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Population and quantitative genomic properties of the USDA soybean germplasm collection

Published online by Cambridge University Press:  23 April 2018

Alencar Xavier ,
Rima Thapa ,
William M. Muir  and
Katy Martin Rainey
Alencar Xavier
Affiliation:
Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA Quantitative Genetics, Dow AgroSciences, Indianapolis, IN 46268, USA
Rima Thapa
Affiliation:
Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
William M. Muir
Affiliation:
Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
Katy Martin Rainey*
Affiliation:
Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
*
*Corresponding author. E-mail: krainey@purdue.edu
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Abstract

This study is the first assessment of the entire soybean [Glycine max (L.) Merr] collection of the United State Department of Agriculture National Plant Germplasm System (USDA) reporting quantitative and population genomic parameters. It also provides a new insight into soybean germplasm structure. Germplasm studies enable plant breeders to incorporate novel genetic resources into breeding pipelines to improve valuable agronomic traits. We conducted comprehensive analyses on the 19,652 soybean accessions in the USDA-ARS germplasm collection, genotyped with the SoySNP50 K iSelect BeadChip SNP array, to elucidate the quantitative properties of existing subpopulations inferred through hierarchical clustering performed with Ward's D agglomeration method and Nei's standard genetic distance. We found the effective population size to be approximately 106 individuals based on the linkage disequilibrium of unlinked loci. The cladogram indicated the existence of eight major clusters. Each cluster displays particular properties with regard to major quantitative traits. Among those, cluster 3 represents the tropical and semi-tropical genetic material, cluster 5 displays large seeds and may represent food-grade germplasm, and cluster 7 represents the undomesticated material in the germplasm collection. The average FST among clusters was 0.22 and a total of 914 SNPs were exclusive to specific clusters. Our classification and characterization of the germplasm collection into major clusters provides valuable information about the genetic resources available to soybean breeders and researchers.

Keywords

fixation indexgenetic correlationphylogenomicsstructureunsupervised machine learning
Type
Research Article
Information
Plant Genetic Resources , Volume 16 , Issue 6 , December 2018 , pp. 513 - 523
Copyright
Copyright © NIAB 2018 

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