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Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L

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 histori...

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Autores principales: Sant’Ana, Gustavo C., Pereira, Luiz F. P., Pot, David, Ivamoto, Suzana T., Domingues, Douglas S., Ferreira, Rafaelle V., Pagiatto, Natalia F., da Silva, Bruna S. R., Nogueira, Lívia M., Kitzberger, Cintia S. G., Scholz, Maria B. S., de Oliveira, Fernanda F., Sera, Gustavo H., Padilha, Lilian, Labouisse, Jean-Pierre, Guyot, Romain, Charmetant, Pierre, Leroy, Thierry
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764960/
https://www.ncbi.nlm.nih.gov/pubmed/29323254
http://dx.doi.org/10.1038/s41598-017-18800-1
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author Sant’Ana, Gustavo C.
Pereira, Luiz F. P.
Pot, David
Ivamoto, Suzana T.
Domingues, Douglas S.
Ferreira, Rafaelle V.
Pagiatto, Natalia F.
da Silva, Bruna S. R.
Nogueira, Lívia M.
Kitzberger, Cintia S. G.
Scholz, Maria B. S.
de Oliveira, Fernanda F.
Sera, Gustavo H.
Padilha, Lilian
Labouisse, Jean-Pierre
Guyot, Romain
Charmetant, Pierre
Leroy, Thierry
author_facet Sant’Ana, Gustavo C.
Pereira, Luiz F. P.
Pot, David
Ivamoto, Suzana T.
Domingues, Douglas S.
Ferreira, Rafaelle V.
Pagiatto, Natalia F.
da Silva, Bruna S. R.
Nogueira, Lívia M.
Kitzberger, Cintia S. G.
Scholz, Maria B. S.
de Oliveira, Fernanda F.
Sera, Gustavo H.
Padilha, Lilian
Labouisse, Jean-Pierre
Guyot, Romain
Charmetant, Pierre
Leroy, Thierry
author_sort Sant’Ana, Gustavo C.
collection PubMed
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.
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spelling pubmed-57649602018-01-17 Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L Sant’Ana, Gustavo C. Pereira, Luiz F. P. Pot, David Ivamoto, Suzana T. Domingues, Douglas S. Ferreira, Rafaelle V. Pagiatto, Natalia F. da Silva, Bruna S. R. Nogueira, Lívia M. Kitzberger, Cintia S. G. Scholz, Maria B. S. de Oliveira, Fernanda F. Sera, Gustavo H. Padilha, Lilian Labouisse, Jean-Pierre Guyot, Romain Charmetant, Pierre Leroy, Thierry Sci Rep Article 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. Nature Publishing Group UK 2018-01-11 /pmc/articles/PMC5764960/ /pubmed/29323254 http://dx.doi.org/10.1038/s41598-017-18800-1 Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Sant’Ana, Gustavo C.
Pereira, Luiz F. P.
Pot, David
Ivamoto, Suzana T.
Domingues, Douglas S.
Ferreira, Rafaelle V.
Pagiatto, Natalia F.
da Silva, Bruna S. R.
Nogueira, Lívia M.
Kitzberger, Cintia S. G.
Scholz, Maria B. S.
de Oliveira, Fernanda F.
Sera, Gustavo H.
Padilha, Lilian
Labouisse, Jean-Pierre
Guyot, Romain
Charmetant, Pierre
Leroy, Thierry
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
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_short 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
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764960/
https://www.ncbi.nlm.nih.gov/pubmed/29323254
http://dx.doi.org/10.1038/s41598-017-18800-1
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