Genetic features of lycopene content associated with flesh color in watermelon

Recent interest has focused on different flesh colors in watermelon due to one of rich resources for the antioxidant cis-isomeric lycopene, one of the carotenoids. The formation of lycopene is a major step in carotenoid biosynthesis, in which lycopene β-cyclase (LCY-B) and lycopene ε-cyclase (LYC-E) enzymes are involved in the formation of lycopene, and LYC-B is involved in the formation of β-carotene. This study is to elucidate genetic relationship among watermelon genotypes with red, yellow or orange flesh color from the whole genome resequencing data. An elevated level of lycopene was noted in all red flesh watermelon lines ranging from 333 to 477 µg/g, while orange-fleshed watermelons have previously been reported to contain mainly β-carotene (91~171 µg/g), with traces of lycopene and phytoene. In the present study, we selected 2369 SNPs with lower PIC values (0.1-0.38) to discriminate 24 genotypes that exhibited different flesh colors. A cluster analysis indicated that red flesh genotypes with a high lycopene content was separated from the non-red flesh inbred lines, such as yellow or orange with a low lycopene content. We randomly selected several SNPs on protein coding genes that presented polymorphism between red flesh and non-red flesh types. Results revealed that these SNP-carrying genes presented preferential and stage-specific expression between red and yellow genotypes. The selected SNP-linked to red flesh loci were further validated, and those SNPs were converted into cleavage amplified polymorphic sequence (CAPS) markers which allows marker-assisted selection of watermelons with high lycopene content.