool for improvement of soybean cultivars worldwide.