Construction and comparison of three reference-quality genome assemblies for soybean
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AbstractWe report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and one of Glycine soja, the closest wild relative of G. max. The G. max assemblies are for widely used U.S. 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 SNPs/kb between Wm82 and Lee, and 4.7 SNPs/kb between these lines and G. soja. SNP distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgressions and haplotype structure. Comparisons against the U.S. germplasm collection shows 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 ~40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and ~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 soybean's domestication and improvement, serving as a basis for future research and crop improvement efforts for this important crop species.
All Author(s) ListValliyodan B, Cannon SB, Bayer PE, Shu S, Brown AV, Ren L, Jenkins J, Chung CYL, Chan TF, Daum CG, Plott C, Hastie A, Baruch K, Barry KW, Huang W, Patil G, Varshney RK, Hu H, Batley J, Yuan Y, Song Q, Stupar RM, Goodstein DM, Stacey G, Lam HM, Jackson SA, Schmutz J, Grimwood J, Edwards D, Nguyen HT
Journal namePlant Journal
Year2019
Month12
Volume Number100
Issue Number5
Pages1066 - 1082
ISSN0960-7412
LanguagesEnglish-United Kingdom
KeywordsGlycine max, Glycine soja, soybean, genome assembly, domestication, comparative genomics

Last updated on 2020-09-07 at 00:44