Genetic dissection of domestication-related traits in soybean through genotyping-by-sequencing of two interspecific mapping populations

Key message A total of 132 domestication-related QTLs, of which 41 were novel, were identified through genotyping-by-sequencing of two Glycine max × Glycine soja populations. Abstract Soybean [ Glycine max (L.) Merr.] was domesticated in East Asia from the wild progenitor Glycine soja . The domestication process led to many distinct morphological changes that adapt it to cultivation. These include larger seeds, erect growth, larger stem diameter, reduced pod shattering, and altered growth habit. The objective of this study was to identify QTLs controlling key domestication-related traits (DRTs) using interspecific mapping populations. A total of 151 RILs from Williams 82 × PI 468916 and 510 RILs from Williams 82 × PI 479752 were utilized for QTL mapping. These lines were genotyped using a genotyping-by-sequencing protocol which resulted in approximately 5000 polymorphic SNP markers. The number of QTLs detected for each of the eleven DRTs ranged between 0–4 QTLs in the smaller Williams 82 × PI 468916 population and 3–16 QTLs in the larger Williams 82 × PI 479752 population. A total of 132 QTLs were detected, of which 51 are associated with selective sweeps previously related to soybean domestication. These QTLs were detected across all 20 chromosomes within 42 genomic regions. This study identifies 41 novel QTLs not detected in previous studies using smaller populations while also confirming the quantitative nature for several of the important DRTs in soybeans. These results would enable more effective use of the wild germplasm for soybean improvement.