Description: Genetic variant data derived from whole genome resequencing data of 1,502 diverse accessions from G. max and G. soja.
SoyBase ID SoyBase.C2021.04; Data Store ID Zhang_Jiang_2020
Project page: 1502 Accession Genotyping
Description: Genotyping results using the 180K SoyaSNP array are presented, with valication tests, in application to 222 diverse soybean lines.
SoyBase ID SoyBase.C2021.02; Data Store ID Lee_Jeong_2015
Project page: 180K Axiom SNP Array
Description: The objectives of this study were to determine the abundance of SSRs in the soybean genome and to develop and test soybean SSR markers to create a database of locus-specific markers with a high likelihood of polymorphism. A total of 210,990 SSRs with di-, tri-, and tetranucleotide repeats of five or more were identified in the soybean whole genome sequence (WGS) which included 61,458 SSRs consisting of repeat units of di- (≥10), tri- (≥8), and tetranucleotide (≥7). Among the 61,458 SSRs, (AT)n, (ATT)n and (AAAT)n were the most abundant motifs among di-, tri-, and tetranucleotide SSRs, respectively. After screening for a number of factors including locus-specificity using e-PCR, a soybean SSR database (BARCSOYSSR_1.0) with the genome position and primer sequences for 33,065 SSRs was created.
SoyBase ID SoyBase.barcsoyssr; Data Store ID Song_Cregan_2010
Project page: BARC Soybean Potential SSR
Description: Glycine max root nodules of different ages were sequenced to investigate the involvement of cysteine proteases and cystatins in the processes of nodule development and senescence.
SoyBase ID SoyBase.A2014.01; Data Store ID vanWyk_DuPlessis_2014
Project page: Cysteine protease and cystatin expression
Description: Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a paleopolyploidy (whole-genome duplication [WGD]) event, approximately 56.5 million years ago, followed by a genus Glycine-specific polyploidy, approximately 10 million years ago. Cytosine methylation is an epigenetic mark that plays an important role in the regulation of genes and transposable elements (TEs); however, the role of DNA methylation in the fate/evolution of genes following polyploidy and speciation has not been fully explored. Whole-genome bisulfite sequencing was used to produce nucleotide resolution methylomes for soybean and common bean. Reference methylomes for both soybean and common bean were constructed, providing resources for investigating epigenetic variation in legume crops. Also, the analysis of methylation patterns of duplicated and single-copy genes has provided insights into the functional consequences of polyploidy and epigenetic regulation in plant genomes.
SoyBase ID SoyBase.E2017.01; Data Store ID Kim_Baidouri_2015
Project page: DNA Methylomes of Two Legume Species
Description: A local cultivar Hedou 12 was resequenced to develop indel and SNP markers using the Williams 82 assembly 1 sequence as reference.
SoyBase ID SoyBase.B2014.01; Data Store ID Song_Wei_2015
Project page: Development of INDEL markers
Description: This project focuses on genetic mechanisms to address biotic and abiotic stresses, with the goal of developing cultivars with robust responses to biotic and abiotic stresses, by identifying useful alleles from across a broad germplasm collection. The project wil also evaluate the feasibility of engineering the effector-triggered immunity for enhancing disease resistance against four serious soybean pathogens through gene editing.
SoyBase ID SoyBase.C2018.01; Data Store ID Bhattacharyya_2018
Project page: Improving Biotic and Abiotic Stress Tolerance
Description: High-quality genome assemblies for soybean (Glycine max) and wild soybean (Glycine soja). These provide complements to the primary reference assembly for Glycine max cv. Williams 82 (Wm82.a2). The G. max assembly is for cultivar Lee, which has been used a parent in many southern U.S. breeding projects. The G. soja assembly is for accession PI 483463. This line was chosen for its high genotypic dissimilarity with respect to cultivated soybean. It originates from Shanxi Province, in north-central China.
SoyBase ID SoyBase.B2018.01; Data Store ID Valliyodan_Cannon_2016
Project page: Lee and PI 483463 Reference Genomes
Description: This project aims to identify determinants of yield potential of soybean varieties. Through resequencing of 79 cultivars that represent milestone parents, as well as the 41 SoyNAM parents, the project detects the genetic signatures of breeding work. Copy number variants (CNV) and in single nucleotide polymorphisms (SNP) are identified and presented interactively.
SoyBase ID SoyBase.C2016.01; Data Store ID MilestoneReseq_2016
Project page: Milestone Cultivar Sequencing
Description: Genotyping results based on the NJAU 355K SoySNP array, applied to 367 soybean accessions, including 105 wild soybeans and 262 cultivated soybeans. Trait analysis focuses on seed weight and selective sweeps during domestication.
SoyBase ID SoyBase.C2021.03; Data Store ID Wang_Chu_2016
Project page: NJAU 335 SNP Array
Description: Sclerotinia stem rot (SSR) resistance was evaluated and genetically characterized in a diverse collection of 101 soybean lines, mostly composed of plant introductions (PIs) and some of which had previously been reported to be resistant to sclerotinia stem rot.
SoyBase ID SoyBase.C2014.01; Data Store ID Iquira_Humira_2015
Project page: Sclerotinia stem rot resistance
Description: 48 high protein soybean accessions in seven MGs (000 to IV) were mated to a matching MG high yield cultivar of ordinary protein content. Selective genotyping of multiple bi-parental populations was used to identify QTL for seed protein and oil.
SoyBase ID SoyBase.D2016.01; Data Store ID Phansak_Soonsuwon_2016
Project page: Seed Protein and Oil QTLs
Description: The objective of this project was to assemble a soybean pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genome-wide changes in gene and allele frequency during domestication and breeding.
SoyBase ID SoyBase.C2020.02; Data Store ID Bayer_Valliyodan_2021
Project page: Sequencing the USDA core soybean collection
Description:The NSF-funded SoyMap II project, led by Scott Jackson, involved sequencing corresponding regions around six regions of interest from eight Glycine species, to gain insights into the polyploid and perennial genome evolution and genetic potential for soybean improvement. This project finished in 2012. See more information about the project, including pictures of the focal species and descriptions of the target regions, at legacy.soybase.org/soymap2.
A subsequent project, led by Jianxin Ma and Dajian Zhang, with funding primarily from the Shandong Province (China), completed the genome assemblies for the species used in the SoyMap II project. The Zhuang, Wang et al. (2022) paper below describes the genome assemblies and analyses from the second project. See references therein for further citations and descriptions of the species and objectives for both projects.
Description: This project identifies the genes and locations that control yield and other important agronomic traits in both domestic and exotic germplasm using association mapping, with a nested association mapping (NAM) population. Please also see the dedicated SoyNAM page, with additional information and plant images. To request seed, see that section below. Note that a Material Transfer Agreement (MTA) may be required; see details below at "request Parent seed".
SoyBase ID SoyBase.C2014.02; Data Store ID SoyNAM_2014
Project page: SoyNAM
Description: In order to provide genetic diversity and resources for identifying important genes, a new ethyl methane sulfonate (EMS) mutagenized soybean population was generated using the newly released germplasm, JTN-5203 (maturity group V). After harvest of a muagenized population, seed traits were evaluated including total oil, protein, starch, moisture content, fatty acid and amino acid compositions. Phenotypic variations observed in this population include changes in leaf morphology, plant architecture, seed compositions, and yield. We identified plants with increased amounts of total protein (50% vs. 41% for control) and plants with higher amounts of total oil (25% vs. 21.2% control). We also identified plants with increases in oleic acid content and decreases in linoleic acid and linolenic acid. This EMS mutant population will be used for further studies including screening for various traits such as amino acid pathways, allergens, phytic acids, and other important soybean agronomic traits.
SoyBase ID SoyBase.P2019.01; Data Store ID Espina_Ahmed_2018
Project page: Soybean EMS Mutagenized Population
Description: Compiled here are over 20,000 independent soybean fast neutron mutant lines derived from M92-220 developed for use in soybean functional genomics. Within the catalog are mutants with observed phenotypic variation in seed composition, maturity, morphology, pigmentation, roots and nodulation. This population was first used for a forward screen of seed protein and oil mutants. In the meantime, it was revitalized as a resource for phenome analysis and future forward and reverse genetics screens. Analysis of genomic DNA from a subset of mutants for deletions and additions by comparative genome hybridization are also displayed on this site.
SoyBase ID ; Data Store ID FN_mutants_2011
Project page: Soybean Fast Neutron Mutants
Description: Haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1,007 soybean accessions yielding close to 15 million SNPs. This haplotype map serves as a unique worldwide resource for soybean genomics and breeding. The HaplotypeMiner tool allows for selection of SNPs useful in defining genes at a given loci in germplasm collections.
SoyBase ID SoyBase.C2020.01; Data Store ID Torkamaneh_Laroche_2021
Project page: Soybean Haplotype Map
Description: The Soybean Transposable Elements database, SoyTEdb, described in SoyTEdb: a comprehensive database of transposable elements in the soybean genome (Du, Grant et al., 2010), contains transposable elements identified in the Williams 82 genome assembly 1, including 32,552 retrotransposons (Class I) and 6,029 DNA transposons (Class II). Linked files provide the named and classified sequences, as well as a reduced set clustered at 60% identity and represented by centroid sequences from each cluster.
SoyBase ID ; Data Store ID SoyTEdb_2010
Project page: Soybean Transposable Elements / SoyTEdb