Development and application of InDels and SNPs markers based on whole-genome resequencing in Chinese cabbage

Abstract Chinese cabbage (Brassica rapa L. syn. B. campestris L., AA, 2n=20) is highly popular green leafy vegetable in the triangle of U, with China serving as its primary center of origin and diversification. Plant height, rosette leaf diameter, and disease resistance have always been important selection criteria for Chinese cabbage. In this study, we conducted re-sequencing on 55 Chinese cabbage accessions collected from China, Japan and Korea, followed population genetic evolutionary analysis and genome-wide association study (GWAS). Our findings unveiled a lack of significant population structure among these accessions, implying a possible evolutionary link or hybridization between Japanese and Korean Chinese cabbages with their Chinese counterparts. GWAS analysis results revealed that BrASD1, BrZHD13, BrGH3.3, and BrGH3.6 regarded as potential candidate genes highly associated with plant height in Chinese cabbage. Moreover, we also identified two single nucleotide polymorphisms (SNPs) loci associated with rosette leaf diameter and one SNP locus associated with downy mildew resistance, respectively. Furthermore, a novel tightly linked Insertion-deletion (InDel) marker on the end of A04 chromosome in B. rapa, SMB.4, has been developed. And SMB.4 can potentially serve as a useful molecular marker screening the genetic resources with downy mildew resistance and application for the downy mildew resistance breeding of Brassica crops.