A 48 SNP set for grapevine cultivar identification

Autor: Juan Carreño, Mark R. Thomas, Diego Lijavetzky, Iván Carreño, Javier Ibáñez, Leonor Ruiz-García, Gema Bravo, Angelica M. Jermakow, Virginia Rodríguez, Dolores Vélez, José Antonio Cabezas, José M. Martínez-Zapater
Přispěvatelé: Fundación Genoma España, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ministerio de Ciencia e Innovación (España), Commonwealth Scientific and Industrial Research Organisation (Australia)
Rok vydání: 2011
Předmět:
Zdroj: Repositorio de Resultados de Investigación del INIA
INIA: Repositorio de Resultados de Investigación del INIA
BMC Plant Biology, Vol 11, Iss 1, p 153 (2011)
RIUR: Repositorio Institucional de la Universidad de La Rioja
Universidad de La Rioja (UR)
Digital.CSIC. Repositorio Institucional del CSIC
instname
RIUR. Repositorio Institucional de la Universidad de La Rioja
CONICET Digital (CONICET)
Consejo Nacional de Investigaciones Científicas y Técnicas
instacron:CONICET
BMC Plant Biology
Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA
ISSN: 2009-0021
Popis: [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.
This study was financially supported by Grapegen and the 14322 Agreement Projects from Genoma España as well as the VIN01-025 Project from the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria from MICINN (Spanish Ministry for Science and Innovation) and in part by CSIRO Plant Industry and the Grape and Wine Research and Development Corporation (GWRDC). We also thank MICINN for a bilateral collaborative grant with Argentina (AR2009-0021), Applied Biosystems for their support in the design of the 48 SNPlex set and the Centro Nacional de Genotipado http://www.cegen.org for SNPlex genotyping. The research group participates in COST Action FA1003.
Databáze: OpenAIRE
Externí odkaz: