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Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

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Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

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dc.contributor.author Gramazio, Pietro es_ES
dc.contributor.author Blanca Postigo, José Miguel es_ES
dc.contributor.author Ziarsolo Areitioaurtena, Pello es_ES
dc.contributor.author Herraiz García, Francisco Javier es_ES
dc.contributor.author Plazas Ávila, María de la O es_ES
dc.contributor.author Prohens Tomás, Jaime es_ES
dc.contributor.author Vilanova Navarro, Santiago es_ES
dc.date.accessioned 2018-01-02T09:41:55Z
dc.date.available 2018-01-02T09:41:55Z
dc.date.issued 2016 es_ES
dc.identifier.issn 1471-2164 es_ES
dc.identifier.uri http://hdl.handle.net/10251/93708
dc.description.abstract [EN] Background: Solanum incanum is a close wild relative of S. melongena with high contents of bioactive phenolics and drought tolerance. S. aethiopicum is a cultivated African eggplant cross-compatible with S. melongena. Despite their great interest in S. melongena breeding programs, the genomic resources for these species are scarce. Results: RNA-Seq was performed with NGS from pooled RNA of young leaf, floral bud and young fruit tissues, generating more than one hundred millions raw reads per species. The transcriptomes were assembled in 83,905 unigenes for S. incanum and in 87,084 unigenes for S. aethiopicum with an average length of 696 and 722 bp, respectively. The unigenes were structurally and functionally annotated based on comparison with public databases by using bioinformatic tools. The single nucleotide variant calling analysis (SNPs and INDELs) was performed by mapping our S. incanum and S. aethiopicum reads, as well as reads from S. melongena and S. torvum available on NCBI database (National Center for Biotechnology Information), against the eggplant genome. Both intraspecific and interspecific polymorphisms were identified and subsets of molecular markers were created for all species combinations. 36 SNVs were selected for validation in the S. incanum and S. aethiopicum accessions and 96 % were correctly amplified confirming the polymorphisms. In addition, 976 and 1,278 SSRs were identified in S. incanum and S. aethiopicum transcriptomes respectively, and a set of them were validated. Conclusions: This work provides a broad insight into gene sequences and allelic variation in S. incanum and S. aethiopicum. This work is a first step toward better understanding of target genes involved in metabolic pathways relevant for eggplant breeding. The molecular markers detected in this study could be used across all the eggplant genepool, which is of interest for breeding programs as well as to perform marker-trait association and QTL analysis studies. es_ES
dc.description.sponsorship This work has been partially funded by Spanish Ministerio de Economia y Competitividad and FEDER (grant AGL2015-64755-450 R).
dc.language Inglés es_ES
dc.publisher Springer (Biomed Central Ltd.) es_ES
dc.relation.ispartof BMC Genomics es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Solanum incanum es_ES
dc.subject S. aethiopicum es_ES
dc.subject Eggplant genepool es_ES
dc.subject De novo transcriptome es_ES
dc.subject Gene annotation es_ES
dc.subject Molecular marker discovery es_ES
dc.subject.classification GENETICA es_ES
dc.title Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s12864-016-2631-4 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//AGL2015-64755-R/ES/MEJORA GENETICA DE LA CALIDAD FUNCIONAL Y APARENTE DE LA BERENJENA/
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 Gramazio, P.; Blanca Postigo, JM.; Ziarsolo Areitioaurtena, P.; Herraiz García, FJ.; Plazas Ávila, MDLO.; Prohens Tomás, J.; Vilanova Navarro, S. (2016). Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding. BMC Genomics. 17(300). https://doi.org/10.1186/s12864-016-2631-4 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1186/s12864-016-2631-4 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 17 es_ES
dc.description.issue 300 es_ES
dc.identifier.pmid 27108408 en_EN
dc.identifier.pmcid PMC4841963
dc.relation.pasarela S\311224 es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
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