Genome-wide association mapping reveals stable genomic regions associated with fruit quality traits in tomato (Solanum lycopersicum L.)

Fruit quality has become a primary breeding objective in tomato because it determines consumer acceptance, processing efficiency, and market value. However, quality-related traits are quantitatively inherited and strongly influenced by environmental conditions, making genetic improvement challenging. In this study, genome-wide association studies (GWAS) was conducted to elucidate the genetic architecture of six economically important fruit quality traits, including luminosity, hue, chroma, soluble solids content (°Brix), titratable acidity, and fruit fresh weight (FW), using a diverse panel of 305 tomato accessions evaluated over two growing seasons. Substantial phenotypic variation was observed for all traits, with significant effects of genotype, year, and genotype × year interaction, indicating that fruit quality is governed by both genetic and environmental factors. Fruit weight, luminosity, hue, chroma, and °Brix exhibited high broad-sense heritability, whereas titratable acidity showed moderate heritability. Correlation analysis revealed strong positive relationships among color-related traits, while °Brix was positively associated with acidity but negatively correlated with fruit color attributes and FW. Skim sequencing generated 4,618 high-quality single nucleotide polymorphisms (SNPs), and GWAS was performed using multiple models. GWAS identified 15 non-redundant marker-trait associations (MTAs) across chromosomes, with several loci consistently detected across statistical models. A prominent locus, SL4.0ch03_12722521, on chromosome 3 was associated with luminosity, hue, and chroma, explaining up to 53.86% of phenotypic variation (PVE), suggesting pleiotropic regulation of fruit color. Stable loci controlling FW and soluble solids were also identified on chromosome 5, explaining up to 52.88% PVE. Candidate genes of significant MTAs included sucrose synthase, sec14p-like phosphatidylinositol transfer protein, bHLH transcription factor, and chitinase genes, indicating potential roles in carbohydrate metabolism, fruit development, cell wall remodeling, pigmentation, and ripening. These findings provide valuable genomic resources for improving fruit quality and accelerating the development of elite tomato cultivars.