The Genetic and Metabolic Changes Associated with the Tangerine Virescent Mutation in Tomato

Ripe tomatoes (Solanum lycopersicum) are usually identified by their red color, caused by the accumulation of the carotenoid lycopene. Varieties of the tangerine tomato have bright orange ripe fruit due to the accumulation of prolycopene, a tetra-cis lycopene isomer, instead of trans-lycopene. The tetra-cis isomer appears to be more bioavailable and therefore is of interest in the formulation of functional food. Tangerine varieties bear mutations in the carotenoid isomerase gene (CRTISO) that block conversion of prolycopene to trans-lycopene. The best characterized allele (t also t³¹⁸³) contains a 348 bp deletion spanning part of the promoter and first exon. Tangerine virescent (t^v), another allele, has been associated with a poor taste. We used next generation sequencing and metabolic profiling to characterize progeny segregating for t and t^v alleles and for the ripening inhibitor, rin.  An in silico bulking approach allowed us to detect the known mutations associated with t and rin.  In addition we identified the basis of t^v as a point insertion at the end of the second exon, recently described as t³⁰⁰². The alleles of tangerine are also associated with SNPs and insertion/deletion mutations linked to the putative functional mutations, defining both linkage drag in our population and the context of the original mutations. Metabolic profiles indicate that t and t^v are associated with changes in carotenoid profiles, suggesting the two alleles regulate flux through the pathway differently.