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

Authors: VALLIYODAN, BABU - University Of Missouri; Cannon, Steven; BAYER, PHILIPP - University Of Western Australia; SHU, SHENGQIANG - Energy Joint Genome Institute; Brown, Anne; REN, LONGHUI - Iowa State University; JENKINS, JERRY - Hudsonalpha Institute For Biotechnology; CHUNG, CLAIRE - The Chinese University Of Hong Kong (CUHK); CHANG, TING-FUNG - The Chinese University Of Hong Kong (CUHK); DAUM, CHRISTOPHER - Energy Joint Genome Institute; PLOTT, CHRISTOPHER - Hudsonalpha Institute For Biotechnology; HASTIE, ALEX - Bionano Genomics, Inc; BARUCH, KOBI - Nrgene; BARRY, KERRIE - Energy Joint Genome Institute; HUANG, WEI - Iowa State University; GUNVANT, PATIL - University Of Missouri; RAJEEV, VARSHNEY - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; HU, HAIFEI - University Of Western Australia; BATLEY, JACQUELINE - University Of Western Australia; YUAN, YUXUAN - University Of Western Australia; Song, Qijian; STUPAR, ROBERT - University Of Minnesota; GOODSTEIN, DAVID - Energy Joint Genome Institute; STACEY, GARY - University Of Missouri; LAM, HON-MING - The Chinese University Of Hong Kong (CUHK); JACKSON, SCOTT - University Of Georgia; SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology; GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology; EDWARDS, DAVE - University Of Western Australia; NGUYEN, HENRY - University Of Missouri

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/17/2019
Publication Date: 8/21/2019
Citation: Valliyodan, B., Cannon, S.B., Bayer, P.E., Shu, S., Brown, A.V., Ren, L., Jenkins, J., Chung, C.Y.L., Chan, T.F., Daum, C.G., Plott, C., Hastie, A., Baruch, K., Barry, K.W., Huang, W., Gunvant, P., Varshney, R.K., Hu, H., Batley, J., Yuan, Y., Song, Q., Stupar, R.M., Goodstein, D.M., Stacey, G., Lam, H.M., Jackson, S.A., Schmutz, J., Grimwood, J., Edwards, D., Nguyen, H.T. 2019. Construction and comparison of three new reference-quality genome assemblies for soybean. Plant Journal. 100(5):1066-1082. https://doi.org/10.1111/tpj.14500.
DOI: https://doi.org/10.1111/tpj.14500

Interpretive Summary: Plant breeders and scientists increasingly rely on genome sequences to identify and select for important traits such as yield, disease resistance, and plant growth characteristics. For soybean, a version of the genome sequence for a widely-used variety ('Williams 82') has been available for about eight years, but there were numerous known gaps and errors in the approximately one-billion DNA bases that comprise the genome assembly. The research in this paper describes major improvements to the Williams 82 reference genome sequence, as well as new genome assemblies for two other varieties: one for the U.S. southern cultivar 'Lee', and another for the closest wild relative of soybean, Glycine soja. These three genome sequences can be used to identify similarities and differences that underlie important traits - that breeders focus on to produce varieties that are more nutritious and robust, for the benefit of farmers and consumers.

Technical Abstract: This research describes reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and one of Glycine soja, closely related to the wild ancestor of G. max. The G. max assemblies are for widely used U.S. cultivars: the northern line ‘Williams 82’; and the southern line ‘Lee’, which have both been used extensively in soybean breeding. The Williams 82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show low diversity between the two cultivated lines as well as structural conservation with the G. soja accession, with notable exceptions, some of which have identifiable biological consequences. We investigated a group of loci that have been important for the domestication of this crop. For each locus, alleles with functional differences are seen between G. soja and the two domesticated accessions. The combination of 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. These new reference-quality assemblies will serve as a basis for future research and crop improvement efforts for this important crop species.