In silico analysis of cDNA libraries SH2 and SH3 for the identification of genes responsive to drought in coffee
Autor(a) principal: | |
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Data de Publicação: | 2012 |
Outros Autores: | , |
Tipo de documento: | Artigo |
Idioma: | por |
Título da fonte: | Coffee Science (Online) |
Texto Completo: | https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155 |
Resumo: | Brazil is the largest producer and exporter of coffee and coffee production is a major source of income for small farmers. Drought, which has become increasingly intense over the years, affects the production of these farmers, as it reduces productivity and can even cause entire crop loss. Aiming at the development of drought tolerant crops, several research groups are currently studying the genetic factors involved in plant responses to drought. The construction and sequencing of EST libraries (Expressed Sequence Tags) is a quick and effective way to obtain information about most expressed genes. The functional genome of coffee made available by cDNA sequencing (ESTs), allowed the construction of a large EST database of three different Coffea species . The Coffee EST Database provides a rich source of information for genetic and physiological studies of coffee plants. The goal of this study was to identify genes potentially involved in the response of coffee plants to water stress by means of an (in silico) analysis of available ESTs of the coffee genome database. The methodology was based on in silico comparisons between EST data from libraries SH2 (Coffea arabica) and SH3 (Coffea canephora), with the aid of bioinformatics tools available at the Coffee Genome Database. With the methodology used, several candidate genes have been identified and may be subject to further experimental studies aiming at the establishment of a breeding program based on marker assisted selection for quick development of drought tolerant varieties of coffee. |
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In silico analysis of cDNA libraries SH2 and SH3 for the identification of genes responsive to drought in coffeeAnálise in silico das bibliotecas de cDNA SH2 e SH3 para a identificação de genes responsivos à seca em cafeeiroCoffea arabicaCoffea canephoracDNA sequencingbioinformaticsdrought stress.Coffea arabicaCoffea canephoracDNA sequencingbioinformaticsdrought stressBrazil is the largest producer and exporter of coffee and coffee production is a major source of income for small farmers. Drought, which has become increasingly intense over the years, affects the production of these farmers, as it reduces productivity and can even cause entire crop loss. Aiming at the development of drought tolerant crops, several research groups are currently studying the genetic factors involved in plant responses to drought. The construction and sequencing of EST libraries (Expressed Sequence Tags) is a quick and effective way to obtain information about most expressed genes. The functional genome of coffee made available by cDNA sequencing (ESTs), allowed the construction of a large EST database of three different Coffea species . The Coffee EST Database provides a rich source of information for genetic and physiological studies of coffee plants. The goal of this study was to identify genes potentially involved in the response of coffee plants to water stress by means of an (in silico) analysis of available ESTs of the coffee genome database. The methodology was based on in silico comparisons between EST data from libraries SH2 (Coffea arabica) and SH3 (Coffea canephora), with the aid of bioinformatics tools available at the Coffee Genome Database. With the methodology used, several candidate genes have been identified and may be subject to further experimental studies aiming at the establishment of a breeding program based on marker assisted selection for quick development of drought tolerant varieties of coffee.O Brasil é o maior produtor e exportador de café no mundo e a cafeicultura é uma fonte de renda importante, para pequenos produtores. A seca, que vem se tornando cada vez mais intensa ao longo dos na os, prejudica a produção desses agricultores. Para auxiliar o desenvolvimento de plantas tolerantes à seca, vários grupos de pesquisa buscam uma melhor compreensão dos fatores genéticos envolvidos na resposta das plantas à seca. A construção e sequenciamento de bibliotecas ESTs (Expressed Sequence Tags) é um meio rápido e efetivo de se obter informações acerca da maioria dos genes expressos. O genoma funcional, do cafeeiro realizado por meio do sequenciamento de cDNAs (ESTs), possibilitou a construção de um amplo banco de dados de ESTs com sequências de três espécies distintas de Coffea. A base de dados do genoma café constitui uma rica fonte de informações para estudos genéticos e fisiológicos do cafeeiro. Objetivou-se, no presente trabalho identificar genes candidatos (GC), potencialmente envolvidos na resposta ao estresse hídrico em cafeeiro, a partir de uma análise in silico dos ESTs disponíveis na base de dados do genoma café. Para essas análises foram utilizadas comparações in silico entre os dados de ESTs das bibliotecas SH2 (Coffea arabica) e SH3 (Coffea canephora), com o auxílio das ferramentas de bioinformática disponíveis na base de dados do genoma café. Com a metodologia utilizada, vários GC foram identificados e podem ser objeto de estudos experimentais posteriores, visando a seleção assistida por marcadores moleculares e para a rápida obtenção de variedades de café tolerantes à seca.Editora UFLA2012-06-27info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfimage/tiffimage/tiffimage/tiffimage/tiffimage/tiffimage/tiffhttps://coffeescience.ufla.br/index.php/Coffeescience/article/view/155Coffee Science - ISSN 1984-3909; Vol. 7 No. 1 (2012); 1-19Coffee Science; Vol. 7 Núm. 1 (2012); 1-19Coffee Science; v. 7 n. 1 (2012); 1-191984-3909reponame:Coffee Science (Online)instname:Universidade Federal de Lavras (UFLA)instacron:UFLAporhttps://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/pdfhttps://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/976https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/977https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/978https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/979https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/980https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/981Copyright (c) 2012 Coffee Science - ISSN 1984-3909https://creativecommons.org/info:eu-repo/semantics/openAccessVinecky, FelipeSilva, Felipe Rodrigues daAndrade, Alan Carvalho2013-02-24T12:41:59Zoai:coffeescience.ufla.br:article/155Revistahttps://coffeescience.ufla.br/index.php/CoffeesciencePUBhttps://coffeescience.ufla.br/index.php/Coffeescience/oaicoffeescience@dag.ufla.br||coffeescience@dag.ufla.br|| alvaro-cozadi@hotmail.com1984-39091809-6875opendoar:2024-05-21T19:53:32.013852Coffee Science (Online) - Universidade Federal de Lavras (UFLA)true |
dc.title.none.fl_str_mv |
In silico analysis of cDNA libraries SH2 and SH3 for the identification of genes responsive to drought in coffee Análise in silico das bibliotecas de cDNA SH2 e SH3 para a identificação de genes responsivos à seca em cafeeiro |
title |
In silico analysis of cDNA libraries SH2 and SH3 for the identification of genes responsive to drought in coffee |
spellingShingle |
In silico analysis of cDNA libraries SH2 and SH3 for the identification of genes responsive to drought in coffee Vinecky, Felipe Coffea arabica Coffea canephora cDNA sequencing bioinformatics drought stress. Coffea arabica Coffea canephora cDNA sequencing bioinformatics drought stress |
title_short |
In silico analysis of cDNA libraries SH2 and SH3 for the identification of genes responsive to drought in coffee |
title_full |
In silico analysis of cDNA libraries SH2 and SH3 for the identification of genes responsive to drought in coffee |
title_fullStr |
In silico analysis of cDNA libraries SH2 and SH3 for the identification of genes responsive to drought in coffee |
title_full_unstemmed |
In silico analysis of cDNA libraries SH2 and SH3 for the identification of genes responsive to drought in coffee |
title_sort |
In silico analysis of cDNA libraries SH2 and SH3 for the identification of genes responsive to drought in coffee |
author |
Vinecky, Felipe |
author_facet |
Vinecky, Felipe Silva, Felipe Rodrigues da Andrade, Alan Carvalho |
author_role |
author |
author2 |
Silva, Felipe Rodrigues da Andrade, Alan Carvalho |
author2_role |
author author |
dc.contributor.author.fl_str_mv |
Vinecky, Felipe Silva, Felipe Rodrigues da Andrade, Alan Carvalho |
dc.subject.por.fl_str_mv |
Coffea arabica Coffea canephora cDNA sequencing bioinformatics drought stress. Coffea arabica Coffea canephora cDNA sequencing bioinformatics drought stress |
topic |
Coffea arabica Coffea canephora cDNA sequencing bioinformatics drought stress. Coffea arabica Coffea canephora cDNA sequencing bioinformatics drought stress |
description |
Brazil is the largest producer and exporter of coffee and coffee production is a major source of income for small farmers. Drought, which has become increasingly intense over the years, affects the production of these farmers, as it reduces productivity and can even cause entire crop loss. Aiming at the development of drought tolerant crops, several research groups are currently studying the genetic factors involved in plant responses to drought. The construction and sequencing of EST libraries (Expressed Sequence Tags) is a quick and effective way to obtain information about most expressed genes. The functional genome of coffee made available by cDNA sequencing (ESTs), allowed the construction of a large EST database of three different Coffea species . The Coffee EST Database provides a rich source of information for genetic and physiological studies of coffee plants. The goal of this study was to identify genes potentially involved in the response of coffee plants to water stress by means of an (in silico) analysis of available ESTs of the coffee genome database. The methodology was based on in silico comparisons between EST data from libraries SH2 (Coffea arabica) and SH3 (Coffea canephora), with the aid of bioinformatics tools available at the Coffee Genome Database. With the methodology used, several candidate genes have been identified and may be subject to further experimental studies aiming at the establishment of a breeding program based on marker assisted selection for quick development of drought tolerant varieties of coffee. |
publishDate |
2012 |
dc.date.none.fl_str_mv |
2012-06-27 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155 |
url |
https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155 |
dc.language.iso.fl_str_mv |
por |
language |
por |
dc.relation.none.fl_str_mv |
https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/pdf https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/976 https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/977 https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/978 https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/979 https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/980 https://coffeescience.ufla.br/index.php/Coffeescience/article/view/155/981 |
dc.rights.driver.fl_str_mv |
Copyright (c) 2012 Coffee Science - ISSN 1984-3909 https://creativecommons.org/ info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Copyright (c) 2012 Coffee Science - ISSN 1984-3909 https://creativecommons.org/ |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf image/tiff image/tiff image/tiff image/tiff image/tiff image/tiff |
dc.publisher.none.fl_str_mv |
Editora UFLA |
publisher.none.fl_str_mv |
Editora UFLA |
dc.source.none.fl_str_mv |
Coffee Science - ISSN 1984-3909; Vol. 7 No. 1 (2012); 1-19 Coffee Science; Vol. 7 Núm. 1 (2012); 1-19 Coffee Science; v. 7 n. 1 (2012); 1-19 1984-3909 reponame:Coffee Science (Online) instname:Universidade Federal de Lavras (UFLA) instacron:UFLA |
instname_str |
Universidade Federal de Lavras (UFLA) |
instacron_str |
UFLA |
institution |
UFLA |
reponame_str |
Coffee Science (Online) |
collection |
Coffee Science (Online) |
repository.name.fl_str_mv |
Coffee Science (Online) - Universidade Federal de Lavras (UFLA) |
repository.mail.fl_str_mv |
coffeescience@dag.ufla.br||coffeescience@dag.ufla.br|| alvaro-cozadi@hotmail.com |
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1799874918399082496 |