A 48 SNP set for grapevine cultivar identification

Abstract

BackgroundRapid and consistent genotyping is an important requirement for cultivar identification in many crop species. Among them grapevine cultivars have been the subject of multiple studies given the large number of synonyms and homonyms generated during many centuries of vegetative multiplication and exchange. Simple sequence repeat (SSR) markers have been preferred until now because of their high level of polymorphism, their codominant nature and their high profile repeatability. However, the rapid application of partial or complete genome sequencing approaches is identifying thousands of single nucleotide polymorphisms (SNP) that can be very useful for such purposes. Although SNP markers are bi-allelic, and therefore not as polymorphic as microsatellites, the high number of loci that can be multiplexed and the possibilities of automation as well as their highly repeatable results under any analytical procedure make them the future markers of choice for any type of genetic identification.ResultsWe analyzed over 300 SNP in the genome of grapevine using a re-sequencing strategy in a selection of 11 genotypes. Among the identified polymorphisms, we selected 48 SNP spread across all grapevine chromosomes with allele frequencies balanced enough as to provide sufficient information content for genetic identification in grapevine allowing for good genotyping success rate. Marker stability was tested in repeated analyses of a selected group of cultivars obtained worldwide to demonstrate their usefulness in genetic identification.ConclusionsWe have selected a set of 48 stable SNP markers with a high discrimination power and a uniform genome distribution (2-3 markers/chromosome), which is proposed as a standard set for grapevine (Vitis vinifera L.) genotyping. Any previous problems derived from microsatellite allele confusion between labs or the need to run reference cultivars to identify allele sizes disappear using this type of marker. Furthermore, because SNP markers are bi-allelic, allele identification and genotype naming are extremely simple and genotypes obtained with different equipments and by different laboratories are always fully comparable.

Identification by SNP Analysis of a Major Role for Cayetana Blanca in the Genetic Network of Iberian Peninsula Grapevine Varieties

“…This system is plex-based and each plex contains 48 markers. Each variety was genotyped using seven plexes (336 SNPs minus four, which were repeated: 332 SNPs), as described in Cabezas et al (2011). Twenty nuclear microsatellites and four chloroplast microsatellites were also analyzed in some samples through the use of multiplex PCR and run in an Applied Biosystems 310 Genetic Analyzer ).…”

“…Compared to conventional nuclear SSR, SNPs have several features appropriate for large-scale genetic studies: they are abundant in most genomes surveyed (Brumfield et al 2003) and they have relatively low costs and the data are very easily scored, allowing a more feasible exchange of data between laboratories. SNPs have been used recently in grapevine for individual identification, integration of genetic and physical maps, and paternity inference (Cabezas et al 2011, Lijavetzky et al 2007) and in the study of genetic structure and domestication history of grape (Myles et al 2011). The power of SNPs for parentage inference has been reported previously (Anderson and Garza 2006), but almost exclusively in animal studies.…”

Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

“…Microsatellite and SNP markers have become in the last years the markers of choice for genetic analyses in grapevine, including genetic mapping and QTL identification (Huang et al 2012;Doligez et al 2013;Battilana et al 2013;Barba et al 2014), linkage disequilibrium and association analyses (Emanuelli et al 2010;Barnaud et al 2010;Cardoso et al 2012;Vargas et al 2013), and varietal identification (Myles et al 2010;Cabezas et al 2011;Laucou et al 2011;Migliaro et al 2012). As in many other woody plant species, genetic mapping in grapevine has been carried out using mainly the double pseudo test-cross strategy (Grattapaglia et al 1995), which is based on the study of allelic segregation of markers found in heterozygosis in one or both progenitors of an F 1 progeny.…”

Genotyping of Vitis vinifera L. within the Slovak national collection of genetic resources

“…Moreover, wine quality control and falsification, respectively, can be analysed from DNA extracted from wine [28]. Other DNA markers such as AFLPs, M-AFLPs, SAMPLs, ISSRs, and SNPs [29] have also been suggested for studies of genetic variation accumulated over centuries of cultivation and selection in different environments.…”