Identification and development of a core set of informative genic SNP markers for assaying genetic diversity in Chinese cabbage

Rapid, economical, and reliable genotyping is an important requirement for germplasm analysis and cultivar identification in crop species. Chinese cabbage (Brassica rapa L. subsp. pekinensis (Lour.) Hanelt) originated in China and is now an economically important vegetable crop worldwide, especially in East Asia. In this study, we evaluated 1167 single nucleotide polymorphisms (SNPs) among 166 representative Chinese cabbage inbred lines using a KASP genotyping assay. On the basis of polymorphisms and principal component analysis, we selected 60 core SNPs distributed on all Brassica rapa chromosomes with allele frequencies sufficiently balanced so as to provide adequate information for genetic identification. The core set of SNPs was used for construction of a neighbor-joining dendrogram, in which the 166 inbred lines were clustered into spring, summer, and autumn ecotype groups. Clustering of the ecotype groups was better resolved than that achieved with 1167 and 360 polymorphic SNP datasets. Stability and resolution of the core SNP markers were tested using 178 commercial hybrid Chinese cabbage cultivars to confirm their utility in genetic identification. The set of 60 informative and stable SNP markers showed high discriminatory power and relatively uniform genomic distribution (4–9 markers per chromosome). The SNPs represent a cost-efficient and accurate marker set for germplasm analysis and cultivar identification and are suitable for molecular marker-assisted breeding in Chinese cabbage.