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 LiuDavid Edwards, Dong Xu, Trupti Joshi, Steven B. Cannon, Henry T. Nguyen

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

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.

Original languageEnglish
Article number50
JournalScientific Data
Volume8
Issue number1
DOIs
StatePublished - Dec 2021

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