Using Soybean Pedigrees to Identify Genomic Selection Signatures Associated with Long-Term Breeding for Cultivar Improvement

Genetic hitchhiking uncovers selection signatures related to traits of agronomic importance in crops. It has been primarily used at the level of domestication by comparing groups of wild germplasm to landraces or elite breeding lines. In this study, we compared two groups of cultivars defined by an elite Canadian soybean cultivar, OAC Bayfield, to identify selection signatures related to long-term breeding within a specific region. Cultivars were assigned to either a pre- or post-OAC Bayfield group. Of the 162 simple sequence repeat (SSR) markers used to genotype members of the pedigree, 14 were fixed and 19 exhibited a selective signature. An in silico analysis comparing our results to quantitative trait loci (QTL) reported in SoyBase showed that 18 out of the 19 markers with a selective signature were associated with at least one QTL. From the 80 QTL associated with the 18 markers, half were related to plant architecture, yield or maturity. In addition, the number and type of QTL associated with the fix...