Caracterização de seqüências expressas do genoma café potencialmente relacionadas com a resistência a doenças
Autor(a) principal: | |
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Data de Publicação: | 2007 |
Tipo de documento: | Dissertação |
Idioma: | por |
Título da fonte: | LOCUS Repositório Institucional da UFV |
Texto Completo: | http://locus.ufv.br/handle/123456789/4825 |
Resumo: | Sequences potentially involved with the coffee resistance were identified, by in silico analyses, using information generated by the Projeto Brasileiro do Genoma Café (PBGC). For that, three strategies were used. Initially, keywords related to the plants resistance mechanism to pathogens were searched in scientific literature and used as drivers for data mining. Using the available tools at the PBGC bioinformatics platform, ESTs (Expressed Sequence Tags) related to each one of these words were identified. The search for similarities between some published sequences and sequences from the PBGC, by using the BLAST program was another strategy. The Electronic Northern, a tool developed by the Laboratório de Genômica e Expressão (LGE), was also used. Those strategies allowed the identification of 14,060 sequences of the PBGC. These sequences were similar to proteins known to be related to de plant disease defense process, for instance chitinase, kinase protein, cytochrome P450, disease resistance protein, pathogenesis related protein, LRR and NBS proteins, hypersensibility induced protein among others. The biological processes with witch these sequences are involved included metabolism, transport, transcription regulation, protein folding, biosynthesis and others. The ontology-based global analysis for molecular function showed that the genes are involved with metabolism, external stimulus response, cellular differentiation, nucleic acid binding, nucleotide binding, defense response, apoptosis and others. Aiming to verify the involvement of these sequences with the coffee tree resistance to leaf rust, 40 primers were designed to amplify the mined sequences. The primers were synthesized using the computational program Primer3 and their stability was tested by the program PrimerSelect. Different PCR conditions were tested. Using optimized reaction and amplification conditions, those 40 primers were tested in 12 resistant and 12 susceptible genotypes to Hemileia vastatrix, fungus that causes coffee leaf rust. Twenty nine of those resulted in unique and sharp bands, and only one of these was polymorphic. The 40 primers permitted to find one molecular marker polymorphic between the resistant and susceptible genotypes. This marker amplifies a region of the DNA which corresponds to a Coffea Arabica ORF for disease resistance protein. |
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Alvarenga, Samuel Mazzinghyhttp://lattes.cnpq.br/6208150945096223Caixeta, Eveline Teixeirahttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4728636Z7Zambolim, Eunize Macielhttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4783380J6Sakiyama, Ney Sussumuhttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4781483H8Cruz, Cosme Damiãohttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4788274A6Silva, Felipe Rodrigues dahttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4733948J92015-03-26T13:42:37Z2007-12-132015-03-26T13:42:37Z2007-07-16ALVARENGA, Samuel Mazzinghy. Caracterization of expressed sequences from coffee genome potentially related with the resistance to diseases. 2007. 123 f. Dissertação (Mestrado em Genética animal; Genética molecular e de microrganismos; Genética quantitativa; Genética vegetal; Me) - Universidade Federal de Viçosa, Viçosa, 2007.http://locus.ufv.br/handle/123456789/4825Sequences potentially involved with the coffee resistance were identified, by in silico analyses, using information generated by the Projeto Brasileiro do Genoma Café (PBGC). For that, three strategies were used. Initially, keywords related to the plants resistance mechanism to pathogens were searched in scientific literature and used as drivers for data mining. Using the available tools at the PBGC bioinformatics platform, ESTs (Expressed Sequence Tags) related to each one of these words were identified. The search for similarities between some published sequences and sequences from the PBGC, by using the BLAST program was another strategy. The Electronic Northern, a tool developed by the Laboratório de Genômica e Expressão (LGE), was also used. Those strategies allowed the identification of 14,060 sequences of the PBGC. These sequences were similar to proteins known to be related to de plant disease defense process, for instance chitinase, kinase protein, cytochrome P450, disease resistance protein, pathogenesis related protein, LRR and NBS proteins, hypersensibility induced protein among others. The biological processes with witch these sequences are involved included metabolism, transport, transcription regulation, protein folding, biosynthesis and others. The ontology-based global analysis for molecular function showed that the genes are involved with metabolism, external stimulus response, cellular differentiation, nucleic acid binding, nucleotide binding, defense response, apoptosis and others. Aiming to verify the involvement of these sequences with the coffee tree resistance to leaf rust, 40 primers were designed to amplify the mined sequences. The primers were synthesized using the computational program Primer3 and their stability was tested by the program PrimerSelect. Different PCR conditions were tested. Using optimized reaction and amplification conditions, those 40 primers were tested in 12 resistant and 12 susceptible genotypes to Hemileia vastatrix, fungus that causes coffee leaf rust. Twenty nine of those resulted in unique and sharp bands, and only one of these was polymorphic. The 40 primers permitted to find one molecular marker polymorphic between the resistant and susceptible genotypes. This marker amplifies a region of the DNA which corresponds to a Coffea Arabica ORF for disease resistance protein.Seqüências potencialmente envolvidas na resistência do cafeeiro a doenças foram identificadas, por meio de análise in silico, a partir das informações geradas pelo Projeto Brasileiro do Genoma Café (PBGC). Para isso foram usadas três estratégias. Inicialmente, palavras-chave correspondentes a termos relacionados aos mecanismos de resistência de plantas a patógenos foram identificadas na literatura e utilizadas como iscas para a mineração dos dados. Com o auxílio de ferramentas disponíveis na plataforma de bioinformática do PBGC, foram identificadas ESTs (Expressed Sequence Tags) relacionadas a cada uma destas palavras. Outra estratégia utilizada foi a busca por similaridades entre algumas seqüências públicas envolvidas com a resistência do cafeeiro a doenças com as seqüências do PBGC, por meio do programa BLAST. Utilizou-se, também, o Electronic Northern, uma ferramenta desenvolvida pelo Laboratório de Genômica e Expressão (LGE). A mineração, usando as três estratégias, identificou 14.060 seqüências do PBGC. Essas seqüências apresentaram similaridade com proteínas conhecidamente relacionadas com o processo de defesa da planta contra doenças como, por exemplo, quitinase, proteína quinase, citocromo P450, proteína de resistência a doenças, proteína relacionada com patogênese, proteínas com domínio LRR e NBS, proteínas induzidas por hipersensibilidade, entre outras. Os processos biológicos com os quais essas seqüências estão envolvidas incluíram metabolismo, transporte, regulação da transcrição, enovelamento de proteínas, biossíntese entre outros. A análise global baseada em ontologia de função molecular das seqüências obtidas mostrou que os genes estão envolvidos com metabolismo, resposta a estímulos externos, diferenciação celular, ligação a ácidos nucléicos, ligação a nucleotídeos, resposta de defesa, apoptose entre outras. Visando verificar o envolvimento destas seqüências com a resistência do cafeeiro à ferrugem foram desenhados 40 primers para amplificar algumas das seqüências mineradas. Os primers foram desenhados com o programa computacional Primer3 e a estabilidade desses foi verificada por meio do programa PrimerSelect. Diferentes concentrações dos componentes da reação de PCR foram analisadas. Utilizando as condições de reação e amplificação otimizadas, os 40 primers foram testados em 12 genótipos resistentes e 12 susceptíveis a Hemileia vastatrix, fungo causador da ferrugem. Vinte e nove destes 40 primers resultaram em bandas únicas e bem definidas, sendo um polimórfico. Este trabalho permitiu obter, até o momento, um marcador molecular polimórfico entre os indivíduos resistentes e susceptíveis. Esse marcador, denominado CARF 005, amplifica uma região do DNA que corresponde a uma ORF parcial de Coffea arabica que codifica uma proteína de resistência a doenças.Coordenação de Aperfeiçoamento de Pessoal de Nível Superiorapplication/pdfporUniversidade Federal de ViçosaMestrado em Genética e MelhoramentoUFVBRGenética animal; Genética molecular e de microrganismos; Genética quantitativa; Genética vegetal; MeCoffeaGenômicaMarcadores molecularesCoffeaGenomeMolecular markersCNPQ::CIENCIAS BIOLOGICAS::GENETICA::GENETICA VEGETALCaracterização de seqüências expressas do genoma café potencialmente relacionadas com a resistência a doençasCaracterization of expressed sequences from coffee genome potentially related with the resistance to diseasesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/openAccessreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFVORIGINALtexto completo.pdfapplication/pdf1133771https://locus.ufv.br//bitstream/123456789/4825/1/texto%20completo.pdf640defa7d0749c719bdf5d760421654aMD51TEXTtexto completo.pdf.txttexto completo.pdf.txtExtracted texttext/plain277189https://locus.ufv.br//bitstream/123456789/4825/2/texto%20completo.pdf.txtdd28a62cd9b5fe02f791dade1dd4f4a8MD52THUMBNAILtexto completo.pdf.jpgtexto completo.pdf.jpgIM Thumbnailimage/jpeg3812https://locus.ufv.br//bitstream/123456789/4825/3/texto%20completo.pdf.jpgf86bc5d506147ffac2b320f50296714aMD53123456789/48252016-04-10 23:17:28.375oai:locus.ufv.br:123456789/4825Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452016-04-11T02:17:28LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false |
dc.title.por.fl_str_mv |
Caracterização de seqüências expressas do genoma café potencialmente relacionadas com a resistência a doenças |
dc.title.alternative.eng.fl_str_mv |
Caracterization of expressed sequences from coffee genome potentially related with the resistance to diseases |
title |
Caracterização de seqüências expressas do genoma café potencialmente relacionadas com a resistência a doenças |
spellingShingle |
Caracterização de seqüências expressas do genoma café potencialmente relacionadas com a resistência a doenças Alvarenga, Samuel Mazzinghy Coffea Genômica Marcadores moleculares Coffea Genome Molecular markers CNPQ::CIENCIAS BIOLOGICAS::GENETICA::GENETICA VEGETAL |
title_short |
Caracterização de seqüências expressas do genoma café potencialmente relacionadas com a resistência a doenças |
title_full |
Caracterização de seqüências expressas do genoma café potencialmente relacionadas com a resistência a doenças |
title_fullStr |
Caracterização de seqüências expressas do genoma café potencialmente relacionadas com a resistência a doenças |
title_full_unstemmed |
Caracterização de seqüências expressas do genoma café potencialmente relacionadas com a resistência a doenças |
title_sort |
Caracterização de seqüências expressas do genoma café potencialmente relacionadas com a resistência a doenças |
author |
Alvarenga, Samuel Mazzinghy |
author_facet |
Alvarenga, Samuel Mazzinghy |
author_role |
author |
dc.contributor.authorLattes.por.fl_str_mv |
http://lattes.cnpq.br/6208150945096223 |
dc.contributor.author.fl_str_mv |
Alvarenga, Samuel Mazzinghy |
dc.contributor.advisor-co1.fl_str_mv |
Caixeta, Eveline Teixeira |
dc.contributor.advisor-co1Lattes.fl_str_mv |
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4728636Z7 |
dc.contributor.advisor-co2.fl_str_mv |
Zambolim, Eunize Maciel |
dc.contributor.advisor-co2Lattes.fl_str_mv |
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4783380J6 |
dc.contributor.advisor1.fl_str_mv |
Sakiyama, Ney Sussumu |
dc.contributor.advisor1Lattes.fl_str_mv |
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4781483H8 |
dc.contributor.referee1.fl_str_mv |
Cruz, Cosme Damião |
dc.contributor.referee1Lattes.fl_str_mv |
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4788274A6 |
dc.contributor.referee2.fl_str_mv |
Silva, Felipe Rodrigues da |
dc.contributor.referee2Lattes.fl_str_mv |
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4733948J9 |
contributor_str_mv |
Caixeta, Eveline Teixeira Zambolim, Eunize Maciel Sakiyama, Ney Sussumu Cruz, Cosme Damião Silva, Felipe Rodrigues da |
dc.subject.por.fl_str_mv |
Coffea Genômica Marcadores moleculares |
topic |
Coffea Genômica Marcadores moleculares Coffea Genome Molecular markers CNPQ::CIENCIAS BIOLOGICAS::GENETICA::GENETICA VEGETAL |
dc.subject.eng.fl_str_mv |
Coffea Genome Molecular markers |
dc.subject.cnpq.fl_str_mv |
CNPQ::CIENCIAS BIOLOGICAS::GENETICA::GENETICA VEGETAL |
description |
Sequences potentially involved with the coffee resistance were identified, by in silico analyses, using information generated by the Projeto Brasileiro do Genoma Café (PBGC). For that, three strategies were used. Initially, keywords related to the plants resistance mechanism to pathogens were searched in scientific literature and used as drivers for data mining. Using the available tools at the PBGC bioinformatics platform, ESTs (Expressed Sequence Tags) related to each one of these words were identified. The search for similarities between some published sequences and sequences from the PBGC, by using the BLAST program was another strategy. The Electronic Northern, a tool developed by the Laboratório de Genômica e Expressão (LGE), was also used. Those strategies allowed the identification of 14,060 sequences of the PBGC. These sequences were similar to proteins known to be related to de plant disease defense process, for instance chitinase, kinase protein, cytochrome P450, disease resistance protein, pathogenesis related protein, LRR and NBS proteins, hypersensibility induced protein among others. The biological processes with witch these sequences are involved included metabolism, transport, transcription regulation, protein folding, biosynthesis and others. The ontology-based global analysis for molecular function showed that the genes are involved with metabolism, external stimulus response, cellular differentiation, nucleic acid binding, nucleotide binding, defense response, apoptosis and others. Aiming to verify the involvement of these sequences with the coffee tree resistance to leaf rust, 40 primers were designed to amplify the mined sequences. The primers were synthesized using the computational program Primer3 and their stability was tested by the program PrimerSelect. Different PCR conditions were tested. Using optimized reaction and amplification conditions, those 40 primers were tested in 12 resistant and 12 susceptible genotypes to Hemileia vastatrix, fungus that causes coffee leaf rust. Twenty nine of those resulted in unique and sharp bands, and only one of these was polymorphic. The 40 primers permitted to find one molecular marker polymorphic between the resistant and susceptible genotypes. This marker amplifies a region of the DNA which corresponds to a Coffea Arabica ORF for disease resistance protein. |
publishDate |
2007 |
dc.date.available.fl_str_mv |
2007-12-13 2015-03-26T13:42:37Z |
dc.date.issued.fl_str_mv |
2007-07-16 |
dc.date.accessioned.fl_str_mv |
2015-03-26T13:42:37Z |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/masterThesis |
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masterThesis |
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dc.identifier.citation.fl_str_mv |
ALVARENGA, Samuel Mazzinghy. Caracterization of expressed sequences from coffee genome potentially related with the resistance to diseases. 2007. 123 f. Dissertação (Mestrado em Genética animal; Genética molecular e de microrganismos; Genética quantitativa; Genética vegetal; Me) - Universidade Federal de Viçosa, Viçosa, 2007. |
dc.identifier.uri.fl_str_mv |
http://locus.ufv.br/handle/123456789/4825 |
identifier_str_mv |
ALVARENGA, Samuel Mazzinghy. Caracterization of expressed sequences from coffee genome potentially related with the resistance to diseases. 2007. 123 f. Dissertação (Mestrado em Genética animal; Genética molecular e de microrganismos; Genética quantitativa; Genética vegetal; Me) - Universidade Federal de Viçosa, Viçosa, 2007. |
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Universidade Federal de Viçosa |
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UFV |
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BR |
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Genética animal; Genética molecular e de microrganismos; Genética quantitativa; Genética vegetal; Me |
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Universidade Federal de Viçosa |
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