Exploring Signatures of Domestication in the Soybean Genome

Domestication and ongoing breeding of crop species have resulted in the selection of agriculturally beneficial alleles that may contribute to domestication syndrome and affect traits such as yield and quality.  Positive selection for these alleles has resulted in selective sweeps, leaving distinct patterns of linkage disequilibrium and allele frequency changes throughout the genome.  These patterns were used to identify the selected loci. Using re-sequencing data from 32 accessions of soybean and its nearest wild relative (Lam et al. 2010. Nature Genetics. 42: 1053-9; Kim et al. 2010. PNAS. 107:22032-7), we have conducted genome-wide scans for selective sweeps and identified loci that may have been critical to the domestication of soybean. Within these regions of selective sweeps, specific genes and regulatory regions exhibiting signatures of positive selection were identified. These genes likely played a role in the process of soybean domestication.