Unraveling the Genetic Basis of Soluble Sugar Accumulation in Tomato Fruits via Genome-Wide Association Studies

Soluble sugars, primarily glucose and fructose, are crucial determinants of tomato taste and flavor. To elucidate the genetic mechanisms regulating soluble sugar content, we conducted genome-wide association studies (GWAS) on the variations in soluble solids content (SSC), glucose and fructose among 234 tomato germplasms. 4,284,885 high-quality single-nucleotide polymorphisms (SNPs) were screened for associations with these traits. Significant loci were predominantly located on chromosomes 1, 3, 6 and 9. Beyond confirming known genes (SFP5 and Lin5) in these mapped genomic regions, six candidate genes were newly associated with sugar content based on haplotypes showing significant positive associations with the traits. Functional predictions suggest these genes are involved in sugar transport (Solyc01G003192, Solyc01G003198), sugar metabolism (Solyc01G003200, Solyc01G003201 and Solyc09G000424) and the production of sugar synthesis substrates (Solyc09G002436), indicating their potential roles in regulating soluble sugar content. The results expand the molecular basis of sugar accumulation in tomatoes, offering practical avenues for genetically improving fruit sugar content.