Kompetitive allele-specific PCR (KASP) genotyping and heterotic group classification of 244 inbred lines in cabbage (Brassica oleracea L. var. capitata)

Abstract

Cabbage is a globally cultivated vegetable with obvious heterosis. The main method used for cabbage breeding is the creation of hybrid combinations with inbred lines, and how to combine the parents plays a crucial role in cabbage breeding. Therefore, it is urgent to classify heterotic groups by molecular markers. In this study, single nucleotide polymorphism (SNP) markers were developed on the basis of whole-genome resequencing data of 50 inbred lines. A total of 2.54 × 106 SNP loci were obtained by aligning resequencing data to the reference genome of cabbage. Finally, five hundred SNP markers among 50 re-sequenced genotypes were further selected on the basis of a high polymorphism information content, a high minor allele frequency, a wide average distribution and low heterozygosity. Then, 442 SNP markers were successfully converted into kompetitive allele-specific PCR (KASP) markers, accounting for 88.4% of all 500 SNP markers. The cabbage inbred lines included three ecotypes: spring cabbage, autumn cabbage and winter cabbage. Based on the KASP genotyping data, the genetic similarity among inbred lines was analyzed, and the heterotic groups within each ecotype were classified. Seven heterotic groups were identified for spring cabbage (77); six, for autumn cabbage (70); and five, for winter cabbage (97). In addition, we found parents of 48 developed elite combinations were all from different heterotic groups or subgroups, which verified that the group classification was accurate and useful. Therefore, we suggest that the parents of combinations should be selected from different heterotic groups or subgroups, which will guide parental selection in cabbage breeding and improve breeding efficiency.