Glycine (soybean)

The best-known species in Glycine is the cultivated soybean, G. max, which was domesticated in Central and East Asia. The majority of the species in the genus are found only in Australia, while a few species extend from Australia to East Asia.

NCBI taxonomy ID: 3847

Overview - soybean genome and annotation statistics and nomenclature

Since the release of the first full soybean genome assembly in 2010, assemblies have been generated for more than 50 accessions, including multiple assemblies for the first reference, Williams 82 (Wm82).

There are several nomenclature patterns for the assemblies and annotations. The pattern used by the DOE-JGI and SoyBase has generally taken the form Wm82.a4.v1, with the middle field ("a4") indicating assembly version and the last field (v1) indicating the annotation version. Within the SoyBase and LegumeInfo Data Store, the pattern takes the form Wm82.gnm4.ann1 -- again, with the middle field ("gnm4") indicating assembly version and the last field (ann1) indicating the annotation version.

Access the genome and annotation data for download via the DATA COLLECTIONS tab.

Access the genome and annotation via JBrowse the GENOMICS tab.

See additional details about the main reference assemblies at the Genome Assembly page.

To examine statistics about all genome assemblies and annotations held at SoyBase, use these two links:

Tools and resources for the genus as a whole

GlycineMine: InterMine interface for accessing genetic and genomic data for several species in Glycine.
ZZBrowse: Association viewers (QTL, GWAS)
GCViT: Genotype comparison visualization tool
Genome Context Viewer: Browser for dynamically discovering and viewing genomic synteny across selected species.
Grin Data Explorer: Tool to facilitate searches of GRIN Descriptor Data
SoyMapII project: SoyMap II project to sequence perennial relatives of soybean.

Tools and resources for particular species

Glycine max: soybean

Soybean (Glycine max), the predominant oil-seed legume worldwide, was likely domesticated in East Asia, ~6000-9000 years ago (Sedivy et al., 2017; https://doi.org/10.1111/nph.14418). It has many culinary and industrial uses. Some of the culinary uses include: for direct consumption of the green seed (i.e. edamame) and leaves (cooked, much like spinach); for tofu, soymilk, textured vegetable protein, soy sauce, tempeh, natto, and vegetable oil. Industrial uses include: oils, soap, cosmetics, and biodiesel. Soybean is also used as a high-protein forage, and can be prepared for fish- and animal-feed.

NCBI taxonomy ID: 3847

Glycine max resources

GlycineMine: InterMine interface for accessing genetic and genomic data for several species in Glycine.
ZZBrowse: Association viewers (QTL, GWAS)
GCViT: Genotype comparison visualization tool
Genome Context Viewer: Browser for dynamically discovering and viewing genomic synteny across selected species.
Grin Data Explorer: Tool to facilitate searches of GRIN Descriptor Data

Glycine max accessions

Reference - Williams 82

Wm82.gnm6

Glycine max accession Williams 82 (ISU01) genome assembly v6; renamed from Wm82 ISU-01 v2.1; JGI name Wm82.a6.v1

Genome Browser

Wm82.gnm5

Glycine max accession Williams 82 (Wm82), genome assembly 5 doi.org/10.1002/tpg2.20382

Genome Browser

Wm82.gnm4

Glycine max accession Williams 82 genome assembly v4.0; JGI name Wm82.a4.v1 doi.org/10.1111/tpj.14500

Genome Browser

Wm82.gnm2

Glycine max accession Williams 82 genome assembly v2.0; JGI name Wm82.a2.v1 doi.org/10.1038/nature08670

Genome Browser

Wm82.gnm1

Glycine max accession Williams genome assembly v1.0; JGI name Glycine max v1.1 doi.org/10.1038/nature08670

Genome Browser

Reference - Lee

Lee.gnm3

Glycine max accession Lee, genome assembly 3 doi.org/10.1002/tpg2.20382

Genome Browser

Lee.gnm2

Glycine max genotype Lee genome assembly v2.0 doi.org/10.1016/j.jare.2021.10.009

Genome Browser

Lee.gnm1

Glycine max accession Lee Genome assembly 1; JGI name Lee v1.1 doi.org/10.1111/tpj.14500

Genome Browser

Reference - Fiskeby III

FiskebyIII.gnm1

Glycine max genotype Fiskeby III genome assembly 1; JGI name Fiskeby v1.1

Genome Browser

Reference - Zhonghuang 13

Zh13.gnm2

Genome assembly version 2 files for cultivar Zhonghuang 13, Shen et al. (2019) doi.org/10.1007/s11427-019-9822-2

Genome Browser

Zh13.gnm1

Genome assembly files for cultivar Zhonghuang 13, Shen et al. (2018) doi.org/10.1007/s11427-018-9360-0

Genome Browser

Reference - Hwangkeum

Hwangkeum.gnm1

Glycine max genotype Hwangkeum genome assembly v1.0 doi.org/10.1093/g3journal/jkab272

Genome Browser

Reference - Jidou 17

JD17.gnm1

Glycine max accession Jidou 17 (JD17), genome assembly 1 doi.org/10.1093/g3journal/jkac017

Genome Browser

Chu, Peng et al., 2021

Citation (DOI) for this accession group: doi.org/10.1038/s41597-021-00947-2

Hefeng25_IGA1002.gnm1

Genome assembly files for cultivar Hefeng 25 (Hefeng25_IGA1002 in publication; WHFS_GmHF25_1.0 in the GenBank assembly record)

Genome Browser

Huaxia3_IGA1007.gnm1

Genome assembly files for cultivar Huaxia3 (Huaxia3_IGA1007 in publication; WHFS_GmHX3_1.0 in the GenBank assembly record)

Genome Browser

Jinyuan_IGA1006.gnm1

Genome assembly files for cultivar Jinyuan (Jinyuan_IGA100 in the publication; 6HFS_GmJY_1.0 in the GenBank assembly record)

Genome Browser

Wenfeng7_IGA1001.gnm1

Genome assembly files for cultivar Wenfeng 7 (Wenfeng7_IGA1001 in publication; WHFS_GmWF7_1.0 in the GenBank assembly record); Chu et al. (2021)

Genome Browser

Wm82_IGA1008.gnm1

Genome assembly files for cultivar Williams 82 (Wm82_IGA1008 in publication; WHFS_GmW82_1.0 in the GenBank assembly record)

Genome Browser

Zh13_IGA1005.gnm1

Genome assembly files for cultivar Zhonghuang 13 (Zh13_IGA1005 in publication; WHFS_GmZH13_1.0 in the GenBank assembly record)

Genome Browser

Zh35_IGA1004.gnm1

Genome assembly files for cultivar Zhonghuang 35 (Zh35_IGA1004 in publication; WHFS_GmZH35_1.0 in the GenBank assembly record)

Genome Browser

Liu, Du et al., 2020

Citation (DOI) for this accession group: doi.org/10.1016/j.cell.2020.05.023

58-161.gnm1

Genome assembly for Glycine max accession 58-161 (SoyL04)

Genome Browser

Amsoy.gnm1

Genome assembly for Glycine max accession Amsoy (SoyC05)

Genome Browser

DongNongNo_50.gnm1

Genome assembly for Glycine max accession DongNongNo_50 (SoyC12)

Genome Browser

FengDiHuang.gnm1

Genome assembly for Glycine max accession FengDiHuang (SoyL07)

Genome Browser

HanDouNo_5.gnm1

Genome assembly for Glycine max accession HanDouNo_5 (SoyC09)

Genome Browser

HeiHeNo_43.gnm1

Genome assembly for Glycine max accession HeiHeNo_43 (SoyC13)

Genome Browser

JiDouNo_17.gnm1

Genome assembly for Glycine max accession JiDouNo_17 (SoyC11)

Genome Browser

JinDouNo_23.gnm1

Genome assembly for Glycine max accession JinDouNo_23 (SoyC07)

Genome Browser

JuXuanNo_23.gnm1

Genome assembly for Glycine max accession JuXuanNo_23 (SoyC03)

Genome Browser

KeShanNo_1.gnm1

Genome assembly for Glycine max accession KeShanNo_1 (SoyC14)

Genome Browser

PI_398296.gnm1

Genome assembly for Glycine max accession PI_398296 (SoyL05)

Genome Browser

PI_548362.gnm1

Genome assembly for Glycine max accession PI_548362 (SoyC10)

Genome Browser

QiHuangNo_34.gnm1

Genome assembly for Glycine max accession QiHuangNo_34 (SoyC08)

Genome Browser

ShiShengChangYe.gnm1

Genome assembly for Glycine max accession ShiShengChangYe (SoyL09)

Genome Browser

TieFengNo_18.gnm1

Genome assembly for Glycine max accession TieFengNo_18 (SoyC02)

Genome Browser

TieJiaSiLiHuang.gnm1

Genome assembly for Glycine max accession TieJiaSiLiHuang (SoyL08)

Genome Browser

TongShanTianEDan.gnm1

Genome assembly for Glycine max accession TongShanTianEDan (SoyL03)

Genome Browser

WanDouNo_28.gnm1

Genome assembly for Glycine max accession WanDouNo_28 (SoyC04)

Genome Browser

XuDouNo_1.gnm1

Genome assembly for Glycine max accession XuDouNo_1 (SoyC01)

Genome Browser

YuDouNo_22.gnm1

Genome assembly for Glycine max accession YuDouNo_22 (SoyC06)

Genome Browser

ZhangChunManCangJin.gnm1

Genome assembly for Glycine max accession ZhangChunManCangJin (SoyL06)

Genome Browser

Zhutwinning2.gnm1

Genome assembly for Glycine max accession Zhutwinning2 (SoyL01)

Genome Browser

ZiHuaNo_4.gnm1

Genome assembly for Glycine max accession ZiHuaNo_4 (SoyL02)

Genome Browser

Wm82_NJAU.gnm1

Glycine max accession Williams 82 from Nanjing Agricultural University (Wm82-NJAU), genome assebly v1 doi.org/10.1016/j.molp.2023.08.012

Genome Browser

Glycine soja: soybean

Glycine soja is the closest wild relative of soybean, Glycine max. Populations of G. soja exist in the wild in China, Japan, Korea, and Russia. Analysis of genetic differences between the two species suggests that the two separated approximately 200 thousand years ago. The species remain interfertile, and G. soja accessions are used in breeding projects in order to introgress traits such as tolerance to particular diseases or environmental stresses.

NCBI taxonomy ID: 3848

Glycine soja resources

GlycineMine: InterMine interface for accessing genetic and genomic data for several species in Glycine.
ZZBrowse: Association viewers (QTL, GWAS)
GCViT: Genotype comparison visualization tool
Genome Context Viewer: Browser for dynamically discovering and viewing genomic synteny across selected species.
Grin Data Explorer: Tool to facilitate searches of GRIN Descriptor Data

Glycine soja accessions

Valliyodan, Cannon et al., 2019

Citation (DOI) for this accession group: doi.org/10.1111/tpj.14500

PI483463.gnm1

Glycine soja accession PI 483463 genome assembly, v1.0; JGI name Glycine soja v1.1

Genome Browser

Xie, Chung et al., 2019

Citation (DOI) for this accession group: doi.org/10.1038/s41467-019-09142-9

W05.gnm1

Genome assembly files for cultivar W05 from Xie, Lam et al. (2019): A reference-grade wild soybean genome

Genome Browser

Chu, Peng et al., 2021

Citation (DOI) for this accession group: doi.org/10.1038/s41597-021-00947-2

F_IGA1003.gnm1

Genome assembly files for Glycine soja F (F_IGA1003 in publication; WHFS_GsojaF_1.0 in the GenBank assembly record)

Genome Browser

Liu, Du et al., 2020

Citation (DOI) for this accession group: doi.org/10.1016/j.cell.2020.05.023

PI_549046.gnm1

Genome assembly for Glycine soja accession PI_549046 (SoyW02)

Genome Browser

PI_562565.gnm1

Genome assembly for Glycine soja accession PI_562565 (SoyW01)

Genome Browser

PI_578357.gnm1

Genome assembly for Glycine soja accession PI_578357 (SoyW03)

Genome Browser

Glycine cyrtoloba: soybean

G. cyrotoloba (Tind) is a perennial plant with twining and stiff stems. G. cyrotoloba pods are curved and somewhat mottled in appearance containing 3-9 seeds that and are dark brown to black in color (Tindale, MD et al., 1984). G. cyrotoloba is a diploid (2n=40) member of the C-genome of Glycine. It is found along the coast of Queensland and Northern New South Wales (Ratnaparkhe et al 2011 ; Gonzalez-Orozco et al., 2012).

NCBI taxonomy ID: 45689

Glycine cyrtoloba resources

SoyMap II project: SoyMap II project to sequence perennial relatives of soybean.
SoyMap2 Diversity Browser on Glyma.Wm82.a1 (Gmax1.01): GBrowse for G. cyrtoloba Bac End Sequence alignments on Glyma.Wm82.a1 (Gmax1.01)
SoyMap2 Diversity Browser on Glyma.Wm82.a2 (Gmax2.0): GBrowse for G. cyrtoloba Bac End Sequence alignments on Glyma.Wm82.a2 (Gmax2.0)

Glycine cyrtoloba accessions

Zhuang, Wang et al., 2022

Citation (DOI) for this accession group: doi.org/10.1038/s41477-022-01102-4

G1267.gnm1

Genome assemblies for Glycine cyrtoloba, accession G1267

Genome Browser

Glycine dolichocarpa: soybean

Glycine dolichocarpa (Tateishi & Ohashi) is a twining plant with long straight dark brown pods with 5-7 seeds. Seeds are square and dark brown in color. G. dolichocarpa is an allotetraploid (2n = 4x = 80) formed by hybridizatoin between G. syndetika and G. tomentella D3 (both 2n = 40). (This species was formerly part of the Glycine tomentella species complex and was referred to as G. tomentella T2.) It has a limited Australian range in Queensland, but like several other Glycine allopolyploids, has colonized islands of the Pacific Ocean (in this case Taiwan) where no perennial diploid Glycine species have been found ( Ratnaparkhe et al 2011; Harbert et al 2014).

NCBI taxonomy ID: 82538

Glycine dolichocarpa resources

SoyMap2 Diversity Browser on Glyma.Wm82.a1 (Gmax1.01): GBrowse for G. dolichocarpa Bac End Sequence alignments on Glyma.Wm82.a1 (Gmax1.01)
SoyMap2 Diversity Browser on Glyma.Wm82.a2 (Gmax2.0): GBrowse for G. dolichocarpa Bac End Sequence alignments on Glyma.Wm82.a2 (Gmax2.0)
SoyMap II project: SoyMap II project to sequence perennial relatives of soybean.

Glycine dolichocarpa accessions

Zhuang, Wang et al., 2022

Citation (DOI) for this accession group: doi.org/10.1038/s41477-022-01102-4

G1134.gnm1

Genome assemblies for Glycine dolichocarpa, accession G1134

Genome Browser

Glycine falcata: soybean

Glycine falcata (Benth.) is unique among perennial Glycine species in that it does not form a vine but rather short, erect stems from a fibrous woody root system instead of the more common taproot. Seeds are round and smooth similar to the annual species. G. falcata is a diploid (2n = 40) and is the sole member of the F-genome. It is sister to the remainder of subgenus Glycine, and is distinctive ecologically, characteristically growing in the black soil region of Queensland and possessing both chasmogamous and below- ground cleistogamous flowers, the latter producing geocarpic fruits (Ratnaparkhe et al 2011; Gonzalez-Orozco et al., 2012).

NCBI taxonomy ID: 45690

Glycine falcata resources

SoyMap2 Diversity Browser on Glyma.Wm82.a1 (Gmax1.01): GBrowse for G. falcata Bac End Sequence alignments on Glyma.Wm82.a1 (Gmax1.01)
SoyMap2 Diversity Browser on Glyma.Wm82.a2 (Gmax2.0): GBrowse for G. falcata Bac End Sequence alignments on Glyma.Wm82.a2 (Gmax2.0)
SoyMap II project: SoyMap II project to sequence perennial relatives of soybean.

Glycine falcata accessions

Zhuang, Wang et al., 2022

Citation (DOI) for this accession group: doi.org/10.1038/s41477-022-01102-4

G1718.gnm1

Genome assemblies for Glycine falcata, accession G1718

Genome Browser

Glycine stenophita: soybean

Glycine stenophita (B.E. Pfeil & Tind.) is a scrambling or climbing perennial that is glabrous or with sparse white hairs covering the stems. Pods are 4 to 6 seeded and seeds are generally barrel shaped with some variation in shape from elliptical to square. G. stenophita is a diploid (2n = 40) member of the B-genome group. It occurs in the Australian states of Queensland and New South Wales (Ratnaparkhe et al 2011; Gonzalez-Orozco et al., 2012).

NCBI taxonomy ID: 96944

Glycine stenophita resources

SoyMap2 Diversity Browser on Glyma.Wm82.a1 (Gmax1.01): GBrowse for G. stenophita Bac End Sequence alignments on Glyma.Wm82.a1 (Gmax1.01)
SoyMap2 Diversity Browser on Glyma.Wm82.a2 (Gmax2.0): GBrowse for G. stenophita Bac End Sequence alignments on Glyma.Wm82.a2 (Gmax2.0)
SoyMap II project: SoyMap II project to sequence perennial relatives of soybean.

Glycine stenophita accessions

Zhuang, Wang et al., 2022

Citation (DOI) for this accession group: doi.org/10.1038/s41477-022-01102-4

G1974.gnm1

Genome assemblies for Glycine stenophita, accession G1974

Genome Browser

Glycine syndetika: soybean

Glycine syndetika (B.E. Pfeil & Craven) is a twining perennial plant with three leathery, often persistent leaflets. Flowers are somewhat clustered towards to the top of the inflorescences and pods contain 4-9 relatively large square seeds (Pfeil. BE et al., 2006). G. syndetika is diploid (2n = 40) member of the A-genome clade. (This species was formerly part of the Glycine tomentella species complex and was referred to as G. tomentella D4. ) It is has a restricted range in the Eastern Queensland region of Australia (Ratnaparkhe et al 2011; Gonzalez-Orozco et al., 2012).

NCBI taxonomy ID: 713886

Glycine syndetika resources

SoyMap2 Diversity Browser on Glyma.Wm82.a1 (Gmax1.01): GBrowse for G. syndetika Bac End Sequence alignments on Glyma.Wm82.a1 (Gmax1.01)
SoyMap2 Diversity Browser on Glyma.Wm82.a2 (Gmax2.0): GBrowse for G. syndetika Bac End Sequence alignments on Glyma.Wm82.a2 (Gmax2.0)
SoyMap II project: SoyMap II project to sequence perennial relatives of soybean.

Glycine syndetika accessions

Zhuang, Wang et al., 2022

Citation (DOI) for this accession group: doi.org/10.1038/s41477-022-01102-4

G1300.gnm1

Genome assemblies for Glycine syndetika, accession G1300

Genome Browser

Glycine D3-tomentella: soybean

A complex of diploid and tetraploid taxa are lumped under the name "G. tomentella" but are each reproductively isolated species, e.g. G. tomentella D3 belongs to the D-genome, whereas D1 G. tomentella belongs to the E-genome.

NCBI taxonomy ID: 2908013

Glycine D3-tomentella resources

SoyMap2 Diversity Browser on Glyma.Wm82.a1 (Gmax1.01): GBrowse for G. tomentella Bac End Sequence alignments on Glyma.Wm82.a1 (Gmax1.01)
SoyMap2 Diversity Browser on Glyma.Wm82.a2 (Gmax2.0): GBrowse for G. tomentella Bac End Sequence alignments on Glyma.Wm82.a2 (Gmax2.0)
SoyMap II: SoyMap II project to sequence perennial relatives of soybean.

Glycine D3-tomentella accessions

Zhuang, Wang et al., 2022

Citation (DOI) for this accession group: doi.org/10.1038/s41477-022-01102-4

G1403.gnm1

Genome assemblies for Glycine D3 tomentella, accession G1403

Genome Browser