Algorithms for discovery of cis-eQTL signals in woody species: the vine (Vitis vinifera L.) as a study model

Abstract

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 genetics of gene expression of complex phenotypes. eQTLs analysis are common in human studies and in model species such as mice, rats and yeast but are very scarce in wood crop species such as fruit trees or grapevines. In this study a comprehensive bioinformatic pipeline has been carried out using genomics and expression data from 10 genotypes of grape, which has been used as model species. As a result of this study a total of 10,618 genetic variants that regulate gene expression levels of 525 genes were detected. A 78% of them, 411, received a functional annotation from UniProtKB or DAVID, between the annotated protein-coding genes are Germin-like proteins (GLPs), auxin-regulatory factors, GRFS, ANK_REP_REGION domain-containing protein, Kinesin motor domain-containing protein or RPP13like protein 2(LOC100852873). This new inventory of cis eQTLs influencing gene expression during the ripening of fruits of Vitis vinifera L. will be an important resource for future research to understand the mechanistic basis for variation in gene regulation in this species. In the future, this methodology may be applied to other woody species, once the necessary databases are generated.