Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing

Valliyodan, B and Brown, A V and Wang, J and Patil, G and Liu, Y and Otyama, P I and Nelson, R T and Vuong, T and Song, Q and Musket, T A and Wagner, R and Marri, P and Reddy, S and Sessions, A and Wu, X and Grant, D and Bayer, P E and Roorkiwal, M and Varshney, R K and Liu, X and Edwards, D and Xu, D and Joshi, T and Cannon, S B and Nguyen, H T (2021) Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data (TSI), 8 (1). pp. 1-9. ISSN 2052-4463

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Abstract

We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the resequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.

Item Type:	Article
Divisions:	Research Program : Genetic Gains
CRP:	UNSPECIFIED
Uncontrolled Keywords:	soybean, Genetics, Genomics
Subjects:	Others > Genetics and Genomics Others > Legume Crops
Depositing User:	Mr Arun S
Date Deposited:	18 May 2021 09:17
Last Modified:	18 May 2021 09:17
URI:	http://oar.icrisat.org/id/eprint/11806
Official URL:	https://doi.org/10.1038/s41597-021-00834-w
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	We acknowledge funding support from the United Soybean Board for the large-scale sequencing of soybean genomes (project #1320-532-5615) and two private companies: Bayer (previously Monsanto and Bayer) and Corteva (previously Dow AgroSciences).The authors would like to thank Andrew Wilkey for his help with GCViT and figure production and Prasanna Vaduvathiriyan, Biomedical Librarian, University of Kansas Medical Center for her help with formatting the references. We acknowledge Dr. Paul Chomet for his comments and suggestions on the soybean re-sequencing project plan, while he was working at the Monsanto Company. In-kind support for analysis was provided by the USDA Agricultural Research Service project 5030-21000-062-00D. The USDA is an equal opportunity provider and employer.
Links:	Google Scholar

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