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Genetic diversity, population structure and relationships in a collection of pepper (Capsicum spp.) landraces from the Spanish centre of diversity revealed by genotyping-by-sequencing (GBS)

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Genetic diversity, population structure and relationships in a collection of pepper (Capsicum spp.) landraces from the Spanish centre of diversity revealed by genotyping-by-sequencing (GBS)

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dc.contributor.author Pereira-Días, Leandro es_ES
dc.contributor.author Vilanova Navarro, Santiago es_ES
dc.contributor.author Fita, Ana es_ES
dc.contributor.author Prohens Tomás, Jaime es_ES
dc.contributor.author Rodríguez Burruezo, Adrián es_ES
dc.date.accessioned 2020-12-12T04:31:45Z
dc.date.available 2020-12-12T04:31:45Z
dc.date.issued 2019-05-01 es_ES
dc.identifier.uri http://hdl.handle.net/10251/156935
dc.description.abstract [EN] Pepper (Capsicum spp.) is one of the most important vegetable crops; however, pepper genomic studies lag behind those of other important Solanaceae. Here we present the results of a high-throughput genotyping-by-sequencing (GBS) study of a collection of 190 Capsicum spp. accessions, including 183 of five cultivated species (C. annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens) and seven of the wild form C. annuum var. glabriusculum. Sequencing generated 6,766,231 high-quality read tags, of which 40.7% were successfully aligned to the reference genome. SNP calling yielded 4083 highly informative segregating SNPs. Genetic diversity and relationships of a subset of 148 accessions, of which a complete passport information was available, was studied using principal components analysis (PCA), discriminant analysis of principal components (DAPC), and phylogeny approaches. C. annuum, C. baccatum, and C. chinense were successfully separated by all methods. Our population was divided into seven clusters by DAPC, where C. frutescens accessions were clustered together with C. chinense. C. annuum var. glabriusculum accessions were spread into two distinct genetic pools, while European accessions were admixed and closely related. Separation of accessions was mainly associated to differences in fruit characteristics and origin. Phylogeny studies showed a close relation between Spanish and Mexican accessions, supporting the hypothesis that the first arose from a main genetic flow from the latter. Tajima's D statistic values were consistent with positive selection in the C. annuum clusters, possibly related to domestication or selection towards traits of interest. This work provides comprehensive and relevant information on the origin and relationships of Spanish landraces and for future association mapping studies in pepper. es_ES
dc.description.sponsorship This work has been financed by INIA projects RTA2013-00022-C02, RTA2014-00041-C02-02, and RF2010-00025-00-00, FEDER funds. Authors are also grateful to the different Research Institutions, scientists, and breeders, and PDOs and GPIs Regulatory Boards, included on Supplementary Data: Table 1 for providing part of the materials studied here. es_ES
dc.language Inglés es_ES
dc.publisher Springer Nature es_ES
dc.relation.ispartof Horticulture Research es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject.classification GENETICA es_ES
dc.title Genetic diversity, population structure and relationships in a collection of pepper (Capsicum spp.) landraces from the Spanish centre of diversity revealed by genotyping-by-sequencing (GBS) es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1038/s41438-019-0132-8 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//RF2010-00025-00-00/ES/Consecución de una colección nuclear de pimiento y especies relacionadas (Capsicum spp.) basada en marcadores AFLPs y SSRs/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//RTA2013-00022-C02-02/ES/Obtención de patrones de pimiento tolerantes a bajos insumos de fósforo y genética de la adaptación radicular a estreses abióticos/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//RTA2014-00041-C02-02/ES/Selección y mejora de variedades tradicionales de pimiento (Capsicum annuum L.) para rendimiento y calidad de fruto y adaptadas a cultivo ecológico/ 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 Pereira-Días, L.; Vilanova Navarro, S.; Fita, A.; Prohens Tomás, J.; Rodríguez Burruezo, A. (2019). Genetic diversity, population structure and relationships in a collection of pepper (Capsicum spp.) landraces from the Spanish centre of diversity revealed by genotyping-by-sequencing (GBS). Horticulture Research. 6:1-13. https://doi.org/10.1038/s41438-019-0132-8 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1038/s41438-019-0132-8 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 13 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 6 es_ES
dc.identifier.eissn 2052-7276 es_ES
dc.identifier.pmid 31044080 es_ES
dc.identifier.pmcid PMC6491490 es_ES
dc.relation.pasarela S\386183 es_ES
dc.contributor.funder European Regional Development Fund es_ES
dc.contributor.funder Ministerio de Ciencia e Innovación es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
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