Genomic history of the origin and domestication of common bean unveils its closest sister species.
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
Texto Completo: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/1078520 |
Resumo: | 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. |
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Genomic history of the origin and domestication of common bean unveils its closest sister species.Genomic introgressionAdaptive traitsFeijãoPhaseolus vulgarisDomesticationBiological speciationGenomicsBackground: 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.MARTHA RENDÓN-ANAYA, CINVESTAV, México; JOSAPHAT M. MONTERO-VARGAS, CINVESTAV, México; SOLEDAD SABURIDO-ALVAREZ, CINVESTAV, México; ANNA VLASOVA, CENTRE FOR GENOMIC REGULATION, Barcelona; SALVADOR CAPELLA-GUTIERREZ, CENTRE FOR GENOMIC REGULATION, Barcelona; JOSE JUAN ORDAZ-ORTIZ, CINVESTAV, México; O. MARIO AGUILAR, UNLP-CONICET, Argentina; ROSANA PEREIRA VIANELLO, CNPAF; MARTA SANTALLA, NATIONAL SPANISH RESEARCH COUNCIL, Espanha; LUIS DELAYE, CINVESTAV, México; TONI GABALDON, CENTRE FOR GENOMIC REGULATION, Barcelona; PAUL GEPTS, UNIVERSITY OF CALIFORNIA, Davis; ROBERT WINKLER, CINVESTAV, México; RODERIC GUIGÓ, CENTRE FOR GENOMIC REGULATION, Barcelona; ALFONSO DELGADO-SALINAS, UNIVERSIDAD NACIONAL AUTÓNOMA DE MEXICO; ALFREDO HERRERA-ESTRELLA, CINVESTAV, México.RENDÓN-ANAYA, M.MONTERO-VARGAS, J. M.SABURIDO-ALVAREZ, S.VLASOVA, A.CAPELLA-GUTIERREZ, S.ORDAZ-ORTIZ, J. J.AGUILAR, O. M.VIANELLO, R. P.SANTALLA, M.DELAYE, L.GABALDÓN, T.GEPTS, P.WINKLER, R.GUIGÓ, R.DELGADO-SALINAS, A.HERRERA-ESTRELLA, A.2017-11-02T08:59:47Z2017-11-02T08:59:47Z2017-10-3120172017-11-02T08:59:47Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleGenome Biology, v. 18, n. 1, p. 1-17, Mar. 2017.http://www.alice.cnptia.embrapa.br/alice/handle/doc/10785200.1186/s13059-017-1190-6enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2017-11-02T08:59:55Zoai:www.alice.cnptia.embrapa.br:doc/1078520Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542017-11-02T08:59:55falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542017-11-02T08:59:55Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false |
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, M. Genomic introgression Adaptive traits Feijão Phaseolus vulgaris Domestication Biological speciation Genomics |
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. |
author |
RENDÓN-ANAYA, M. |
author_facet |
RENDÓN-ANAYA, M. MONTERO-VARGAS, J. M. SABURIDO-ALVAREZ, S. VLASOVA, A. CAPELLA-GUTIERREZ, S. ORDAZ-ORTIZ, J. J. AGUILAR, O. M. VIANELLO, R. P. SANTALLA, M. DELAYE, L. GABALDÓN, T. GEPTS, P. WINKLER, R. GUIGÓ, R. DELGADO-SALINAS, A. HERRERA-ESTRELLA, A. |
author_role |
author |
author2 |
MONTERO-VARGAS, J. M. SABURIDO-ALVAREZ, S. VLASOVA, A. CAPELLA-GUTIERREZ, S. ORDAZ-ORTIZ, J. J. AGUILAR, O. M. VIANELLO, R. P. SANTALLA, M. DELAYE, L. GABALDÓN, T. GEPTS, P. WINKLER, R. GUIGÓ, R. DELGADO-SALINAS, A. HERRERA-ESTRELLA, A. |
author2_role |
author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
MARTHA RENDÓN-ANAYA, CINVESTAV, México; JOSAPHAT M. MONTERO-VARGAS, CINVESTAV, México; SOLEDAD SABURIDO-ALVAREZ, CINVESTAV, México; ANNA VLASOVA, CENTRE FOR GENOMIC REGULATION, Barcelona; SALVADOR CAPELLA-GUTIERREZ, CENTRE FOR GENOMIC REGULATION, Barcelona; JOSE JUAN ORDAZ-ORTIZ, CINVESTAV, México; O. MARIO AGUILAR, UNLP-CONICET, Argentina; ROSANA PEREIRA VIANELLO, CNPAF; MARTA SANTALLA, NATIONAL SPANISH RESEARCH COUNCIL, Espanha; LUIS DELAYE, CINVESTAV, México; TONI GABALDON, CENTRE FOR GENOMIC REGULATION, Barcelona; PAUL GEPTS, UNIVERSITY OF CALIFORNIA, Davis; ROBERT WINKLER, CINVESTAV, México; RODERIC GUIGÓ, CENTRE FOR GENOMIC REGULATION, Barcelona; ALFONSO DELGADO-SALINAS, UNIVERSIDAD NACIONAL AUTÓNOMA DE MEXICO; ALFREDO HERRERA-ESTRELLA, CINVESTAV, México. |
dc.contributor.author.fl_str_mv |
RENDÓN-ANAYA, M. MONTERO-VARGAS, J. M. SABURIDO-ALVAREZ, S. VLASOVA, A. CAPELLA-GUTIERREZ, S. ORDAZ-ORTIZ, J. J. AGUILAR, O. M. VIANELLO, R. P. SANTALLA, M. DELAYE, L. GABALDÓN, T. GEPTS, P. WINKLER, R. GUIGÓ, R. DELGADO-SALINAS, A. HERRERA-ESTRELLA, A. |
dc.subject.por.fl_str_mv |
Genomic introgression Adaptive traits Feijão Phaseolus vulgaris Domestication Biological speciation Genomics |
topic |
Genomic introgression Adaptive traits Feijão Phaseolus vulgaris Domestication Biological speciation Genomics |
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 |
2017-11-02T08:59:47Z 2017-11-02T08:59:47Z 2017-10-31 2017 2017-11-02T08:59:47Z |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
Genome Biology, v. 18, n. 1, p. 1-17, Mar. 2017. http://www.alice.cnptia.embrapa.br/alice/handle/doc/1078520 0.1186/s13059-017-1190-6 |
identifier_str_mv |
Genome Biology, v. 18, n. 1, p. 1-17, Mar. 2017. 0.1186/s13059-017-1190-6 |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1078520 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA |
instname_str |
Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
instacron_str |
EMBRAPA |
institution |
EMBRAPA |
reponame_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
collection |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
repository.name.fl_str_mv |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
repository.mail.fl_str_mv |
cg-riaa@embrapa.br |
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1794503443685048320 |