Abstract
BackgroundBerry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds.ResultsThirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). These markers were selected from SNP/InDel found among segregants from a Ruby x Sultanina population with contrasting phenotypes for berry size. The set of 38 SNP and InDel markers was distributed in eight chromosomes. Genotype-phenotype association analyses were performed using a set of 13 RxS segregants and 41 table grapes varieties with different genetic backgrounds during three seasons. The results showed several degrees of association of these markers with berry size (10.2 to 30.7%) as other berry-related traits such as length and width. The co-localization of SNP and /or InDel markers and previously reported QTLs and candidate genes associated with berry size were analysed.ConclusionsWe identified a set of informative and transferable SNP and InDel markers associated with berry size. Our results suggest the suitability of SNPs and InDels as candidate markers for berry weight in seedless table grape breeding. The identification of genomic regions associated with berry weight in chromosomes 8, 15 and 17 was achieved with supporting evidence derived from a transcriptome experiment focused on SNP/InDel search, as well as from a QTL-linkage mapping approach. New regions possibly associated with berry weight in chromosomes 3, 6, 9 and 14 were identified.
Highlights
Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences
single nucleotide polymorphisms (SNPs) and insertion/ deletions (InDels) density varied among chromosomes; the highest density was observed for both polymorphisms in chr 8 (2.15 SNPs per Kb, 0.32 InDels per Kb), while the lowest density for both was observed in chr 9 (1.32 SNPs per Kb, 0.18 InDels per Kb) (Additional file 6: Figure S5)
Using an integrated analysis based on RNASeq, SNP/InDel search and validation on table grape segregants and grape varieties with different genetic backgrounds, we identified a set of informative and transferable SNP and InDel markers associated with berry size
Summary
Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. The grape is a long-lived liana adapted to a diverse range of climates [2,3,4,5] It has a high level of genetic and phenotypic diversity, represented by the estimated 5000–10, 000 existing cultivars of grapes [6, 7], including the whole genus Vitis with over 50 species [8,9,10]. Juvenility of grapes delays phenotypic evaluation a few years, in particular when fruit characteristics are the main target This represents a high cost in labor and land space dedicated to the segregant maintenance and evaluation. The use of molecular tools providing phenotypic information at early stages of development for new lines can assist the selection (or discarding) of a subset of genotypes, and save resources and time
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