Genetic Dissection of Anthocyanin Accumulation in Tomato Using GWAS and Hybridization Probe Melting (HPM) for Marker-Assisted Breeding

Tomato fruit color is primarily influenced by the accumulation of pigments such as carotenoids and anthocyanins, which are regulated by a complex network of genes and environmental factors. The presence of anthocyanins, in particular, contributes to the purple phenotype in tomatoes, which has been associated with improved nutritional quality and disease resistance. Previous studies have identified key regulatory genes, including SlMYBATV and SlANT1, that control anthocyanin biosynthesis in tomatoes. A total of 48 tomato accessions were selected, including both anthocyanin-producing and non-producing cultivars, to assess genetic variation in relation to fruit color. GWAS analysis identified significant associations between single-nucleotide polymorphisms (SNPs) on chromosomes 7 and 10 and the purple fruit phenotype. These genomic regions contained key anthocyanin regulatory genes, SlMYBATV on chromosome 7 and SlANT1 on chromosome 10, confirming their roles in anthocyanin biosynthesis. Linkage disequilibrium (LD) analysis further revealed strong correlations between SNPs within these regions, facilitating the selection of representative SNPs for genotyping. The genotyping of SNPs Ch07_60981501 and Ch10_64354129 using HPM demonstrated clear differentiation between purple and non-purple cultivars based on melting temperature differences, validating the functional significance of the identified loci. The results confirmed that the nonfunctional SlMYBATV allele at the atv locus allows for enhanced anthocyanin accumulation by relieving repression of anthocyanin activators like SlANT1. This interaction between the Aft and atv loci drives light-dependent anthocyanin biosynthesis in purple tomatoes. HPM genotyping offers a cost-effective tool for allele identification, supporting breeding programs for anthocyanin-rich tomatoes. SNP markers enable marker-assisted selection (MAS) for improved nutritional and aesthetic traits. This study highlights SlMYBATV and SlANT1 in anthocyanin biosynthesis, advancing efforts to develop enriched tomato varieties and supporting agricultural productivity and health.