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Genomic history of the origin and domestication of common bean unveils its closest sister species

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dc.contributor.author Rendón-Anaya, Martha
dc.contributor.author Montero-Vargas, Josaphat M.
dc.contributor.author Saburido-Álvarez, Soledad
dc.contributor.author Vlasova, Anna
dc.contributor.author Capella Gutiérrez, Salvador Jesús, 1985-
dc.contributor.author Ordaz-Ortiz, José Juan
dc.contributor.author Aguilar, O. Mario
dc.contributor.author Vianello-Brondani, Rosana P.
dc.contributor.author Santalla, Marta
dc.contributor.author Delaye, Luis
dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
dc.contributor.author Gepts, Paul
dc.contributor.author Winkler, Robert
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author Delgado-Salinas, Alfonso
dc.contributor.author Herrera-Estrella, Alfredo
dc.date.accessioned 2017-05-26T07:52:35Z
dc.date.available 2017-05-26T07:52:35Z
dc.date.issued 2017
dc.identifier.citation Rendón-Anaya M, Montero-Vargas JM, Saburido-Álvarez S, Vlasova A, Capella Gutiérrez SJ, Ordaz-Ortiz JJ et al. Genomic history of the origin and domestication of common bean unveils its closest sister species. Genome Biology. 2017;18:60. DOI: 10.1186/s13059-017-1190-6
dc.identifier.issn 1474-760X
dc.identifier.uri http://hdl.handle.net/10230/32167
dc.description.abstract Background: Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. Results: We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres. Conclusions: We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the “wild ancestor” of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.
dc.description.sponsorship This work was supported by the Ibero-American Programme for Science, Technology and Development - CYTED (PhasIbeAm project); Spanish Government - Ministry of Economy and Competitiveness (EUI2009-04052, BIO2011-26205), “Centro de Excelencia Severo Ochoa 2013-2017,” SEV-2012-0208 and Project PT13/0001/0021 (ISCIII - Subdirección General de Evaluación y Fomento de la Investigación/FEDER “Una Manera de hacer Europa”); Brazilian Government—National Council for Scientific and Technological Development - CNPq/Prosul (490725/2010-4); Ministerio de Ciencia, Tecnología e Innovación Productiva de la República Argentina; Consejo Nacional de Ciencia y Tecnología - Conacyt, Mexico (J010-214-2009, Fronteras 2015-2/814); and U.S. government: USDA National Institute of Food and Agriculture (2013-67013-21224. M. R-A. and J.M.M.-V. are indebted to Conacyt for a doctoral fellowship.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof Genome Biology. 2017;18:60
dc.rights This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title Genomic history of the origin and domestication of common bean unveils its closest sister species
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/s13059-017-1190-6
dc.subject.keyword Common bean
dc.subject.keyword Domestication
dc.subject.keyword Genomic introgression
dc.subject.keyword Adaptive traits
dc.subject.keyword Speciation
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2011-26205
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV-2012-0208
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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