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Transcriptome sequencing for SNP discovery across Cucumis melo

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Transcriptome sequencing for SNP discovery across Cucumis melo

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dc.contributor.author Blanca Postigo, José Miguel es_ES
dc.contributor.author Esteras Gómez, Cristina es_ES
dc.contributor.author Ziarsolo Areitioaurtena, Pello es_ES
dc.contributor.author Perez, Daniel es_ES
dc.contributor.author Fernández-Pedrosa, Victoria es_ES
dc.contributor.author Collado, Carmen es_ES
dc.contributor.author Rodríguez de Pablos, Raquel es_ES
dc.contributor.author Ballester, Alida es_ES
dc.contributor.author Roig Montaner, Mª Cristina es_ES
dc.contributor.author Cañizares Sales, Joaquín es_ES
dc.contributor.author Picó Sirvent, María Belén
dc.date.accessioned 2013-09-04T06:59:53Z
dc.date.available 2013-09-04T06:59:53Z
dc.date.issued 2012
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10251/31731
dc.description.abstract Background: Melon (Cucumis melo L.) is a highly diverse species that is cultivated worldwide. Recent advances in massively parallel sequencing have begun to allow the study of nucleotide diversity in this species. The Sanger method combined with medium-throughput 454 technology were used in a previous study to analyze the genetic diversity of germplasm representing 3 botanical varieties, yielding a collection of about 40,000 SNPs distributed in 14,000 unigenes. However, the usefulness of this resource is limited as the sequenced genotypes do not represent the whole diversity of the species, which is divided into two subspecies with many botanical varieties variable in plant, flowering, and fruit traits, as well as in stress response. As a first step to extensively document levels and patterns of nucleotide variability across the species, we used the high-throughput SOLiD¿ system to resequence the transcriptomes of a set of 67 genotypes that had previously been selected from a core collection representing the extant variation of the entire species.Results: The deep transcriptome resequencing of all of the genotypes, grouped into 8 pools (wild African agrestis, Asian agrestis and acidulus, exotic Far Eastern conomon, Indian momordica and Asian dudaim and flexuosus, commercial cantalupensis, subsp. melo Asian and European landraces, Spanish inodorus landraces, and Piel de Sapo breeding lines) yielded about 300 M reads. Short reads were mapped to the recently generated draft genome assembly of the DHL line Piel de Sapo (inodorus) x Songwhan Charmi (conomon) and to a new version of melon transcriptome. Regions with at least 6X coverage were used in SNV calling, generating a melon collection with 303,883 variants. These SNVs were dispersed across the entire C. melo genome, and distributed in 15,064 annotated genes. The number and variability of in silico SNVs differed considerably between pools. Our finding of higher genomic diversity in wild and exotic agrestis melons from India and Africa as compared to commercial cultivars, cultigens and landraces from Eastern Europe, Western Asia and the Mediterranean basin is consistent with the evolutionary history proposed for the species. Group-specific SNVs that will be useful in introgression programs were also detected. In a sample of 143 selected putative SNPs, we verified 93% of the polymorphisms in a panel of 78 genotypes.Conclusions: This study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial) melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity. This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties. © 2012 Blanca et al.; licensee BioMed Central Ltd. es_ES
dc.description.sponsorship This project was carried out in the frame of the MELONOMICS project (2009-2012) of the Fundacion Genoma Espana. 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 Nucleotide es_ES
dc.subject Transcriptome es_ES
dc.subject Article es_ES
dc.subject Cultivar es_ES
dc.subject Exotic species es_ES
dc.subject Gene mapping es_ES
dc.subject Gene targeting es_ES
dc.subject Genetic variability es_ES
dc.subject Genotype es_ES
dc.subject High throughput screening es_ES
dc.subject Introgression es_ES
dc.subject Melon es_ES
dc.subject Nonhuman es_ES
dc.subject Plant genome es_ES
dc.subject Single nucleotide polymorphism es_ES
dc.subject Wild plant es_ES
dc.subject Cucumis es_ES
dc.subject Cucumis melo es_ES
dc.subject Melo es_ES
dc.subject Momordica es_ES
dc.subject.classification GENETICA es_ES
dc.title Transcriptome sequencing for SNP discovery across Cucumis melo es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/1471-2164-13-280
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 Blanca Postigo, JM.; Esteras Gómez, C.; Ziarsolo Areitioaurtena, P.; Perez, D.; Fernández-Pedrosa, V.; Collado, C.; Rodríguez De Pablos, R.... (2012). Transcriptome sequencing for SNP discovery across Cucumis melo. BMC Genomics. 13(280):1-18. doi:10.1186/1471-2164-13-280 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://dx.doi.org/10.1186/1471-2164-13-280 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 18 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 13 es_ES
dc.description.issue 280 es_ES
dc.relation.senia 224479
dc.identifier.pmid 22726804 en_EN
dc.identifier.pmcid PMC3473316 en_EN
dc.contributor.funder Fundación Genoma España es_ES


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