Genomic technologies uncover inter-varietalstructural variation in grapevine

Grapevine (Vitis vinifera L.) is one of the most important crop plants in the world because of its economically valuable role in fruit and wine production; for this reason, great interest has recently been shown in identifying genomic variations and their functional effects on inter-varietal phenotypic differences. Discovery and characterization of all genetic variations is critical to reach a full understanding of the genetic basis of phenotypic differences. Using an approach developed for the analysis of human and mammalian genomes, which combines high-throughput sequencing (HTS), array comparative genomic hybridization (aCGH), fluorescent in situ hybridization (FISH), and quantitative PCR (qPCR), we were able to create an inter-varietal atlas of structural variations and single nucleotide variants (SNVs) for the grapevine genome analyzing four economically and genetically relevant table grapevine varieties. We found 4.8 million SNVs and detected roughly 8% of the grapevine genome affected by genomic variations. We identified more than 700 copy number variation (CNV) regions, and searching for gene content in these regions, we were able to find more than 2000 genes subjected to CNV as potential candidates for phenotypic differences between varieties. For example, we found a polymorphic region at chromosome 18_random containing six different genes belonging to the germacrene D synthase family and a flavonol synthase gene, which showed the highest rate of duplication in the Italia cultivar. Since Italia is the only cultivar (among those analyzed in this study) showing aromatic taste, this finding could be related to berry flavor trait. Likewise, comparison among the different grape genomes showed differences in gene dosages playing critical roles in response to biotic and abiotic stresses. Overall our data highlight the significance of these genome-wide studies on CNVs in the grapevine genome and identify candidate genes for some of the most complex and desired traits in breeding. We paired-end sequenced four table grape cultivars: Autumn royal (AR), Italia (It), Red globe (RG), and Thompson seedless (TS) and alignment of the obtained reads against the PN40024 Pinot noir reference genome (Table 1 and Figure 1). SNPs identification and WSSD analysis We identified 4,478,098 SNPs and 262,395 INDELs. Similar percentages of duplication (average 16%) and deletion (average 3%) were found in the four table grape varieties and in the PN40024 reference.