SNP-discovery by RAD-sequencing in a germplasm collection of cultivated and wild grapevine accessions

The discovery and use of genome-wide molecular markers across many individuals is crucial for evaluation of patterns and processes in evolutionary changes. RESTRICTION-SITE ASSOCIATED DNA SEQUENCING (RAD-seq) may be a suitable approach due to its ability to identify and get genotyped several markers simultaneously. A novel protocol of RAD-seq was set-up on 5500 SOLiD™ System introducing a biotinylated adapter. Afterwards the novel RAD-seq protocol was applied to a grapevine germplasm collection of 51 cultivars (Vitis vinifera subsp. sativa) and 45 wild accessions (V. vinifera subsp. sylvestis). The resulting 561’843’350 reads were aligned on the V. vinifera ‘PN40024’ reference genome sequence and almost all the predicted RE sites were covered. UNIFIEDGENOTYPER of Genome Analysis Toolkit was used to identify Single Nucleotide Polymorphisms (SNP). A final dataset of 52’644 good quality SNPs was obtained, among which 32’977 SNPs revealed a Minor Allele Frequence higher than 0.05. Based on the new grapevine gene prediction v2.1, 27’902 SNPs were intergenic, 5’649 missense, 240 nonsense and 3’106 synonymous. The genetic diversity analysis revealed how the RAD-seq markers are able to collect and show some undisclosed differences among wild and cultivated grapevine accessions. Therefore, the RAD-seq is a candidate approach to disclose the relationship between ancestor and domesticated species, helping to clarify the process of domestication.