Genomic Consequences of Selection and Genome-Wide Association Mapping in Soybean.

Soybean is widely grown as a major source of edible oil and protein for human consumption and livestock feed. Domestication and subsequent breeding improvement have likely left detectable signatures within the genome of modern soybean. We genotyped 342 landraces and 1062 improved lines with the SoySNP50K Illumina BeadChip containing 52,041 single nucleotide polymorphisms (SNPs), and systematically phenotyped these genotypes for 9 agronomic traits. A cross-population composite likelihood ratio (XP-CLR) statistical program was used to screen the signals of selective sweeps. A total of 125 candidate selection regions were identified, many of which harbored genes potentially involved in crop improvement. To further investigate whether these candidate regions were in fact enriched for genes (or quantitative trait loci) affected by selection, genome-wide association studies (GWAS) were conducted on 7 selection traits targeted in soybean breeding (grain yield, plant height, lodging, maturity date, seed coat color, seed protein and oil content) and 2 non-selection traits (pubescence and flower color). Major genomic regions associated with selection traits overlapped with candidate selection regions, whereas no overlap of this kind occurred for the non-selection traits, suggesting that the selection sweeps we identified are associated with traits of agronomic importance. Multiple novel loci and refined map locations of known loci related to these traits were also identified. These results illustrate that comparative population genomic analyses, especially when combined with trait-based mapping approaches, are a promising approach to dissect improvement related agronomic traits.