Variable Selection Patterns Associated with Constitutive and GxE Effects for Grain Yield in a Locally Adapted Soybean Population

Abstract It is widely accepted that artificial selection has reduced the overall amount of genetic variation present for most modern crops, including soybeans. How traits with a complex genetic architecture, such as yield, may experience selection pressure differently in accordance with the diverse combination of constitutive and environmentally interactive components, is still unclear. We used data from multi environment yield trials in an elite soybean breeding program along with public sequencing data from other populations to assess the effect of selection among varying combinations of effect types. Genomic regions with higher genetic diversity and lower divergence were significantly associated with higher GxE variance but not constitutive variance, indicating selection is relaxed at these loci. Among GxE effect types we found prominent evidence for both negative and positive selection, and a markedly higher level of selection signatures at conditionally neutral loci, illustrating the complicated nature of response to selection for soybean yield.