Construction and comparison of three reference-quality genome assemblies for soybean

Valliyodan, Babu; Cannon, Steven B.; Bayer, Philipp E.; Shu, Shengqiang; Brown, Anne V.; Ren, Longhui; Jenkins, Jerry; Chung, Claire Y. ‐L.; Chan, Ting‐Fung; Daum, Christopher G.; Plott, Christopher; Hastie, Alex; Baruch, Kobi; Barry, Kerrie W.; Huang, Wei; Patil, Gunvant; Varshney, Rajeev K.; Hu, Haifei; Batley, Jacqueline; Yuan, Yuxuan; Song, Qijian; Stupar, Robert M.; Goodstein, David M.; Stacey, Gary; Lam, Hon‐Ming; Jackson, Scott A.; Schmutz, Jeremy; Grimwood, Jane; Edwards, David; Nguyen, Henry T.

doi:10.1111/tpj.14500

Construction and comparison of three reference-quality genome assemblies for soybean

Journal Article · Wed Aug 21 00:00:00 EDT 2019 · The Plant Journal

DOI:https://doi.org/10.1111/tpj.14500· OSTI ID:1619141

^[1]; Cannon, Steven B. ^[2]; Bayer, Philipp E. ^[3]; Shu, Shengqiang ^[4]; Brown, Anne V. ^[2]; Ren, Longhui ^[5]; Jenkins, Jerry ^[6]; Chung, Claire Y. ‐L. ^[7]; Chan, Ting‐Fung ^[7]; Daum, Christopher G. ^[4]; Plott, Christopher ^[6]; Hastie, Alex ^[8]; Baruch, Kobi ^[9]; Barry, Kerrie W. ^[4]; Huang, Wei ^[5]; Patil, Gunvant ^[10]; ^[11]; Hu, Haifei ^[3]; Batley, Jacqueline ^[3]; Yuan, Yuxuan ^[12] more »

Univ. of Missouri, Columbia, MO (United States); Lincoln Univ., Jefferson City, MO (United States)
US Dept. of Agriculture (USDA)., Ames, IA (United States)
The Univ. of Western Australia, Crawley, WA (Australia)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Iowa State Univ., Ames, IA (United States)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Chinese Univ. of Hong Kong (China)
Bionano Genomics, San Diego, CA (United States)
NRGene Ltd., Ness Ziona (Israel)
Univ. of Missouri, Columbia, MO (United States)
International Crops Research Inst. for the Semi‐Arid Tropics (ICRISAT), Patancheru (India)
School of Biological Sciences The University of Western Australia Crawley 6009 WA Australia
US Dept. of Agriculture (USDA)., Beltsville, MD (United States)
Univ. of Minnesota, St. Paul, MN (United States)
Univ. of Georgia, Athens, GA (United States)

Here, we report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: National Science Foundation (NSF); USDA; USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1619141

Journal Information:: The Plant Journal, Journal Name: The Plant Journal Journal Issue: 5 Vol. 100; ISSN 0960-7412

Publisher:: Society for Experimental BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 2 of Circular RNAs modulate the floral fate acquisition in soybean shoot apical meristem Babaei, Saeid; Singh, Mohan B.; Bhalla, Prem L. figshare https://doi.org/10.6084/m9.figshare.23536090.v1	dataset	January 2023
Additional file 3 of Circular RNAs modulate the floral fate acquisition in soybean shoot apical meristem Babaei, Saeid; Singh, Mohan B.; Bhalla, Prem L. figshare https://doi.org/10.6084/m9.figshare.23536093	dataset	January 2023
Additional file 4 of Circular RNAs modulate the floral fate acquisition in soybean shoot apical meristem Babaei, Saeid; Singh, Mohan B.; Bhalla, Prem L. figshare https://doi.org/10.6084/m9.figshare.23536099	dataset	January 2023
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59 BASIC BIOLOGICAL SCIENCES
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domestication
genome assembly
glycine max
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soybean

Construction and comparison of three reference-quality genome assemblies for soybean

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