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

Autores
Rendón Anaya, Martha; Montero Vargas, Josaphat M.; Saburido Álvarez, Soledad; Vlasova, Anna; Capella Gutierrez, Salvador; Ordaz Ortiz, José Juan; Aguilar, Orlando Mario; Vianello Brondani, Rosana P.; Santalla, Marta; Delaye, Luis; Gabaldón, Toni; Gepts, Paul; Winkler, Robert; Guigó, Roderic; Delgado Salinas, Alfonso; Herrera Estrella, Alfredo
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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.
Fil: Rendón Anaya, Martha. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Fil: Montero Vargas, Josaphat M.. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Fil: Saburido Álvarez, Soledad. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Fil: Vlasova, Anna. Universitat Pompeu Fabra; España. Centre for Genomic Regulation; España
Fil: Capella Gutierrez, Salvador. Universitat Pompeu Fabra; España. Centre for Genomic Regulation; España
Fil: Ordaz Ortiz, José Juan. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Fil: Aguilar, Orlando Mario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Vianello Brondani, Rosana P.. Embrapa Rice and Bean; Brasil
Fil: Santalla, Marta. Consejo Superior de Investigaciones Científicas; España. Mision Biológica de Galicia; España
Fil: Delaye, Luis. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Fil: Gabaldón, Toni. Universitat Pompeu Fabra; España. Centre for Genomic Regulation; España
Fil: Gepts, Paul. University of California at Davis; Estados Unidos
Fil: Winkler, Robert. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Fil: Guigó, Roderic. Universitat Pompeu Fabra; España. Centre for Genomic Regulation; España
Fil: Delgado Salinas, Alfonso. Universidad Nacional Autónoma de México. Departamento de Botánica. Instituto de Biología; México
Fil: Herrera Estrella, Alfredo. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Materia
ADAPTIVE TRAITS
COMMON BEAN
DOMESTICATION
GENOMIC INTROGRESSION
SPECIATION
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/53490
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/53490
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Genomic history of the origin and domestication of common bean unveils its closest sister speciesRendón Anaya, MarthaMontero Vargas, Josaphat M.Saburido Álvarez, SoledadVlasova, AnnaCapella Gutierrez, SalvadorOrdaz Ortiz, José JuanAguilar, Orlando MarioVianello Brondani, Rosana P.Santalla, MartaDelaye, LuisGabaldón, ToniGepts, PaulWinkler, RobertGuigó, RodericDelgado Salinas, AlfonsoHerrera Estrella, AlfredoADAPTIVE TRAITSCOMMON BEANDOMESTICATIONGENOMIC INTROGRESSIONSPECIATIONhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: 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.Fil: Rendón Anaya, Martha. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; MéxicoFil: Montero Vargas, Josaphat M.. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; MéxicoFil: Saburido Álvarez, Soledad. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; MéxicoFil: Vlasova, Anna. Universitat Pompeu Fabra; España. Centre for Genomic Regulation; EspañaFil: Capella Gutierrez, Salvador. Universitat Pompeu Fabra; España. Centre for Genomic Regulation; EspañaFil: Ordaz Ortiz, José Juan. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; MéxicoFil: Aguilar, Orlando Mario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Vianello Brondani, Rosana P.. Embrapa Rice and Bean; BrasilFil: Santalla, Marta. Consejo Superior de Investigaciones Científicas; España. Mision Biológica de Galicia; EspañaFil: Delaye, Luis. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; MéxicoFil: Gabaldón, Toni. Universitat Pompeu Fabra; España. Centre for Genomic Regulation; EspañaFil: Gepts, Paul. University of California at Davis; Estados UnidosFil: Winkler, Robert. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; MéxicoFil: Guigó, Roderic. Universitat Pompeu Fabra; España. Centre for Genomic Regulation; EspañaFil: Delgado Salinas, Alfonso. Universidad Nacional Autónoma de México. Departamento de Botánica. Instituto de Biología; MéxicoFil: Herrera Estrella, Alfredo. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; MéxicoBioMed Central2017-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/53490Rendón Anaya, Martha; Montero Vargas, Josaphat M.; Saburido Álvarez, Soledad; Vlasova, Anna; Capella Gutierrez, Salvador; et al.; Genomic history of the origin and domestication of common bean unveils its closest sister species; BioMed Central; Genome Biology; 18; 1; 3-2017; 1-171474-75961474-760XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1186/s13059-017-1190-6info:eu-repo/semantics/altIdentifier/url/https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1190-6info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:32:11Zoai:ri.conicet.gov.ar:11336/53490instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:32:11.68CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Genomic history of the origin and domestication of common bean unveils its closest sister species
title Genomic history of the origin and domestication of common bean unveils its closest sister species
spellingShingle Genomic history of the origin and domestication of common bean unveils its closest sister species
Rendón Anaya, Martha
ADAPTIVE TRAITS
COMMON BEAN
DOMESTICATION
GENOMIC INTROGRESSION
SPECIATION
title_short Genomic history of the origin and domestication of common bean unveils its closest sister species
title_full Genomic history of the origin and domestication of common bean unveils its closest sister species
title_fullStr Genomic history of the origin and domestication of common bean unveils its closest sister species
title_full_unstemmed Genomic history of the origin and domestication of common bean unveils its closest sister species
title_sort Genomic history of the origin and domestication of common bean unveils its closest sister species
dc.creator.none.fl_str_mv Rendón Anaya, Martha
Montero Vargas, Josaphat M.
Saburido Álvarez, Soledad
Vlasova, Anna
Capella Gutierrez, Salvador
Ordaz Ortiz, José Juan
Aguilar, Orlando Mario
Vianello Brondani, Rosana P.
Santalla, Marta
Delaye, Luis
Gabaldón, Toni
Gepts, Paul
Winkler, Robert
Guigó, Roderic
Delgado Salinas, Alfonso
Herrera Estrella, Alfredo
author Rendón Anaya, Martha
author_facet Rendón Anaya, Martha
Montero Vargas, Josaphat M.
Saburido Álvarez, Soledad
Vlasova, Anna
Capella Gutierrez, Salvador
Ordaz Ortiz, José Juan
Aguilar, Orlando Mario
Vianello Brondani, Rosana P.
Santalla, Marta
Delaye, Luis
Gabaldón, Toni
Gepts, Paul
Winkler, Robert
Guigó, Roderic
Delgado Salinas, Alfonso
Herrera Estrella, Alfredo
author_role author
author2 Montero Vargas, Josaphat M.
Saburido Álvarez, Soledad
Vlasova, Anna
Capella Gutierrez, Salvador
Ordaz Ortiz, José Juan
Aguilar, Orlando Mario
Vianello Brondani, Rosana P.
Santalla, Marta
Delaye, Luis
Gabaldón, Toni
Gepts, Paul
Winkler, Robert
Guigó, Roderic
Delgado Salinas, Alfonso
Herrera Estrella, Alfredo
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv ADAPTIVE TRAITS
COMMON BEAN
DOMESTICATION
GENOMIC INTROGRESSION
SPECIATION
topic ADAPTIVE TRAITS
COMMON BEAN
DOMESTICATION
GENOMIC INTROGRESSION
SPECIATION
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv 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.
Fil: Rendón Anaya, Martha. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Fil: Montero Vargas, Josaphat M.. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Fil: Saburido Álvarez, Soledad. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Fil: Vlasova, Anna. Universitat Pompeu Fabra; España. Centre for Genomic Regulation; España
Fil: Capella Gutierrez, Salvador. Universitat Pompeu Fabra; España. Centre for Genomic Regulation; España
Fil: Ordaz Ortiz, José Juan. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Fil: Aguilar, Orlando Mario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Vianello Brondani, Rosana P.. Embrapa Rice and Bean; Brasil
Fil: Santalla, Marta. Consejo Superior de Investigaciones Científicas; España. Mision Biológica de Galicia; España
Fil: Delaye, Luis. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Fil: Gabaldón, Toni. Universitat Pompeu Fabra; España. Centre for Genomic Regulation; España
Fil: Gepts, Paul. University of California at Davis; Estados Unidos
Fil: Winkler, Robert. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
Fil: Guigó, Roderic. Universitat Pompeu Fabra; España. Centre for Genomic Regulation; España
Fil: Delgado Salinas, Alfonso. Universidad Nacional Autónoma de México. Departamento de Botánica. Instituto de Biología; México
Fil: Herrera Estrella, Alfredo. Instituto Politécnico Nacional. Centro de Investigación y de Estudios Avanzados; México
description 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.
publishDate 2017
dc.date.none.fl_str_mv 2017-03
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/53490
Rendón Anaya, Martha; Montero Vargas, Josaphat M.; Saburido Álvarez, Soledad; Vlasova, Anna; Capella Gutierrez, Salvador; et al.; Genomic history of the origin and domestication of common bean unveils its closest sister species; BioMed Central; Genome Biology; 18; 1; 3-2017; 1-17
1474-7596
1474-760X
CONICET Digital
CONICET
url http://hdl.handle.net/11336/53490
identifier_str_mv Rendón Anaya, Martha; Montero Vargas, Josaphat M.; Saburido Álvarez, Soledad; Vlasova, Anna; Capella Gutierrez, Salvador; et al.; Genomic history of the origin and domestication of common bean unveils its closest sister species; BioMed Central; Genome Biology; 18; 1; 3-2017; 1-17
1474-7596
1474-760X
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1186/s13059-017-1190-6
info:eu-repo/semantics/altIdentifier/url/https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1190-6
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
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reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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