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

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

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Abstract

We 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. This article is protected by copyright. All rights reserved.

Original languageEnglish
Pages (from-to)1066-1082
Number of pages39
JournalThe Plant Journal
Volume100
Issue number5
DOIs
Publication statusPublished - Dec 2019

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