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
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GlycineMine
- InterMine interface for accessing genetic and genomic data for several species in Glycine.
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ZZBrowse
- Association viewers (QTL, GWAS)
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GCViT
- Genotype comparison visualization tool
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Genome Context Viewer
- Browser for dynamically discovering and viewing genomic synteny across selected species.
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Grin Data Explorer
- Tool to facilitate searches of GRIN Descriptor Data
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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
Wm82.gnm5
Glycine max accession Williams 82 (Wm82), genome assembly 5
doi.org/10.1002/tpg2.20382
Wm82.gnm4
Glycine max accession Williams 82 genome assembly v4.0; JGI name Wm82.a4.v1
doi.org/10.1111/tpj.14500
Wm82.gnm2
Glycine max accession Williams 82 genome assembly v2.0; JGI name Wm82.a2.v1
doi.org/10.1038/nature08670
Wm82.gnm1
Glycine max accession Williams genome assembly v1.0; JGI name Glycine max v1.1
doi.org/10.1038/nature08670
Reference - Lee
Lee.gnm3
Glycine max accession Lee, genome assembly 3
doi.org/10.1002/tpg2.20382
Lee.gnm2
Glycine max genotype Lee genome assembly v2.0
doi.org/10.1016/j.jare.2021.10.009
Lee.gnm1
Glycine max accession Lee Genome assembly 1; JGI name Lee v1.1
doi.org/10.1111/tpj.14500
Reference - Fiskeby III
FiskebyIII.gnm1
Glycine max genotype Fiskeby III genome assembly 1; JGI name Fiskeby v1.1
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
Zh13.gnm1
Genome assembly files for cultivar Zhonghuang 13, Shen et al. (2018)
doi.org/10.1007/s11427-018-9360-0
Reference - Hwangkeum
Hwangkeum.gnm1
Glycine max genotype Hwangkeum genome assembly v1.0
doi.org/10.1093/g3journal/jkab272
Reference - Jidou 17
JD17.gnm1
Glycine max accession Jidou 17 (JD17), genome assembly 1
doi.org/10.1093/g3journal/jkac017
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)
Huaxia3_IGA1007.gnm1
Genome assembly files for cultivar Huaxia3 (Huaxia3_IGA1007 in publication; WHFS_GmHX3_1.0 in the GenBank assembly record)
Jinyuan_IGA1006.gnm1
Genome assembly files for cultivar Jinyuan (Jinyuan_IGA100 in the publication; 6HFS_GmJY_1.0 in the GenBank assembly record)
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)
Wm82_IGA1008.gnm1
Genome assembly files for cultivar Williams 82 (Wm82_IGA1008 in publication; WHFS_GmW82_1.0 in the GenBank assembly record)
Zh13_IGA1005.gnm1
Genome assembly files for cultivar Zhonghuang 13 (Zh13_IGA1005 in publication; WHFS_GmZH13_1.0 in the GenBank assembly record)
Zh35_IGA1004.gnm1
Genome assembly files for cultivar Zhonghuang 35 (Zh35_IGA1004 in publication; WHFS_GmZH35_1.0 in the GenBank assembly record)
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)
Amsoy.gnm1
Genome assembly for Glycine max accession Amsoy (SoyC05)
DongNongNo_50.gnm1
Genome assembly for Glycine max accession DongNongNo_50 (SoyC12)
FengDiHuang.gnm1
Genome assembly for Glycine max accession FengDiHuang (SoyL07)
HanDouNo_5.gnm1
Genome assembly for Glycine max accession HanDouNo_5 (SoyC09)
HeiHeNo_43.gnm1
Genome assembly for Glycine max accession HeiHeNo_43 (SoyC13)
JiDouNo_17.gnm1
Genome assembly for Glycine max accession JiDouNo_17 (SoyC11)
JinDouNo_23.gnm1
Genome assembly for Glycine max accession JinDouNo_23 (SoyC07)
JuXuanNo_23.gnm1
Genome assembly for Glycine max accession JuXuanNo_23 (SoyC03)
KeShanNo_1.gnm1
Genome assembly for Glycine max accession KeShanNo_1 (SoyC14)
PI_398296.gnm1
Genome assembly for Glycine max accession PI_398296 (SoyL05)
PI_548362.gnm1
Genome assembly for Glycine max accession PI_548362 (SoyC10)
QiHuangNo_34.gnm1
Genome assembly for Glycine max accession QiHuangNo_34 (SoyC08)
ShiShengChangYe.gnm1
Genome assembly for Glycine max accession ShiShengChangYe (SoyL09)
TieFengNo_18.gnm1
Genome assembly for Glycine max accession TieFengNo_18 (SoyC02)
TieJiaSiLiHuang.gnm1
Genome assembly for Glycine max accession TieJiaSiLiHuang (SoyL08)
TongShanTianEDan.gnm1
Genome assembly for Glycine max accession TongShanTianEDan (SoyL03)
WanDouNo_28.gnm1
Genome assembly for Glycine max accession WanDouNo_28 (SoyC04)
XuDouNo_1.gnm1
Genome assembly for Glycine max accession XuDouNo_1 (SoyC01)
YuDouNo_22.gnm1
Genome assembly for Glycine max accession YuDouNo_22 (SoyC06)
ZhangChunManCangJin.gnm1
Genome assembly for Glycine max accession ZhangChunManCangJin (SoyL06)
Zhutwinning2.gnm1
Genome assembly for Glycine max accession Zhutwinning2 (SoyL01)
ZiHuaNo_4.gnm1
Genome assembly for Glycine max accession ZiHuaNo_4 (SoyL02)
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
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
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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
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
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)
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)
PI_562565.gnm1
Genome assembly for Glycine soja accession PI_562565 (SoyW01)
PI_578357.gnm1
Genome assembly for Glycine soja accession PI_578357 (SoyW03)
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
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SoyMap II project
- SoyMap II project to sequence perennial relatives of soybean.
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SoyMap2 Diversity Browser on Glyma.Wm82.a1 (Gmax1.01)
- GBrowse for G. cyrtoloba Bac End Sequence alignments on Glyma.Wm82.a1 (Gmax1.01)
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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
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
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SoyMap2 Diversity Browser on Glyma.Wm82.a1 (Gmax1.01)
- GBrowse for G. dolichocarpa Bac End Sequence alignments on Glyma.Wm82.a1 (Gmax1.01)
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SoyMap2 Diversity Browser on Glyma.Wm82.a2 (Gmax2.0)
- GBrowse for G. dolichocarpa Bac End Sequence alignments on Glyma.Wm82.a2 (Gmax2.0)
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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
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
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SoyMap2 Diversity Browser on Glyma.Wm82.a1 (Gmax1.01)
- GBrowse for G. falcata Bac End Sequence alignments on Glyma.Wm82.a1 (Gmax1.01)
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SoyMap2 Diversity Browser on Glyma.Wm82.a2 (Gmax2.0)
- GBrowse for G. falcata Bac End Sequence alignments on Glyma.Wm82.a2 (Gmax2.0)
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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
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
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SoyMap2 Diversity Browser on Glyma.Wm82.a1 (Gmax1.01)
- GBrowse for G. stenophita Bac End Sequence alignments on Glyma.Wm82.a1 (Gmax1.01)
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SoyMap2 Diversity Browser on Glyma.Wm82.a2 (Gmax2.0)
- GBrowse for G. stenophita Bac End Sequence alignments on Glyma.Wm82.a2 (Gmax2.0)
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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
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
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SoyMap2 Diversity Browser on Glyma.Wm82.a1 (Gmax1.01)
- GBrowse for G. syndetika Bac End Sequence alignments on Glyma.Wm82.a1 (Gmax1.01)
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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
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
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SoyMap2 Diversity Browser on Glyma.Wm82.a1 (Gmax1.01)
- GBrowse for G. tomentella Bac End Sequence alignments on Glyma.Wm82.a1 (Gmax1.01)
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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