Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1038/s41598-017-18800-1 http://hdl.handle.net/11449/160014 |
Resumo: | Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley. |
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Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica LLipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley.Brazilian Coffee Research ConsortiumCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Ciencia sem FronteirasBrazilian Coffee Research Consortium, INCT CafeConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Inst Agron Parana, Lab Biotecnol Vegetal, BR-86047902 Londrina, PR, BrazilCIRAD, UMR AGAP, F-34398 Montpellier, FranceEmpresa Brasileira Pesquisa Agr, BR-0770901 Brasilia, DF, BrazilUniv Estadual Paulista, Inst Biociencias, BR-13506900 Rio Claro, SP, BrazilUniv Montpellier, IRD, CIRAD, IPME, BP 64501, F-34394 Montpellier, FranceUniv Montpellier, AGAP, CIRAD, INRA,Montpellier SupAgro, Montpellier, FranceUniv Estadual Paulista, Inst Biociencias, BR-13506900 Rio Claro, SP, BrazilCAPES: 1203-001CAPES: ANR-10-LABX-0001-01CAPES: 015/13Ciencia sem Fronteiras: CAPES PVE 084/13Nature Publishing GroupInst Agron ParanaCIRADEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Universidade Estadual Paulista (Unesp)Univ MontpellierSant'Ana, Gustavo C.Pereira, Luiz F. P.Pot, DavidIvamoto, Suzana T. [UNESP]Domingues, Douglas S. [UNESP]Ferreira, Rafaelle V.Pagiatto, Natalia F.Silva, Bruna S. R. daNogueira, Livia M.Kitzberger, Cintia S. G.Scholz, Maria B. S.Oliveira, Fernanda F. deSera, Gustavo H.Padilha, LilianLabouisse, Jean-PierreGuyot, RomainCharmetant, PierreLeroy, Thierry2018-11-26T15:46:08Z2018-11-26T15:46:08Z2018-01-11info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article12application/pdfhttp://dx.doi.org/10.1038/s41598-017-18800-1Scientific Reports. London: Nature Publishing Group, v. 8, 12 p., 2018.2045-2322http://hdl.handle.net/11449/16001410.1038/s41598-017-18800-1WOS:000419941000006WOS000419941000006.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengScientific Reports1,533info:eu-repo/semantics/openAccess2023-11-04T06:11:29Zoai:repositorio.unesp.br:11449/160014Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-11-04T06:11:29Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L |
title |
Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L |
spellingShingle |
Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L Sant'Ana, Gustavo C. |
title_short |
Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L |
title_full |
Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L |
title_fullStr |
Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L |
title_full_unstemmed |
Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L |
title_sort |
Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L |
author |
Sant'Ana, Gustavo C. |
author_facet |
Sant'Ana, Gustavo C. Pereira, Luiz F. P. Pot, David Ivamoto, Suzana T. [UNESP] Domingues, Douglas S. [UNESP] Ferreira, Rafaelle V. Pagiatto, Natalia F. Silva, Bruna S. R. da Nogueira, Livia M. Kitzberger, Cintia S. G. Scholz, Maria B. S. Oliveira, Fernanda F. de Sera, Gustavo H. Padilha, Lilian Labouisse, Jean-Pierre Guyot, Romain Charmetant, Pierre Leroy, Thierry |
author_role |
author |
author2 |
Pereira, Luiz F. P. Pot, David Ivamoto, Suzana T. [UNESP] Domingues, Douglas S. [UNESP] Ferreira, Rafaelle V. Pagiatto, Natalia F. Silva, Bruna S. R. da Nogueira, Livia M. Kitzberger, Cintia S. G. Scholz, Maria B. S. Oliveira, Fernanda F. de Sera, Gustavo H. Padilha, Lilian Labouisse, Jean-Pierre Guyot, Romain Charmetant, Pierre Leroy, Thierry |
author2_role |
author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Inst Agron Parana CIRAD Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Universidade Estadual Paulista (Unesp) Univ Montpellier |
dc.contributor.author.fl_str_mv |
Sant'Ana, Gustavo C. Pereira, Luiz F. P. Pot, David Ivamoto, Suzana T. [UNESP] Domingues, Douglas S. [UNESP] Ferreira, Rafaelle V. Pagiatto, Natalia F. Silva, Bruna S. R. da Nogueira, Livia M. Kitzberger, Cintia S. G. Scholz, Maria B. S. Oliveira, Fernanda F. de Sera, Gustavo H. Padilha, Lilian Labouisse, Jean-Pierre Guyot, Romain Charmetant, Pierre Leroy, Thierry |
description |
Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-11-26T15:46:08Z 2018-11-26T15:46:08Z 2018-01-11 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1038/s41598-017-18800-1 Scientific Reports. London: Nature Publishing Group, v. 8, 12 p., 2018. 2045-2322 http://hdl.handle.net/11449/160014 10.1038/s41598-017-18800-1 WOS:000419941000006 WOS000419941000006.pdf |
url |
http://dx.doi.org/10.1038/s41598-017-18800-1 http://hdl.handle.net/11449/160014 |
identifier_str_mv |
Scientific Reports. London: Nature Publishing Group, v. 8, 12 p., 2018. 2045-2322 10.1038/s41598-017-18800-1 WOS:000419941000006 WOS000419941000006.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Scientific Reports 1,533 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
12 application/pdf |
dc.publisher.none.fl_str_mv |
Nature Publishing Group |
publisher.none.fl_str_mv |
Nature Publishing Group |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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