High-throughput identification of SNPs reveals extensive heterosis with intra-group hybridization and genetic characteristics in a large rapeseed (Brassica napus L.) panel

Genetically diverse germplasm sets are necessary for the identification of heterotic groups in hybrid breeding programs. Assigning parental lines to identified heterotic groups may increase the efficiency of hybrid rapeseed breeding programs. In this study, the genetic diversity, population structure, relationship, and linkage disequilibrium (LD) of 995 rapeseed accessions, including improved breeding lines and parental lines of elite hybrids, were analyzed using a 60K single nucleotide polymorphism array. The whole population was divided into four subgroups according to the parameters of principal component analysis and STRUCTURE. The overall LD decay was fast, and the LD of the A genome decayed faster than that of the C genome. A core set containing 35 accessions was selected using the POWER-CORE program. The heterotic groups were first assessed based on SNPs in the enlarged core set containing core set accessions and parental lines of three elite hybrid. The parental lines were assigned to certain subpopulation (Pop2 in the enlarged core set), in which the accessions are almost the semi-winter or winter OSR lines. The results revealed that the likelihood of developing heterotic hybrids is much higher with intra-group parents. The studies about information regarding the levels of population structure of core sets combined with their ecological adaptability and genetic distance may be useful for the efficient selection of ideal parental lines during rapeseed hybrid breeding program.