Developing new tomato lines in Indigo Rose genetic background with differential anthocyanin and carotenoid production in fruits

Tomato (Solanum lycopersicum) fruit pigmentation during ripening results primarily from carotenoid accumulation and chlorophyll degradation, with flavonoids, particularly anthocyanins in specialized genotypes, contributing to fruit coloration. To develop tomato lines with diverse pigmentation and enhanced nutritional profiles in fruits, we combined conventional breeding with CRISPR/Cas9 editing in the Indigo Rose (IR) background. Four new lines, Red Rose (RR), Pink Rose (PR), Yellow Rose (YR), and Yellow-Purple Rose (YP), were generated by knocking out Aft and Myb12 genes and introducing the PSY1/Unknown allele. RNA-seq analysis revealed extensive tissue-specific transcriptomic remodeling, with peel and flesh diverging during ripening. Gene ontology enrichment indicated altered gene expression in flavonoid and carotenoid biosynthesis pathways. Metabolomic profiling supported these results: IR and YP peels were rich in anthocyanins, including delphinidins, petunidins and malvidins, whereas YR and YP flesh contained reduced total carotenoids but elevated ?-carotene. Integrated analyses demonstrate that targeted modification of key enzyme or regulatory genes can reprogram fruit pigmentation, providing valuable genetic resources for tomato breeding.