ClPSY1 gene-based SNP markers identified from whole-genome resequencing for the determination of orange flesh color and carotenoid content in watermelon

Watermelon (Citrullus lanatus) is an economically important crop worldwide. The color of watermelon flesh is affected by the type and content of carotenoids. Carotenoids are high in antioxidants, which are associated with lower risk of various cancers and cardiovascular diseases and support visual function. Accordingly, the color of watermelon flesh is considered an important characteristic as it not only provides color diversity but also serves as the main motivator of consumer choice in terms of nutrition. Molecular markers have emerged as a powerful tool in plant breeding and the development of markers for selection of important traits and highly desirable. We previously identified genome-wide single nucleotide polymorphism (SNP) by performing whole-genome rese-quencing (WGRS) of 24 inbred watermelon lines with different flesh color traits (PRJNA516776). In this study, we proposed candidate genes for orange flesh color based on SNPs unique to orange flesh genotypes. One SNP in the phytoene synthase (ClPSY1) allele, which mediates the first step in carotenoid biosynthesis, was found to be associated with the orange color of watermelon flesh. Based on the polymorphism present in the ClPSY1 gene, we developed a molecular marker for predicting watermelon flesh color and confirmed the association of the SNP with orange flesh. This marker and markers derived from several other previously reported genes could be useful for the selective breeding of watermelons with a specific flesh color.