Sequence variation in SlMYB12 is associated with fruit peel color in pink tomato cultivars

The peel of pink-colored tomato is transparent due to the lack of accumulation of the flavonoid naringenin chalcone during ripening. A strong correlation was found between flavonoid expression and the function of SlMYB12, which is a transcriptional regulator of flavonoid biosynthesis. Thus, SlMYB12 is a strong candidate gene underlying the pink phenotype. Three allelic variants, a 603 bp deletion, a nucleotide substitution (C > T), and a 1 bp insertion (TG > TAG) in the SlMYB12 gene have been previously reported. We performed PCR genotyping based on these three allelic variations in 47 tomato cultivars displaying either a pink or red phenotype. However, the genotype did not match with the expected phenotype in one pink cultivar “Prime Alexander”. This cultivar was therefore self-pollinated to produce 20 progeny plants. To identify new mutations in SlMYB12, the sequence of genomic DNA and CDS were compared between the progeny 17 and the reference line, Heinz 1706. A novel G > T nucleotide substitution was found in the 2nd intron. This SNP leads to a deletion of 7 bp (GTAACAG) from the end of the 2nd exon, resulting in a premature stop codon. The presence of this SNP associates the pink phenotype with the genotype. This novel SNP will be useful as a genetic marker for marker-assisted breeding of pink tomato.