Supplementary Material - Genome-Wide Association Study Reveals Genomic Regions and Candidate Genes Influencing Berry and Cluster Traits in Grapes (<i>Vitis</i> spp.)

Berry and cluster size are pivotal determinants of grapevine productivity and consumer preferences, remaining major targets in grapevine breeding. However, due to their complexity as quantitative traits under polygenic control, a deeper understanding of their genetic determinants is needed. The Brazilian grapevine gene pool significantly contributes to the enhancement of grapevines in tropical and subtropical regions. To advance beyond traditional quantitative trait loci (QTL) mapping in bi-parental crosses, we conducted a genome-wide association study (GWAS) using a diverse panel of 288 Vitis spp. accessions from a Brazilian breeding program. This panel was phenotyped over 12 years for six critical fruit size traits and genotyped with the Vitis18k SNP array. Using two different algorithms, the GWAS identified 56 significant SNPs distributed across 17 chromosomes (Chr), validating previously identified QTLs and uncovering novel associations. Four closely spaced markers on Chr1 suggest the presence of a QTL influencing five traits simultaneously. A strong association signal, explaining approximately 29-35% of the phenotypic variance (PVE), indicates a major QTL for berry length (BL) and width (BWi) on Chr14. Additionally, major-effect SNP loci were identified with PVE of 18-27% for cluster weight (CW) on Chr1, cluster length (CL) on Chr7 and 14, cluster width (CWi) on Chr6 and 18, and berry weight (BW) on Chr4. Putative candidate genes were identified in genomic regions associated with significant SNPs, with 80 genes predicted for berry traits and 52 genes for cluster traits. Key predicted genes are involved in growth and development regulation, hormonal regulation, protein synthesis, stress response, and other physiological processes crucial for cellular health and functionality. Our results provide valuable insights into the genetic determinants of grape fruit size traits, offering essential data for future functional studies and improving the efficiency of breeding programs aimed at developing grape cultivars with specific berry sizes and cluster architecture.