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Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes

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Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes

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dc.contributor.author Acquadro, Alberto es_ES
dc.contributor.author Barchi, Lorenzo es_ES
dc.contributor.author Gramazio, Pietro es_ES
dc.contributor.author Portis, Ezio es_ES
dc.contributor.author Vilanova Navarro, Santiago es_ES
dc.contributor.author Comino, Cinzia es_ES
dc.contributor.author Plazas Ávila, María de la O es_ES
dc.contributor.author Prohens Tomás, Jaime es_ES
dc.contributor.author Lanteri, Sergio es_ES
dc.date.accessioned 2018-06-18T04:29:31Z
dc.date.available 2018-06-18T04:29:31Z
dc.date.issued 2017 es_ES
dc.identifier.issn 1932-6203 es_ES
dc.identifier.uri http://hdl.handle.net/10251/104264
dc.description.abstract [EN] Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) using a genotype-by-sequencing approach. A total of 210 million useful reads were produced and were successfully aligned to the reference eggplant genome sequence. Out of the 75,399 polymorphic sites identified among the 76 entries in study, 12,859 were associated with coding sequence. A genetic relationships analysis, supported by the output of the FastSTRUCTURE software, identified four major sub-groups as present in the germplasm panel. The first of these clustered S. aethiopicum with its wild ancestor S. anguivi; the second, S. melongena, its wild progenitor S. insanum, and its relatives S. incanum, S. lichtensteinii and S. linneanum; the third, S. macrocarpon and its wild ancestor S. dasyphyllum; and the fourth, the New World species S. sisymbriifolium, S. torvum and S. elaeagnifolium. By applying a hierarchical FastSTRUCTURE analysis on partitioned data, it was also possible to resolve the ambiguous membership of the accessions of S. campylacanthum, S. violaceum, S. lidii, S. vespertilio and S. tomentsum, as well as to genetically differentiate the three species of New World Origin. A principal coordinates analysis performed both on the entire germplasm panel and also separately on the entries belonging to sub-groups revealed a clear separation among species, although not between each of the domesticates and their respective wild ancestors. There was no clear differentiation between either distinct cultivar groups or different geographical provenance. Adopting various approaches to analyze SNP variation provided support for interpretation of results. The genotyping-by-sequencing approach showed to be highly efficient for both quantifying genetic diversity and establishing genetic relationships among and within cultivated eggplants and their wild relatives. The relevance of these results to the evolution of eggplants, as well as to their genetic improvement, is discussed. es_ES
dc.description.sponsorship This work has been funded in part by European Unions Horizon 2020 Research and Innovation Programme under grant agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and by Spanish Ministerio de Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER). Funding has also been received from the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives", which is supported by the Government of Norway. This last project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and implemented in partnership with national and international gene banks and plant breeding institutes around the world. For further information see the project website:http://www.cwrdiversity.org/. Pietro Gramazio is grateful to Universitat Politecnica de Valencia for a pre-doctoral (Programa FPI de la UPV-Subprograma 1/2013 call) contract. Mariola Plazas is grateful to Spanish Ministerio de Economia, Industria y Competitividad for a post-doctoral grant within the Santiago Grisolia Programme (FCJI-2015-24835). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. es_ES
dc.language Inglés es_ES
dc.publisher Public Library of Science es_ES
dc.relation info:eu-repo/grantAgreement/MINECO//AGL2015-64755-R/ES/MEJORA GENETICA DE LA CALIDAD FUNCIONAL Y APARENTE DE LA BERENJENA/ es_ES
dc.relation THE GLOBAL CROP DIVERSITY TRUST/CROP/SC-310-03 es_ES
dc.relation info:eu-repo/grantAgreement/MINECO//FJCI-2015-24835/ES/FJCI-2015-24835/
dc.relation.ispartof PLoS ONE es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject.classification GENETICA es_ES
dc.title Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1371/journal.pone.0180774 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/677379/EU/Linking genetic resources, genomes and phenotypes of Solanaceous crops/ 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 Acquadro, A.; Barchi, L.; Gramazio, P.; Portis, E.; Vilanova Navarro, S.; Comino, C.; Plazas Ávila, MDLO.... (2017). Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes. PLoS ONE. 12(7). https://doi.org/10.1371/journal.pone.0180774 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://doi.org/10.1371/journal.pone.0180774 es_ES
dc.description.upvformatpinicio e0180774 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 12 es_ES
dc.description.issue 7 es_ES
dc.identifier.pmid 28686642
dc.identifier.pmcid PMC5501601
dc.relation.pasarela S\347956 es_ES
dc.contributor.funder Crop Trust es_ES
dc.contributor.funder European Commission es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
dc.contributor.funder European Regional Development Fund
dc.contributor.funder Government of Norway
dc.contributor.funder Universitat Politècnica de València


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