Understanding the genetic control of fruit composition traits in interspecific grapevines (Vitis spp.) is crucial when breeding new cultivars with desirable fruit chemistry. To address this, a genome-wide association study (GWAS) was conducted using 587 genotypes derived from three elite selections. This study spanned 3 years (2020–2022) and with phenotyping conducted at three different timepoints within each season for a total of nine phenotyping events focused on nine fruit traits. Several strong and stable quantitative trait locus (QTL) associations were identified on chromosomes 6, 16, and 17 across multiple phenotyping events for most sugar- and acid-related traits. Notably, putative sugar transporter genes Vitvi16g00860 and Vitvi16g00861 on chromosome 16, which facilitate the movement of sugars and K+ ions across membranes, were found to be associated with all sugar and acid traits studied. Additionally, several QTLs on chromosomes 1–5, 7, 14, and 18 were identified for various fruit quality traits across different phenotyping events. We determined functional connections between traits and scrutinized candidate genes by utilizing gene ontology annotations for genes located near significant SNPs. We also highlighted the effect of different forms of phenotype (best linear unbiased predictions and unmodified) in suppressing certain QTL associations. This GWAS study focused on fruit quality in grapes, establishing a necessary knowledge base regarding the genetic architecture of these traits to aid molecular breeders in further improving them.

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