Genome-wide association analysis to identify genomic regions and predict candidate genes for bunch traits in grapes (Vitis vinifera L.)

•Genome wide association analysis identified major QTLs for grape bunch length on linkage groups 9 and 15 and QTLs for berry weight on linkage groups 3 and 5.•The minor allele at SNP S8_12810131 was significantly associated with longer bunches and a rare allele at S4_13617800 was associated with higher berry length.•Candidate genes having known functions related to several physiological processes crucial for cell growth and development were identified in the genomic region spanning significantly associated markers. Grape quality traits like bunch and berry size are important as they influence consumer acceptance and marketability of the produce. Therefore, a deeper understanding of their genetic determinant is crucial for varietal improvement. In this study, association mapping was performed using SNP marker data and three season phenotyping data of 122 diverse grapevine genotypes. Genotyping by sequencing (GBS) identified 1,08,777 high quality SNPs distributed on all the chromosomes. A good correlation was observed across three seasons for berry size and bunch length. Genome-wide association analysis using six different models identified significantly associated SNPs for each of the traits. We identified 13 significant SNPs associated with bunch length, seven of them were located on linkage groups (LGs) 9 and 15. For berry diameter, 18 significantly associated markers located on LGs 4, 5, 17 and six other LGs were identified. Fourteen SNPs mainly on linkage groups 3 and 5 were identified for berry weight. Three closely linked markers on LG3 explaining about 20-25 % variation suggested presence of major QTL for berry weight on LG3. Candidate genes were mined in the genomic regions containing significant SNPs explaining large phenotypic variation. Twenty-one genes for bunch length, 28 genes for berry length, 22 genes for berry diameter and 25 genes for berry weight were predicted. Several predicted genes were found to have function related to cell enlargement, cell morphogenesis and other physiological processes required for cell growth and development.