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Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

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Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

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dc.contributor.author Blanca Postigo, José Miguel es_ES
dc.contributor.author Cañizares Sales, Joaquín es_ES
dc.contributor.author Roig Montaner, Mª Cristina es_ES
dc.contributor.author Ziarsolo Areitioaurtena, Pello es_ES
dc.contributor.author Nuez Viñals, Fernando es_ES
dc.contributor.author Picó Sirvent, María Belén es_ES
dc.date.accessioned 2013-04-16T07:35:19Z
dc.date.available 2013-04-16T07:35:19Z
dc.date.issued 2011 es_ES
dc.identifier.issn 1471-2164 es_ES
dc.identifier.uri http://hdl.handle.net/10251/27869
dc.description.abstract Background: Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat and vitamins. A broad range of genomic tools are today available for other cucurbits that have become models for the study of different metabolic processes. However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding.Results: We report the generation of a total of 512,751 C. pepo EST sequences, using 454 GS FLX Titanium technology. ESTs were obtained from normalized cDNA libraries (root, leaves, and flower tissue) prepared using two varieties with contrasting phenotypes for plant, flowering and fruit traits, representing the two C. pepo subspecies: subsp. pepo cv. Zucchini and subsp. ovifera cv Scallop. De novo assembling was performed to generate a collection of 49,610 Cucurbita unigenes (average length of 626 bp) that represent the first transcriptome of the species. Over 60% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The distributions of Cucurbita unigenes followed similar tendencies than that reported for Arabidopsis or melon, suggesting that the dataset may represent the whole Cucurbita transcriptome. About 34% unigenes were detected to have known orthologs of Arabidopsis or melon, including genes potentially involved in disease resistance, flowering and fruit quality. Furthermore, a set of 1,882 unigenes with SSR motifs and 9,043 high confidence SNPs between Zucchini and Scallop were identified, of which 3,538 SNPs met criteria for use with high throughput genotyping platforms, and 144 could be detected as CAPS. A set of markers were validated, being 80% of them polymorphic in a set of variable C. pepo and C. moschata accessions.Conclusion: We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed. The transcriptome provides an invaluable new tool for biological research. The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties. © 2011 Blanca et al; licensee BioMed Central Ltd. es_ES
dc.language Inglés
dc.publisher BioMed Central en_EN
dc.relation.ispartof BMC Genomics es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Complementary DNA es_ES
dc.subject Transcriptome es_ES
dc.subject Microsatellite DNA es_ES
dc.subject Plant DNA es_ES
dc.subject Allele es_ES
dc.subject Arabidopsis es_ES
dc.subject Article es_ES
dc.subject DNA library es_ES
dc.subject DNA sequence es_ES
dc.subject Expressed sequence tag es_ES
dc.subject Flowering es_ES
dc.subject Gene expression es_ES
dc.subject Genetic variability es_ES
dc.subject Genotype es_ES
dc.subject Nonhuman es_ES
dc.subject Phenotype es_ES
dc.subject Scallop es_ES
dc.subject Simple sequence repeat es_ES
dc.subject Single nucleotide polymorphism es_ES
dc.subject Squash es_ES
dc.subject Transcriptomics es_ES
dc.subject Flower es_ES
dc.subject Gene expression profiling es_ES
dc.subject Gene library es_ES
dc.subject Genetics es_ES
dc.subject Molecular genetics es_ES
dc.subject Plant gene es_ES
dc.subject Plant leaf es_ES
dc.subject Plant root es_ES
dc.subject Cucumis es_ES
dc.subject Cucurbita es_ES
dc.subject Cucurbita moschata es_ES
dc.subject Cucurbita pepo es_ES
dc.subject Cucurbita pepo var. melopepo es_ES
dc.subject Cucurbitaceae es_ES
dc.subject Pepo es_ES
dc.subject DNA, Plant es_ES
dc.subject Flowers es_ES
dc.subject Genes, Plant es_ES
dc.subject Microsatellite Repeats es_ES
dc.subject Molecular Sequence Annotation es_ES
dc.subject Plant Leaves es_ES
dc.subject Plant Roots es_ES
dc.subject Polymorphism, Single Nucleotide es_ES
dc.subject Sequence Analysis, DNA es_ES
dc.subject.classification GENETICA es_ES
dc.title Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)
dc.type Artículo es_ES
dc.identifier.doi 10.1186/1471-2164-12-104. es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.description.bibliographicCitation Blanca Postigo, JM.; Cañizares Sales, J.; Roig Montaner, MC.; Ziarsolo Areitioaurtena, P.; Nuez Viñals, F.; Picó Sirvent, MB. (2011). Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics. 12:104-117. doi:10.1186/1471-2164-12-104 es_ES
dc.description.accrualMethod Senia es_ES
dc.description.upvformatpinicio 104 es_ES
dc.description.upvformatpfin 117 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 12 es_ES
dc.relation.senia 206206 es_ES
dc.identifier.pmid 21310031 en_EN
dc.identifier.pmcid PMC3049757 en_EN


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