Development and application of the SNP14K array to accelerate Brassica rapa genetic research

Brassica rapa is one of the most important vegetable crops with the largest cultivation area in China. Compared with other genotyping technologies, the Affymetrix Axiom genotyping with single nucleotide polymorphism (SNP) array has become popular due to its high-throughput, flexibility, and efficiency. In this study, we successfully developed the first SNP14K array for B. rapa based on resequencing data from 189 accessions. The array contains 148,399 high-quality SNPs evenly distributed across the genome. Minor Allele Frequency (MAF) analysis indicated that these SNPs are highly polymorphic. Principal component analysis (PCA) clearly distinguished different subspecies among the 189 B. rapa accessions. Population structure and phylogenetic analyses demonstrated that the 148,399 high-quality SNPs are representative. Next, we assessed the genetic relationships of 97 B. rapa varieties using the SNP14K array on the Axiom genotyping system. Phylogenetic analysis showed that these 97 cultivars were divided into seven distinct subpopulations: Chinese cabbage, Pak choi, Wawacai, Baibangkuaicai, Qingbangkuaicai, Caixin, and one mixed type. In addition, major quantitative trait loci (QTLs) related to leaf trichome and flowering time were accurately identified using the SNP14K array. This newly developed SNP14K array provides a valuable new tool for genetic diversity analysis, gene/QTL mapping, and molecular breeding in B . rapa . • The first high-density SNP14K array, which contains 148,399 representative SNPs, has been successfully developed for B. rapa. • The SNP14K array can accurately identify major QTLs associated with leaf trichome and flowering time traits in B. rapa.