Identification of stable quantitative trait loci and candidate genes for sweetness and acidity in tablegrape using a highly saturated single-nucleotide polymorphism-based linkage map

Abstract

Background and Aims

Identifying the genes that participate in the sweetness and acidity of the berry is key, because these traits are quintessential to the flavour and quality of fresh grapes and wine. In this study we focused on the identification of genomic regions that host genes associated with sweetness and acidity in tablegrapes.

Methods and Results

A highly saturated genetic map was prepared using a Ruby Seedless × Sultanina cross (RxS; n = 138) genotyped using an SNPlex-type platform, and quantitative trait loci (QTLs) were mapped. In the integrated map of this population, 1731 markers were distributed along the 19 linkage groups (LGs) of the species. Three significant QTLs, two in LG5 and one in LG8, were associated with fructose/glucose ratio, TA and tartaric acid concentration; these QTLs explained up to 20% of the phenotypic variance for these traits. Eight candidate genes located within the confidence intervals of the sugar and TA QTLs were chosen and their expression profiles analysed from flowering to berry ripening. A Genome-Wide Association Study (GWAS) analysis revealed the association of single-nucleotide polymorphisms in the same regions as QTLs.

Conclusions

Quantitative trait loci significant for sugar and acidity were identified on a tablegrape high-quality genetic map; furthermore, an association between acidity or sugar concentration and expression changes for candidate genes was also observed.

Significance of the Study

These findings could become the basis to develop selection tools for the breeding of these traits in tablegrape.