Evolutionary population structure model reveals pleiotropic effects of GmPDAT for seed oil- and size-related traits in soybean.

Soybean seed oil-related traits are related to nutritional effects linked to human health, as well as to crop domestication. These domesticated traits have significant differences across various evolutionary types. The integration of evolutionary population structure (evolutionary types) with genome-wide association studies increased the power in gene detection and identified one locus for seed oil- and size-related traits on chromosome 13. This domestication locus, along with another domestication locus in a 200 kb region, was confirmed by GEMMA and EMMAX. GmPDAT had higher expressional level in the high-oil and large-seed accessions than in the low-oil and small-seed accessions. Real-time qPCR analysis of GmPDAT showed higher expression levels in overexpression lines and lower expression levels in RNAi lines. Overexpression lines increased seed oil- and size-related traits, whereas RNAi lines decreased seed oil- and size-related traits. In addition, we deduced the molecular mechanism of GmPDAT based on the results from linkage analysis for triacylglycerols and histocytological comparison of transgenic soybean seeds. This result provides a new approach for identifying domestication genes with pleiotropic effects.