High-throughput 18K SNP array to assess genetic variability of the main grapevine cultivars from Sicily

Abstract

The viticulture of Sicily, for its vocation, is one of the most important and ancient forms in Italy. Autochthonous grapevine cultivars, many of which known throughout the world, have always been cultivated in the island from many centuries. With the aim to preserve this large grapevine diversity, previous studies have already started to assess the genetic variability among the Sicilian cultivars by using morphological and microsatellite markers. In this study, simple sequence repeat (SSR) were utilized to verify the true-to-typeness of a large clone collection (101) belonging to 21 biotypes of the most 10 cultivated Sicilian cultivars. Afterwards, 42 Organization Internationale de la Vigne et du Vin (OIV) descriptors and a high-throughput single nucleotide polymorphism (SNP) genotyping array (Vitis18kSNP) were applied to assess genetic variability among cultivars and biotypes of the same cultivar. Ampelographic traits and high-throughput SNP genotyping platforms provided an accuracy estimation of genetic diversity in the Sicilian germplasm, showing the relationships among cultivars by cluster and multivariate analyses. The large SNP panel defined sub-clusters unable to discern among biotypes, previously classified by ampelographic analysis, belonging to each cultivar. These results suggested that a very large number of SNP did not cover the genome regions harboring few morphological traits. Genetic structure of the collection revealed a clear optimum number of groups for K = 3, clustering in the same group a significant portion of family-related genotypes. Parentage analysis highlighted significant relationships among Sicilian grape cultivars and Sangiovese, as already reported, but also the first evidences of the relationships between Nero d'Avola and both Inzolia and Catarratto. Finally, a small panel of highly informative markers (12 SNPs) allowed us to isolate a private profile for each Sicilian cultivar, providing a new tool for cultivar identification.

Design and validation of an STR hexaplex assay for DNA profiling of grapevine cultivars

“…Tetranucleotide repeats are scarce in the grapevine genome but a list of potentially useful microsatellites with a core length of four nucleotides was recently identified [46,66]. While SNPs [67,68] avoid stuttering problems and do not require an allelic ladder for standardized genotyping, we concur with Santos [46] that long core repeat microsatellites and a forensic standardization approach [49] to their profiling still has considerable unexploited potential in grapevine genetics. It remains to be seen whether massively parallel sequencingbased technologies [69] offer sufficient advantages over STRs.…”

Single nucleotide polymorphism profiles reveal an admixture genetic structure of grapevine germplasm from Calabria, Italy, uncovering its key role for the diversification of cultivars in the Mediterranean Basin

“…FastStructure (Raj et al ) was used in an admixture model to highlight the number of putative genetic pools ( K ) present in the data set. The analysis was performed and visualised as described in Mercati et al (), using the input files (.bed, .bim, .fam) generated by PLINK. The package R/SNPRelate (Zheng et al ) was used to evaluate the relationship between cultivars from Calabria and Sicilia previously analysed (Mercati et al ) by computing a principal component analysis (PCA) extracting the first 100 principal components (PCs).…”

“…The analysis was performed and visualised as described in Mercati et al (), using the input files (.bed, .bim, .fam) generated by PLINK. The package R/SNPRelate (Zheng et al ) was used to evaluate the relationship between cultivars from Calabria and Sicilia previously analysed (Mercati et al ) by computing a principal component analysis (PCA) extracting the first 100 principal components (PCs). The Wright's fixation index ( F st ) (Wright ) was evaluated for each genetic background studied (both Calabria and Sicily) using R/HierFstat.…”

“…The development of high‐throughput next generation sequencing (NGS) technologies has made it possible to sequence entire genomes more efficiently, obtaining large‐scale SNP isolation and the advance of efficient SNP genotyping platforms (Schmid et al , Lijavetzky et al , Pindo et al , Verde et al , Yu et al , Melo et al ) useful to detect genetic variations (Myles et al , Sim et al , Winfield et al , Kurokawa et al , Mercati et al ). Large‐scale grape SNP discovery has been reported (Lijavetzky et al , Pindo et al ) leading to the identification of thousands of SNPs validated in a 9 K genotyping array (Myles et al , ).…”

“…Large‐scale grape SNP discovery has been reported (Lijavetzky et al , Pindo et al ) leading to the identification of thousands of SNPs validated in a 9 K genotyping array (Myles et al , ). More recently, the GrapeReSeq Consortium developed a high‐throughput 18 K SNP chip (Le Paslier et al ) and a set of informative SNPs were also identified for cultivar identification and clonal variation studies (Cabezas et al , Carrier et al , Mercati et al ).…”