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A 48 SNP set for grapevine cultivar identification

José A Cabezas16, Javier Ibáñez2, Diego Lijavetzky17, Dolores Vélez3, Gema Bravo1, Virginia Rodríguez1, Iván Carreño4, Angelica M Jermakow5, Juan Carreño4, Leonor Ruiz-García4, Mark R Thomas5 and José M Martinez-Zapater12*

  • * Corresponding author: José M Martinez-Zapater

  • † Equal contributors

Author Affiliations

1 Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain

2 Instituto de Ciencias de la Vid y del Vino (CSIC-Universidad de La Rioja-Gobierno de La Rioja). Complejo Científico Tecnológico. C/Madre de Dios 51. 26006 Logroño. Spain

3 Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA). Finca "El Encín". Ctra A2, Km 38.200. 28800 Alcalá de Henares. Madrid. Spain

4 Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA). Estación Sericícola. C/Mayor, s/n. 30150 La Alberca. Murcia. Spain

5 CSIRO Plant Industry, PO Box 350, Glen Osmond, SA 5064, Australia

6 Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Ctra de A Coruña, Km 7. 28040. Madrid. Spain

7 Instituto de Biología Agrícola de Mendoza, Facultad de Ciencias Agrarias, CONYCET-Universidad Nacional de Cuyo, Almirante Brown 500, M5528AHB Chacras de Coria, Argentina

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BMC Plant Biology 2011, 11:153  doi:10.1186/1471-2229-11-153

Published: 8 November 2011



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.


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.


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.