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. 2011 Nov 8:11:153.
doi: 10.1186/1471-2229-11-153.

A 48 SNP set for grapevine cultivar identification

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A 48 SNP set for grapevine cultivar identification

José A Cabezas et al. BMC Plant Biol. .

Abstract

Background: Rapid 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.

Results: We 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.

Conclusions: We 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.

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Figures

Figure 1
Figure 1
SNP genetic and physical position. For each chromosome, the map on the left (gray bars) shows the physical position of studied SNP markers on the 12X grapevine sequence of the PN40024 near homozygous line [40] indicated in kilobases; and the map on the right (empty bars) shows the genetic position, indicated in centiMorgans, of microsatellites (between brackets) and SNP genetically mapped using the four segregating progenies. Markers with known position in only one of these maps are indicated in bold: in the map on the left, the SNP with known physical position that could not be mapped genetically; and in the map on the right SNP mapped genetically but with unknown or uncertain physical position.
Figure 2
Figure 2
Representation of the genetic distances among varieties. The distances are measured in number of different alleles for the 11,325 pair-wise comparisons among the 151 non-redundant genotypes with 48 SNP. The small window is a zoom of the smallest distance zone.

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