Construction of a SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Abstract

Cauliflower is one of the most important vegetable crops grown worldwide. However, efforts to improve cauliflower are hindered by the lack of genetic diversity information and efficient molecular markers. In this study, we aim to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1,662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. To generate ideal SNP marker sets from the candidates, we developed a program for in silico simulations on 153 core cauliflower germplasm samples. Finally, 41 highly polymorphic KASP markers were selected and applied in the identification of 329 cauliflower cultivars which were mainly collected from public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information of the current cauliflower cultivars.