April 21, 2020  |  

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

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

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

Journal: The Plant journal
DOI: 10.1111/tpj.14500
Year: 2019

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