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Genomic variation in tomato, from wild ancestors to contemporary breeding accessions

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Genomic variation in tomato, from wild ancestors to contemporary breeding accessions

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dc.contributor.author Blanca Postigo, José Miguel es_ES
dc.contributor.author Montero Pau, Javier es_ES
dc.contributor.author Sauvage, Christopher es_ES
dc.contributor.author Bauchet, Guillermo es_ES
dc.contributor.author Illa, Eudald es_ES
dc.contributor.author Díez Niclós, Mª José Teresa de Jesús es_ES
dc.contributor.author Francis, David es_ES
dc.contributor.author Causse, Mathilde es_ES
dc.contributor.author Van Der Knaap, Esther Klazina Maria es_ES
dc.contributor.author Cañizares Sales, Joaquín es_ES
dc.date.accessioned 2016-05-10T10:16:50Z
dc.date.available 2016-05-10T10:16:50Z
dc.date.issued 2015-04-01
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10251/63841
dc.description.abstract [EN] Background: Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection. Results: Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and “cherry tomato” are not synonymous terms. The morphologically-based term “cherry tomato” included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups. Conclusions: This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement. es_ES
dc.description.sponsorship We are grateful to the gene banks for their collections that made this study possible. We thank Syngenta Seeds for providing genotyping data for 42 accessions. We would like to thank the Supercomputing and Bioinnovation Center (Universidad de Malaga, Spain) for providing computational resources to process the SNAPP phylogenetic tree. This research was supported in part by the USDA/NIFA funded SolCAP project under contract number to DF and USDA AFRI 2013-67013-21229 to EvdK and DF. 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 Solanum lycopersicum es_ES
dc.subject Solanum pimpinellifolium es_ES
dc.subject SolCAP array es_ES
dc.subject Origin es_ES
dc.subject Variability es_ES
dc.subject Genome es_ES
dc.subject Fruit size genes es_ES
dc.subject Domestication es_ES
dc.subject.classification GENETICA es_ES
dc.title Genomic variation in tomato, from wild ancestors to contemporary breeding accessions es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s12864-015-1444-1
dc.relation.projectID info:eu-repo/grantAgreement/USDA//USDA AFRI 2013-67013-21229/ es_ES
dc.rights.accessRights Abierto 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.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.description.bibliographicCitation Blanca Postigo, JM.; Montero Pau, J.; Sauvage, C.; Bauchet, G.; Illa, E.; Díez Niclós, MJTDJ.; Francis, D.... (2015). Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics. 16(257):1-19. https://doi.org/10.1186/s12864-015-1444-1 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://dx.doi.org/10.1186/s12864-015-1444-1 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 19 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 16 es_ES
dc.description.issue 257 es_ES
dc.relation.senia 289648 es_ES
dc.identifier.pmid 25880392 en_EN
dc.identifier.pmcid PMC4404671 en_EN
dc.contributor.funder U.S. Department of Agriculture es_ES
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