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Registro Completo |
Biblioteca(s): |
Embrapa Agricultura Digital; Embrapa Café. |
Data corrente: |
20/04/2016 |
Data da última atualização: |
22/02/2017 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Autoria: |
MOFATTO, L. S.; CARNEIRO, F. de A.; VIEIRA, N. G.; DUARTE, K. E.; VIDAL, R. O.; ALEKCEVETCH, J. C.; COTTA, M. G.; VERDEIL, J-L.; LAPEYRE-MONTES, F.; LARTAUD, M.; LEROY, T.; DE BELLIS, F.; POT, D; RODRIGUES, G. C.; CARAZZOLLE, M. F.; PEREIRA, G. A. G.; ANDRADE, A. C.; MARRACCINI, P. |
Afiliação: |
LUCIANA SOUTO MOFATTO, IB/Unicamp; FERNANDA DE ARAÚJO CARNEIRO, CENARGEN; NATALIA GOMES VIEIRA, CENARGEN; KAROLINE ESTEFANI DUARTE, CENARGEN; RAMON OLIVEIRA VIDAL, IB/Unicamp; JEAN CAROS ALEKCEVETCH, CENARGEN; MICHELLE GUITTON COTTA, CENARGEN; JEAN-LUC VERDEIL, CIRAD/UMR/AGAP; FABIENNE LEPEYRE-MONTES, CIRAD/UMR/AGAP; MARC LARTAUD, CIRAD/UMR/AGAP; THIERRY LEROY, CIRAD/UMR/AGAP; FABIEN DE BELLIS, CIRAD/UMR/AGAP; DAVID POT, CIRAD/UMR/AGAP; GUSTAVO COSTA RODRIGUES, CNPTIA; MARCELO FALSARELLA CARAZZOLLE, IB/Unicamp; GONÇALO AMARANTE GUIMARÃES PEREIRA, IB/Unicamp; ALAN CARVALHO ANDRADE, SAPC; PIERRE MARRACCINI, CENARGEN, CIRAD/UMR/AGAP. |
Título: |
Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars. |
Ano de publicação: |
2016 |
Fonte/Imprenta: |
BMC Plant Biology, v. 16, n. 94, p. 1-18, 2016. |
DOI: |
10.1186/s12870-016-0777-5 |
Idioma: |
Inglês |
Conteúdo: |
BACKGROUND: Drought is a widespread limiting factor in coffee plants. It affects plant development, fruit production, bean development and consequently beverage quality. Genetic diversity for drought tolerance exists within the coffee genus. However, the molecular mechanisms underlying the adaptation of coffee plants to drought are largely unknown. In this study, we compared the molecular responses to drought in two commercial cultivars (IAPAR59, drought-tolerant and Rubi, drought-susceptible) of Coffea arabica grown in the field under control (irrigation) and drought conditions using the pyrosequencing of RNA extracted from shoot apices and analysing the expression of 38 candidate genes. RESULTS: Pyrosequencing from shoot apices generated a total of 34.7 Mbp and 535,544 reads enabling the identification of 43,087 clusters (41,512 contigs and 1,575 singletons). These data included 17,719 clusters (16,238 contigs and 1,575 singletons) exclusively from 454 sequencing reads, along with 25,368 hybrid clusters assembled with 454 sequences. The comparison of DNA libraries identified new candidate genes (n = 20) presenting differential expression between IAPAR59 and Rubi and/or drought conditions. Their expression was monitored in plagiotropic buds, together with those of other (n = 18) candidates genes. Under drought conditions, up-regulated expression was observed in IAPAR59 but not in Rubi for CaSTK1 (protein kinase), CaSAMT1 (SAM-dependent methyltransferase), CaSLP1 (plant development) and CaMAS1 (ABA biosynthesis). Interestingly, the expression of lipid-transfer protein (nsLTP) genes was also highly up-regulated under drought conditions in IAPAR59. This may have been related to the thicker cuticle observed on the abaxial leaf surface in IAPAR59 compared to Rubi. CONCLUSIONS: The full transcriptome assembly of C. arabica, followed by functional annotation, enabled us to identify differentially expressed genes related to drought conditions. Using these data, candidate genes were selected and their differential expression profiles were confirmed by qPCR experiments in plagiotropic buds of IAPAR59 and Rubi under drought conditions. As regards the genes up-regulated under drought conditions, specifically in the drought-tolerant IAPAR59, several corresponded to orphan genes but also to genes coding proteins involved in signal transduction pathways, as well as ABA and lipid metabolism, for example. The identification of these genes should help advance our understanding of the genetic determinism of drought tolerance in coffee. MenosBACKGROUND: Drought is a widespread limiting factor in coffee plants. It affects plant development, fruit production, bean development and consequently beverage quality. Genetic diversity for drought tolerance exists within the coffee genus. However, the molecular mechanisms underlying the adaptation of coffee plants to drought are largely unknown. In this study, we compared the molecular responses to drought in two commercial cultivars (IAPAR59, drought-tolerant and Rubi, drought-susceptible) of Coffea arabica grown in the field under control (irrigation) and drought conditions using the pyrosequencing of RNA extracted from shoot apices and analysing the expression of 38 candidate genes. RESULTS: Pyrosequencing from shoot apices generated a total of 34.7 Mbp and 535,544 reads enabling the identification of 43,087 clusters (41,512 contigs and 1,575 singletons). These data included 17,719 clusters (16,238 contigs and 1,575 singletons) exclusively from 454 sequencing reads, along with 25,368 hybrid clusters assembled with 454 sequences. The comparison of DNA libraries identified new candidate genes (n = 20) presenting differential expression between IAPAR59 and Rubi and/or drought conditions. Their expression was monitored in plagiotropic buds, together with those of other (n = 18) candidates genes. Under drought conditions, up-regulated expression was observed in IAPAR59 but not in Rubi for CaSTK1 (protein kinase), CaSAMT1 (SAM-dependent methyltransferase), CaSLP1 (plant deve... Mostrar Tudo |
Palavras-Chave: |
Candidate gene; Coffee; Differential gene expression; Real-time PCR (RT-qPCR); RNA-Seq. |
Thesagro: |
Café; Coffea Arábica; Resistência à seca; Seca. |
Thesaurus Nal: |
Drought; Drought tolerance; Sequence analysis. |
Categoria do assunto: |
-- |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/142466/1/Identification-of-candidate-genes.pdf
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Marc: |
LEADER 03947naa a2200481 a 4500 001 2058399 005 2017-02-22 008 2016 bl uuuu u00u1 u #d 024 7 $a10.1186/s12870-016-0777-5$2DOI 100 1 $aMOFATTO, L. S. 245 $aIdentification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars.$h[electronic resource] 260 $c2016 520 $aBACKGROUND: Drought is a widespread limiting factor in coffee plants. It affects plant development, fruit production, bean development and consequently beverage quality. Genetic diversity for drought tolerance exists within the coffee genus. However, the molecular mechanisms underlying the adaptation of coffee plants to drought are largely unknown. In this study, we compared the molecular responses to drought in two commercial cultivars (IAPAR59, drought-tolerant and Rubi, drought-susceptible) of Coffea arabica grown in the field under control (irrigation) and drought conditions using the pyrosequencing of RNA extracted from shoot apices and analysing the expression of 38 candidate genes. RESULTS: Pyrosequencing from shoot apices generated a total of 34.7 Mbp and 535,544 reads enabling the identification of 43,087 clusters (41,512 contigs and 1,575 singletons). These data included 17,719 clusters (16,238 contigs and 1,575 singletons) exclusively from 454 sequencing reads, along with 25,368 hybrid clusters assembled with 454 sequences. The comparison of DNA libraries identified new candidate genes (n = 20) presenting differential expression between IAPAR59 and Rubi and/or drought conditions. Their expression was monitored in plagiotropic buds, together with those of other (n = 18) candidates genes. Under drought conditions, up-regulated expression was observed in IAPAR59 but not in Rubi for CaSTK1 (protein kinase), CaSAMT1 (SAM-dependent methyltransferase), CaSLP1 (plant development) and CaMAS1 (ABA biosynthesis). Interestingly, the expression of lipid-transfer protein (nsLTP) genes was also highly up-regulated under drought conditions in IAPAR59. This may have been related to the thicker cuticle observed on the abaxial leaf surface in IAPAR59 compared to Rubi. CONCLUSIONS: The full transcriptome assembly of C. arabica, followed by functional annotation, enabled us to identify differentially expressed genes related to drought conditions. Using these data, candidate genes were selected and their differential expression profiles were confirmed by qPCR experiments in plagiotropic buds of IAPAR59 and Rubi under drought conditions. As regards the genes up-regulated under drought conditions, specifically in the drought-tolerant IAPAR59, several corresponded to orphan genes but also to genes coding proteins involved in signal transduction pathways, as well as ABA and lipid metabolism, for example. The identification of these genes should help advance our understanding of the genetic determinism of drought tolerance in coffee. 650 $aDrought 650 $aDrought tolerance 650 $aSequence analysis 650 $aCafé 650 $aCoffea Arábica 650 $aResistência à seca 650 $aSeca 653 $aCandidate gene 653 $aCoffee 653 $aDifferential gene expression 653 $aReal-time PCR (RT-qPCR) 653 $aRNA-Seq 700 1 $aCARNEIRO, F. de A. 700 1 $aVIEIRA, N. G. 700 1 $aDUARTE, K. E. 700 1 $aVIDAL, R. O. 700 1 $aALEKCEVETCH, J. C. 700 1 $aCOTTA, M. G. 700 1 $aVERDEIL, J-L. 700 1 $aLAPEYRE-MONTES, F. 700 1 $aLARTAUD, M. 700 1 $aLEROY, T. 700 1 $aDE BELLIS, F. 700 1 $aPOT, D 700 1 $aRODRIGUES, G. C. 700 1 $aCARAZZOLLE, M. F. 700 1 $aPEREIRA, G. A. G. 700 1 $aANDRADE, A. C. 700 1 $aMARRACCINI, P. 773 $tBMC Plant Biology$gv. 16, n. 94, p. 1-18, 2016.
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Embrapa Agricultura Digital (CNPTIA) |
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Registro Completo
Biblioteca(s): |
Embrapa Territorial; Embrapa Unidades Centrais. |
Data corrente: |
23/11/2012 |
Data da última atualização: |
23/11/2012 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Circulação/Nível: |
A - 2 |
Autoria: |
BOLFE, E. L.; BATISTELLA, M.; FERREIRA, M. C. |
Afiliação: |
EDSON LUIS BOLFE, CNPM; MATEUS BATISTELLA, CNPM; MARCOS CÉSAR FERREIRA, UNICAMP. |
Título: |
Correlação de variáveis espectrais e estoque de carbono da biomassa aérea de sistemas agroflorestais. |
Ano de publicação: |
2012 |
Fonte/Imprenta: |
Pesquisa Agropecuária Brasileira, Brasilia, DF, v. 47, n. 9, p. 1261-1269, set. 2012. |
Idioma: |
Português |
Conteúdo: |
O objetivo deste trabalho foi avaliar a correlação entre variáveis espectrais e o estoque de carbono da biomassa aérea de sistemas agroflorestais da região de Tomé‑Açu, PA. Foram testados 24 índices de vegetação de três grupos (razão simples, diferença normalizada e complexos), gerados a partir de imagens do sensor TM/ Landsat‑5, adquiridas em 2008. As variáveis obtidas foram correlacionadas, por meio de regressão linear simples, ao estoque de carbono de quatro classes de sistemas agroflorestais, de diferentes idades e composições florísticas. As correlações obtidas entre as variáveis espectrais e o estoque de carbono foram significativas em 47% dos índices testados e variaram de acordo com as diferenças de biomassa nos sistemas analisados. As melhores correlações foram obtidas pelos índices de vegetação de razão simples e de diferença normalizada, em sistemas agroflorestais jovens, e pelos índices de vegetação complexos, em sistemas agroflorestais mais antigos. |
Palavras-Chave: |
Crop-livestock-forest integration; Integração lavoura-pecuária-floresta; Land use and land cover; Uso e cobertura da terra. |
Thesagro: |
Sensoriamento remoto. |
Thesaurus NAL: |
Landsat; Remote sensing. |
Categoria do assunto: |
-- |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/70653/1/BolfePAB.pdf
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Marc: |
LEADER 01777naa a2200229 a 4500 001 1940357 005 2012-11-23 008 2012 bl uuuu u00u1 u #d 100 1 $aBOLFE, E. L. 245 $aCorrelação de variáveis espectrais e estoque de carbono da biomassa aérea de sistemas agroflorestais. 260 $c2012 520 $aO objetivo deste trabalho foi avaliar a correlação entre variáveis espectrais e o estoque de carbono da biomassa aérea de sistemas agroflorestais da região de Tomé‑Açu, PA. Foram testados 24 índices de vegetação de três grupos (razão simples, diferença normalizada e complexos), gerados a partir de imagens do sensor TM/ Landsat‑5, adquiridas em 2008. As variáveis obtidas foram correlacionadas, por meio de regressão linear simples, ao estoque de carbono de quatro classes de sistemas agroflorestais, de diferentes idades e composições florísticas. As correlações obtidas entre as variáveis espectrais e o estoque de carbono foram significativas em 47% dos índices testados e variaram de acordo com as diferenças de biomassa nos sistemas analisados. As melhores correlações foram obtidas pelos índices de vegetação de razão simples e de diferença normalizada, em sistemas agroflorestais jovens, e pelos índices de vegetação complexos, em sistemas agroflorestais mais antigos. 650 $aLandsat 650 $aRemote sensing 650 $aSensoriamento remoto 653 $aCrop-livestock-forest integration 653 $aIntegração lavoura-pecuária-floresta 653 $aLand use and land cover 653 $aUso e cobertura da terra 700 1 $aBATISTELLA, M. 700 1 $aFERREIRA, M. C. 773 $tPesquisa Agropecuária Brasileira, Brasilia, DF$gv. 47, n. 9, p. 1261-1269, set. 2012.
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