Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.)

Expression quantitative trait loci (eQTLs) are associations between genetic variants, such as Single Nucleotide Polymorphisms (SNPs), and gene expression. eQTLs are an important tool to understand the genetic variance of gene expression of complex phenotypes. eQTLs analyses are common in biomedical models but are scarce in woody crop species such as fruit trees or grapes. In this study, a comprehensive bioinformatic analysis was conducted leveraging with expression data from two different growth stages, around ripening onset, of 10 genotypes of grape (Vitis vinifera L.). A total of 2170 cis-eQTL were identified in 212 gene modulated at ripening onset. The 48% of these DEGs have a known function. Among the annotated protein-coding genes, terpene synthase, auxin-regulatory factors, GRFS, ANK_REP_REGION domain-containing protein, Kinesin motor domain-containing protein and flavonol synthase were noted. This new inventory of cis-eQTLs influencing gene expression during fruit ripening will be an important resource to examine variation for this trait and will help to elucidate the complex genetic architecture underlying this process in grape.