Identification of candidate genes responsible for earlyripening in grape (Vitis vinifera L.) at genome level

In this study, transcriptional studies were carried out to determine the candidate genes responsible for earliness in grapes at the genome level. RNA sequencing technique was used in 5 cultivars, 3 of which were early ripening and 2 of which were late ripening, with 3 biological repetitions. As a result of sequencing, between 27 million and 34 million clean reads were obtained from the samples with low error rates and high quality scores. A total of 25,736 genes were detected in the early-late comparison groups of gene expression analyzes, of which 8,271 were identified as differentially expressed genes. Among the differentially expressed genes, 4474 were found to have increased expression and 3797 to decreased expression. The genes VIT_05s0029g01480 and VIT_12s0034g00380 were among the genes whose expression increased in all early-late comparison groups. It has been determined that VIT_12s0034g00380 and VIT_05s0029g01480 genes are responsible for the activation of pathogen resistance proteins (TMV resistance protein N-like) and protein kinase domain-containing protein, respectively. A total of 2,466,585 SNPs were detected between the 15 samples studied and the grape reference genome, and 2 SNPs thought to be associated with earliness were determined on the chromosome 12. Among the SNPs in the VIT_12s0034g00380 gene, C/T nucleotide change was observed in all early cultivars relative to the grape reference genome, while it remained the same in late cultivars with the reference genome. Therefore, genetic variation at this point is thought to trigger earliness in grapes. Finally, RNA sequencing data was validated by real-time PCR studies conducted on four randomly selected genes. It is thought that the findings obtained from this study, will serve for the development of markers to be used to determine the early ripening character at the molecular level.