Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

Nat Genet. 2010 Dec;42(12):1053-9. doi: 10.1038/ng.715. Epub 2010 Nov 14.


We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agriculture*
  • Chromosomes, Plant / genetics
  • Genes, Plant / genetics
  • Genetic Variation*
  • Genome, Plant / genetics*
  • Inbreeding
  • Linkage Disequilibrium / genetics
  • Mutation / genetics
  • Phylogeny
  • Polymorphism, Single Nucleotide / genetics
  • Selection, Genetic*
  • Sequence Analysis, DNA*
  • Soybeans / genetics*