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.

A high-density integrated map for grapevine based on three mapping populations genotyped by the Vitis18K SNP chip

“…2 ). A similar under-representation of this region was also encountered in previous maps based on the Vitis 18K SNP chip (Houel et al 2015 ; Duchêne et al 2020 ; Mamani et al 2021 ). This is likely due to the fact that the majority of the markers at the distal end of chromosome 9 originate from the Vitis markers subset and were scored as monomorphic or failed in genotyping.…”

“…In this work, we integrated the BLASTN-derived positions on the ‘PN40024 12X.v2’ assembly for the additional 7859 SNPs (in agreement with those reported at https://urgi.versailles.inra.fr/jbrowse/ ; Table S1). Three genetic maps have been built so far using data derived from the Vitis 18K SNP chip (Houel et al 2015 ; Duchêne et al 2020 ; Mamani et al 2021 ). In these studies, 1122, 1587 and 1737 of the SNPs included in the Vitis 18K SNP chip were mapped; however, the mapping data for only 1587 SNPs are available in tabular format.…”

“…The Vitis 18K SNP chip has been mostly used to assess population genetic diversity, structure, and relatedness (De Lorenzis et al 2015 , 2019 ; Degu et al 2015 ; Mercati et al 2016 , 2021 ; Ruffa et al 2016 ; Laucou et al 2018 ; Marrano et al 2018 ; Sunseri et al 2018 ; Bianchi et al 2020 ; Boccacci et al 2020 ; Crespan et al 2020 , 2021 ; Raimondi et al 2020 ; D’Onofrio et al 2021 ), or to identify somatic variants to explain intra-varietal diversity (De Lorenzis et al 2017 ). The application of the Vitis 18K SNP array to identify marker-trait associations, however, remains limited (Houel et al 2015 ; Duchêne et al 2020 ; Mamani et al 2021 ). Finally, as for many other species, despite the generation of the high-throughput genotyping tools, the position of genotyped SNPs that can be inferred by sequence information still needs mapping validation.…”

Biography of Vitis genomics: recent advances and prospective

“…In the past two decades, a number of studies on grape gene identification have been performed and 941 genes ( Fig. 2 , Supplementary Data Table S1 ) have been identified, which were related to all traits of grape, including berry development [ 39–45 ], berry quality regulation [ 31 , 37 , 42 , 46–59 ], fruit genotypes [ 60 ], sugar and acid content [ 34 , 52 , 61 ], aroma and flavonoids [ 48 , 62–69 ], and biotic and abiotic resistance [ 70–77 ]. Among these genes, the biosynthesis of anthocyanins and flavonoids has received considerable attention from researchers, with 277 candidate genes having been identified [ 62–69 ], followed by disease resistance (123 genes) [ 72–76 ], and plant and berry development (83 genes) [ 31 , 39–45 ].…”