A 48 SNP set for grapevine cultivar identification

  1. Cabezas, J.A. 2
  2. Ibáñez, J. 4
  3. Lijavetzky, D. 23
  4. Vélez, D. 5
  5. Bravo, G. 2
  6. Rodríguez, V. 2
  7. Carreño, I. 6
  8. Jermakow, A.M. 1
  9. Carreño, J. 6
  10. Ruiz-García, L. 6
  11. Thomas, M.R. 1
  12. Martinez-Zapater, J.M. 2
  1. 1 Commonwealth Scientific and Industrial Research Organisation
    info

    Commonwealth Scientific and Industrial Research Organisation

    Canberra, Australia

    ROR https://ror.org/03qn8fb07

  2. 2 Centro Nacional de Biotecnología
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    Centro Nacional de Biotecnología

    Madrid, España

    ROR https://ror.org/015w4v032

  3. 3 Universidad Nacional de Cuyo
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    Universidad Nacional de Cuyo

    Ciudad de Mendoza, Argentina

    ROR https://ror.org/05sn8wf81

  4. 4 Instituto de Ciencias de la Vid y del Vino
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    Instituto de Ciencias de la Vid y del Vino

    Logroño, España

    ROR https://ror.org/01rm2sw78

  5. 5 Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario
    info

    Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario

    Madrid, España

  6. 6 Instituto Murciano de Investigacion y Desarrollo Agrario y Alimentario
    info

    Instituto Murciano de Investigacion y Desarrollo Agrario y Alimentario

    La Alberca de Záncara, España

  7. 7 Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria
    info

    Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

    Madrid, España

    ROR https://ror.org/011q66e29

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Revista:
BMC Plant Biology

ISSN: 1471-2229

Año de publicación: 2011

Volumen: 11

Páginas: 1-12

Tipo: Artículo

DOI: 10.1186/1471-2229-11-153 SCOPUS: 2-s2.0-80455158286 WoS: WOS:000297250700001 GOOGLE SCHOLAR lock_openAcceso abierto editor

Otras publicaciones en: BMC Plant Biology

Repositorio institucional: lock_openAcceso abierto Editor

Resumen

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. © 2011 Cabezas et al; licensee BioMed Central Ltd.