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

Babu Valliyodan; Anne V Brown; Juexin Wang; Gunvant Patil; Yang Liu; Paul I Otyama; Rex T Nelson; Tri Vuong; Qijian Song; Theresa A Musket; Ruth Wagner; Pradeep Marri; Sam Reddy; Allen Sessions; Xiaolei Wu; David Grant; Philipp E Bayer; Manish Roorkiwal; Rajeev K Varshney; Xin Liu; David Edwards; Dong Xu; Trupti Joshi; Steven B Cannon; Henry T Nguyen

doi:10.1038/s41597-021-00834-w

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

Sci Data. 2021 Feb 8;8(1):50. doi: 10.1038/s41597-021-00834-w.

Authors

Babu Valliyodan^#^{1

2}, Anne V Brown^#³, Juexin Wang^#⁴, Gunvant Patil^#^{1

5}, Yang Liu^#⁶, Paul I Otyama⁷, Rex T Nelson³, Tri Vuong¹, Qijian Song⁸, Theresa A Musket¹, Ruth Wagner⁹, Pradeep Marri^{10

11}, Sam Reddy¹⁰, Allen Sessions¹², Xiaolei Wu¹², David Grant^{3

7}, Philipp E Bayer¹³, Manish Roorkiwal¹⁴, Rajeev K Varshney¹⁴, Xin Liu^{15

16}, David Edwards¹³, Dong Xu^{4

6}, Trupti Joshi^{4

6

17}, Steven B Cannon³, Henry T Nguyen¹⁸

Affiliations

¹ Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
² Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, MO, 65101, USA.
³ USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA.
⁴ Department of Electrical Engineering and Computer Science, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
⁵ Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
⁶ MU Institute of Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
⁷ Department of Agronomy, Iowa State University, Ames, IA, 50011, USA.
⁸ USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, 20705, USA.
⁹ Bayer CropScience, St. Louis, MO, 63141, USA.
¹⁰ Corteva Agriscience, Indianapolis, IN, 46268, USA.
¹¹ Pairwise Plants LLC, Durham, NC, 27709, USA.
¹² Bayer CropScience, Research Triangle Park, NC, 27709, USA.
¹³ School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia.
¹⁴ International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India.
¹⁵ Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China.
¹⁶ State Key Laboratory of Agricultural Genomics, China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.
¹⁷ Department of Health Management and Informatics, University of Missouri, Columbia, MO, 65211, USA.
¹⁸ Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA. nguyenhenry@missouri.edu.

^# Contributed equally.

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 re-sequenced 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.

Publication types

Dataset
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Crops, Agricultural / genetics
Fabaceae / genetics
Genome, Plant*
Genotype
Geography
Glycine max / genetics*
Linkage Disequilibrium
Polymorphism, Single Nucleotide*
Selection, Genetic

Abstract

Publication types

MeSH terms

Grants and funding