Haplotype analysis of a major and stable QTL underlying soybean (Glycine max) seed oil content reveals footprint of artificial selection

Abstract

Improvement of soybean seed oil content was a major goal in soybean breeding. In this study, a recombinant inbred line (RIL) population derived from elite cultivar “Jidou 12” and landrace accession “Heidou” was used to identify major and stable QTL underlying oil content via linkage analysis across four environments. Of the six QTL associated with oil content, only qOIL_8_1 flanked by Satt177 and Satt341 was detected across four environments and explained a high percentage of phenotypic variance. The Jidou 12 allele could increase average oil content by 7.2 mg g−1 compared with the Heidou allele and had no significant drag on protein content. Eight quantitative trait nucleotides (QTNs) were associated with oil content underlying qOIL_8_1 via genome wide association study (GWAS) of four soybean panels. Among these, three located in the same haplotype block from Chr08_8291045 to Chr08_8512373. A strong domestication selection footprint in the block was detected as indicated by high Fst values, and significant difference of haplotype frequency between wild and landrace soybean in the region. This study will facilitate selection of soybean parent and breeding lines for seed oil content improvement.