Journal article
Construction and comparison of three reference‐quality genome assemblies for soybean
The Plant Journal, Vol.100(5), pp.1066-1082
2019
Abstract
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.
Details
- Title
- Construction and comparison of three reference‐quality genome assemblies for soybean
- Authors/Creators
- B. Valliyodan (Author/Creator) - University of MissouriS.B. Cannon (Author/Creator) - AmesP.E. Bayer (Author/Creator) - The University of Western AustraliaS. Shu (Author/Creator) - Joint Genome InstituteA.V. Brown (Author/Creator) - Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, 50011, IA, USA.L. Ren (Author/Creator) - Iowa State UniversityJ. Jenkins (Author/Creator)C.Y.L. Chung (Author/Creator) - Chinese University of Hong KongT‐F Chan (Author/Creator)C.G. Daum (Author/Creator) - Joint Genome InstituteC. Plott (Author/Creator) - HudsonAlpha Institute for BiotechnologyA. Hastie (Author/Creator) - BioNano Genomics (United States)K. Baruch (Author/Creator) - NRGene Ltd. Ness Ziona 7403648 IsraelK.W. Barry (Author/Creator) - Joint Genome InstituteW. Huang (Author/Creator) - Iowa State UniversityG. Patil (Author/Creator) - University of MissouriR.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsH. Hu (Author/Creator) - The University of Western AustraliaJ. Batley (Author/Creator) - The University of Western AustraliaY. Yuan (Author/Creator) - The University of Western AustraliaQ. Song (Author/Creator) - United States Department of AgricultureR.M. Stupar (Author/Creator) - University of MinnesotaD.M. Goodstein (Author/Creator) - Joint Genome InstituteG. Stacey (Author/Creator) - University of MissouriH‐M Lam (Author/Creator)S.A. Jackson (Author/Creator) - Applied Genetic Technologies (United States)J. Schmutz (Author/Creator) - HudsonAlpha Institute for BiotechnologyJ. Grimwood (Author/Creator) - HudsonAlpha Institute for BiotechnologyD. Edwards (Author/Creator) - The University of Western AustraliaH.T. Nguyen (Author/Creator) - University of Missouri
- Publication Details
- The Plant Journal, Vol.100(5), pp.1066-1082
- Publisher
- Blackwell Publishing
- Identifiers
- 991005541290107891
- Copyright
- © 2019 The Authors The Plant Journal © 2019 John Wiley & Sons Ltd
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- 3.4.96 QTL
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