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The color of tomato ( Solanum lycopersicum ) fruit flesh is often used as an indicator of quality. Generally, fruit color is determined by the accumulation of carotenoids and flavonoids, along with concomitant degradation of chlorophylls during ripening. Several genes, such as phytoenesynthetase1 ( Psy1 ), STAY-GREEN ( SGR ), and SlMYB12 , have been extensively studied to elucidate the genes controlling fruit coloration. In this study, we observed low carotenoid levels without degradation of chlorophylls in green-fruited tomato caused by mutations in three genes, Psy1 , SGR , and SlMYB12 . We crossed two inbred lines, BUC30 (green-fruited) and KNR3 (red-fruited), to confirm the causal effects of these mutations on fruit coloration. The F₂ population segregated for eight different fruit colors in the proportions expected for three pairs of gene, as confirmed by a chi-square test. Therefore, we developed a population of tomato with diverse fruit colors and used molecular markers to detect the genes responsible for the individual fruit colors. These newly-designed DNA-based markers can be used for selecting desired fruit color genotypes within adapted breeding materials and cultivars for breeding.

Molecular Insights Reveal Psy1, SGR, and SlMYB12 Genes are Associated with Diverse Fruit Color Pigments in Tomato (Solanum lycopersicum L.)