A New SNP Marker for Allelic Selection of Carotenoid Isomerase in Watermelon

Carotenoid isomerase (encoded by CRTISO) catalyzes an isomerization of cis-lycopene into all-trans form in conjunction with desaturations from phytoene to lycopene in the carotenoid biosynthetic pathway of plants. Limited sequence information on CRTISO in other species made it difficult to clone watermelon CRTISO. Over five kb of genomic sequence of watermelon CRTISO contains twelve introns in the coding region. It showed 80% amino acid sequence identity with tomato and 82% with Arabidopsis CRTISO. The sequences of the coding region were aligned between CRTISO of red watermelon and that of salmon yellow watermelon and two single nucleotide polymorphisms (SNPs) were identified. One SNP showed a conserved substitution from tyrosine to phenylalanine and the other SNP resulted in an amino acid substitution from leucine to proline. Alignment of the deduced amino acids showed that leucine is conserved in other crops. Genotyping was performed to validate whether they can distinguish flesh color differences. Different genetic populations and commercial varieties were tested using two SNP markers. One SNP co-segregated with salmon yellow flesh color. This suggested the newly developed SNP marker is very closely linked to causal mutations resulting in salmon yellow flesh color of watermelon and this marker may provide a useful tool for breeding novel watermelon varieties.