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SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium

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SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium

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dc.contributor.author Esteras Gómez, Cristina es_ES
dc.contributor.author Formisano, G. es_ES
dc.contributor.author Roig Montaner, Mª Cristina es_ES
dc.contributor.author Díaz Bermúdez, Aurora es_ES
dc.contributor.author Blanca Postigo, José Miguel es_ES
dc.contributor.author Garcia-Mas, J. es_ES
dc.contributor.author Gomez-Guillamon, M.L. es_ES
dc.contributor.author Lopez-Sese, A. es_ES
dc.contributor.author Lazaro, A. es_ES
dc.contributor.author Monforte Gilabert, Antonio José es_ES
dc.contributor.author Picó Sirvent, María Belén es_ES
dc.date.accessioned 2016-06-02T09:43:58Z
dc.date.available 2016-06-02T09:43:58Z
dc.date.issued 2013-05
dc.identifier.issn 0040-5752
dc.identifier.uri http://hdl.handle.net/10251/65090
dc.description.abstract Novel sequencing technologies were recently used to generate sequences from multiple melon (Cucumis melo L.) genotypes, enabling the in silico identification of large single nucleotide polymorphism (SNP) collections. In order to optimize the use of these markers, SNP validation and large-scale genotyping are necessary. In this paper, we present the first validated design for a genotyping array with 768 SNPs that are evenly distributed throughout the melon genome. This customized Illumina GoldenGate assay was used to genotype a collection of 74 accessions, representing most of the botanical groups of the species. Of the assayed loci, 91 % were successfully genotyped. The array provided a large number of polymorphic SNPs within and across accessions. This set of SNPs detected high levels of variation in accessions from this crop s center of origin as well as from several other areas of melon diversification. Allele distribution throughout the genome revealed regions that distinguished between the two main groups of cultivated accessions (inodorus and cantalupensis). Population structure analysis showed a subdivision into five subpopulations, reflecting the history of the crop. A considerably low level of LD was detected, which decayed rapidly within a few kilobases. Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in melon. Since many of the genotyped accessions are currently being used as the parents of breeding populations in various programs, this set of mapped markers could be used for future mapping and breeding efforts. es_ES
dc.description.sponsorship This project was carried out in the frame of the MELONOMICS project (2009-2012) of the Fundacion Genoma Espana and with the contributions of the PLAT KKBE project PIM2010PKB-00691. en_EN
dc.language Inglés es_ES
dc.publisher Springer Verlag (Germany) es_ES
dc.relation.ispartof TAG Theoretical and Applied Genetics es_ES
dc.rights Reserva de todos los derechos es_ES
dc.subject.classification GENETICA es_ES
dc.title SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1007/s00122-013-2053-5
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//PIM2010PKB-00691/ES/SUGARS AND FRUIT QUALITY IN MELON/ es_ES
dc.rights.accessRights Cerrado es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.description.bibliographicCitation Esteras Gómez, C.; Formisano, G.; Roig Montaner, MC.; Díaz Bermúdez, A.; Blanca Postigo, JM.; Garcia-Mas, J.; Gomez-Guillamon, M.... (2013). SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium. TAG Theoretical and Applied Genetics. 126(5):1285-1303. https://doi.org/10.1007/s00122-013-2053-5 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://dx.doi.org/10.1007/s00122-013-2053-5 es_ES
dc.description.upvformatpinicio 1285 es_ES
dc.description.upvformatpfin 1303 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 126 es_ES
dc.description.issue 5 es_ES
dc.relation.senia 239986 es_ES
dc.contributor.funder Ministerio de Ciencia e Innovación es_ES
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