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High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping

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High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping

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dc.contributor.author Esteras Gómez, Cristina es_ES
dc.contributor.author Gómez, Pedro es_ES
dc.contributor.author Monforte Gilabert, Antonio José es_ES
dc.contributor.author Blanca Postigo, José Miguel es_ES
dc.contributor.author Vicente-Dolera, Nelly es_ES
dc.contributor.author Roig Montaner, Mª Cristina es_ES
dc.contributor.author Nuez Viñals, Fernando es_ES
dc.contributor.author Picó Sirvent, María Belén
dc.date.accessioned 2013-09-04T06:25:27Z
dc.date.available 2013-09-04T06:25:27Z
dc.date.issued 2012
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10251/31716
dc.description.abstract Background: Cucurbita pepo is amember of the Cucurbitaceae family, the second-most important horticultural family in terms of economic importance after Solanaceae. The ¿summer squash¿ types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species. The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). Results: We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species¿ two subspecies: Zucchini (subsp. pepo) ¿ Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. Conclusion: Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps an performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in the coding regions of genes involved in different physiological processes. The platform will also be useful for future mapping and diversity studies, and will be essential in order to accelerate the process of breeding new and better adapted squash varieties. es_ES
dc.description.sponsorship This research was funded by the INIA projects RTA2008-00035-C02-01/02 and RTA2011-00044-C02-1/2 of the Spanish Instituto Nacional de Investigacion y Tecnologia Agraria and FEDER funds (EU). The NVD grant was supported by the Programa de Formacion del Personal Tecnico e Investigador from IFAPA, co-financed with European Social Funds. The authors wish to thank P. Salas and E. Martinez Perez for their technical assistance in the fruit characterization. We are thankful for the kindly suggestions of Dr. Harry Paris for the F<INF>2</INF> C. pepo mapping population. en_EN
dc.language Inglés es_ES
dc.publisher BioMed Central es_ES
dc.relation.ispartof BMC Genomics es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Single nucleotide polymorphisms es_ES
dc.subject Consensus linkage map es_ES
dc.subject Cucumis-sativus l es_ES
dc.subject Melo l es_ES
dc.subject Transcriptome characterization es_ES
dc.subject Germplasm collection es_ES
dc.subject Crop improvement es_ES
dc.subject Aflp markers es_ES
dc.subject Genetic-map es_ES
dc.subject DNA markers es_ES
dc.subject.classification GENETICA es_ES
dc.title High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/1471-2164-13-80
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//RTA2008-00035-C02-01/ES/Mejora competitiva del calabacín por características de calidad de fruto y resistencia a enfermedades: Desarrollo de RILs, marcadores codominantes SSR, CAPS y SNP, y construcción de un mapa genético./ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//RTA2011-00044-C02-01/ES/Desarrollo competitivo de nuevos cultivares de calabacín y ampliación de la plataforma genómica para la mejora de esta hortaliza/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//RTA2011-00044-C02-02/ES/Desarrollo competitivo de nuevos cultivares de calabacín y ampliación de la plataforma genómica para la mejora de esta hortaliza/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana - Institut Universitari de Conservació i Millora de l'Agrodiversitat Valenciana es_ES
dc.description.bibliographicCitation Esteras Gómez, C.; Gómez, P.; Monforte Gilabert, AJ.; Blanca Postigo, JM.; Vicente-Dolera, N.; Roig Montaner, MC.; Nuez Viñals, F.... (2012). High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping. BMC Genomics. 13(80):1-21. https://doi.org/10.1186/1471-2164-13-80 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://dx.doi.org/10.1186/1471-2164-13-80 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 21 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 13 es_ES
dc.description.issue 80 es_ES
dc.relation.senia 224477
dc.identifier.pmid 22356647 en_EN
dc.identifier.pmcid PMC3359225
dc.contributor.funder Ministerio de Ciencia e Innovación es_ES
dc.contributor.funder European Social Fund es_ES
dc.contributor.funder European Regional Development Fund es_ES


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