Abstract
Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26–0.32) and linkage disequilibrium (LD, 28.8–58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine.
Highlights
Grape is nowadays a crop of major economic importance in the world: in 2015, around 7.5 Mha were under cultivation and produced 75.7 Mt of fruits, 56% being processed for wine, juice and spirits and 44% used for fresh or dried raisin consumption [1]
On the reference genome [33], 88.2% (9004) of the single nucleotide polymorphism (SNP) mapped on chromosomes (Fig 1), 8.3% located on unmapped scaffolds (“chrUn” tag) and 3.5% on scaffolds assigned to a chromosome but not mapped
Similar reasons may lay behind the lack of signal for phenology: we found only one SNP weakly associated with budburst-to-veraison time, while no association was found for other phenological traits
Summary
Grape is nowadays a crop of major economic importance in the world: in 2015, around 7.5 Mha were under cultivation and produced 75.7 Mt of fruits, 56% being processed for wine, juice and spirits and 44% used for fresh or dried raisin consumption [1]. A first comprehensive attempt to classify cultivars was achieved by Negrul [23] who took into account mostly geographical information and morphological traits He suggested that the three cultivated “proles” (occidentalis, pontica and orientalis) derived from two pools of V. vinifera subsp. The development of molecular markers allowed characterizing both the genetic diversity and structure in large samples of V. vinifera cultivars [6, 12, 18, 20, 24] All these data are in agreement with Negrul’s morphological classification [23] and allowed us to define a large panel for association mapping [25]. Most of these studies were performed using nuclear microsatellites (nSSRs), some explored the potential of SNP arrays [12, 20]
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