Development and application of KASP molecular markers for Brassica campestris ssp. chinensis based on whole-genome resequencing

【Objective】 The purpose of the study was to develop KASP molecular markers for Brassica campestris ssp. chinensis based on whole genome resequencing data,in order to accumulate and enrich the genetic information of this spe-cies,and provide technical support for the identification of Brassica campestris ssp. chinensis germplasm resource,genemapping and marker-assisted breeding. 【Method】Whole genome resequencing and comparison analysis on 2 Brassica campestris ssp. chinensis high-generation inbred lines C40 and JY70 were conducted. KASP molecular markers weredeveloped by selecting differential SNP loci,and genetic diversity analysis and DNA fingerprint construction were carriedout for 55 Brassica campestris ssp. chinensis germplasm resources. 【Result】 There were 460849 SNP loci with genotypeincompatibility,sequencing depth greater than 10X and homozygous alleles between C40 and JY70. A total of 15 SNP lociwith relatively uniform distribution on each chromosome were selected to be designed as KASP primers, and 150 pairs ofKASP primers were used to detect C40 and JY70 genotype,and 86 pairs of primers were successfully genotyped. Basedon the genotyping results of 55 Brassica campestris ssp. chinensis germplasm resources, 41 KASP molecular markerswith high amplification quality in Brassica campestris ssp. chinensis were selected. The genetic diversity analysis of 55Brassica campestris ssp. chinensis germplasm resources with 41 KASP markers showed that,the minor allele frequencyranged from 0.5000 to 0.9273,with an average of 0.6643; the gene diversity index was 0.1349-0.5000,with an average of0.4257; the polymorphism information content（ PIC） was 0.1258-0.3750,with an average value of 0.3322; and 94.5% ofthe loci had PIC＞0.2500, with fine polymorphism. The clustering analysis results showed that 55 Brassica campestris ssp. chinensis germplasm resources were divided into 3 major groups,germplasm resources of the same type were clustered to-gether, and resources of the same geographical origin were clustered together, which effectively reflected the genetic rela-tionship between germplasms. The DNA fingerprints of 55 Brassica campestris ssp. chinensis germplasm resources wereconstructed by using 15 KASP moecular markers with the highest PIC. 【Conlusion】The 41 KASP molecular markers ofBrassica campestris ssp. chinensis were developed, which can be used for germplasm resource identification, gene map-ping and marker-assisted breeding of Brassica campestris ssp. chinensis.