Genetic relationship and pedigree of Chinese watermelon varieties based on diversity of perfect SNPs

Watermelon (Citrullus lanatus) is one of the world's most important fruit crops, and China produces the most watermelons in the world. Recently, a watermelon variome consisting of 414 key resequenced accessions was reported. However, the genetic relationships and pedigree of Chinese watermelon varieties in the seed market remain unclear. In this study, 241 evenly distributed perfect single nucleotide polymorphisms (SNPs) derived from the watermelon variome were selected for variety identification. The diversity of 247 Chinese watermelon varieties was identified based on their SNP genotypes. The 247 watermelon varieties were clustered into five subpopulations: the East Asian ecotype, intermediate ecotype, small fruit with red flesh ecotype, small fruit with yellow flesh ecotype, and American ecotype. We further established the pedigree of four subpopulations, of which JingXinNo.1, ZaoChunHongYu, HuangXiaoYu and XiaoLan, and Sugarlee were the main doner of the East Asian ecotype, small fruit with red flesh ecotype, small fruit with yellow flesh ecotype, and American ecotype, respectively. Thirty-two core SNPs were selected and applied in watermelon variety identification. They were also validated by the Kompetitive allele-specific PCR (KASPar) platform. The present study furthered our understanding of the genetic relationships and pedigree of watermelon varieties in China, and will help to manage the plant variety protection in watermelon.