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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital; Embrapa Café. |
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Data corrente: |
20/04/2016 |
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Data da última atualização: |
22/02/2017 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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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. |
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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. |
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Título: |
Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars. |
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Ano de publicação: |
2016 |
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Fonte/Imprenta: |
BMC Plant Biology, v. 16, n. 94, p. 1-18, 2016. |
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DOI: |
10.1186/s12870-016-0777-5 |
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Idioma: |
Inglês |
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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 |
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Palavras-Chave: |
Candidate gene; Coffee; Differential gene expression; Real-time PCR (RT-qPCR); RNA-Seq. |
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Thesagro: |
Café; Coffea Arábica; Resistência à seca; Seca. |
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Thesaurus Nal: |
Drought; Drought tolerance; Sequence analysis. |
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Categoria do assunto: |
-- |
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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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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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| 122. |  | TARRAND, J. J.; KRIEG, N. R.; DOBEREINER, J. A taxonomic study of the Spirillum lipoferum group, with descriptions of a new genus, Azospirillum gen. nov. and two species, Azospirillum lipoferum (Beijerinck) comb. nov. and Azospirillum brasilense sp. nov. Canadian Journal of Microbiology, v.24, n.8, p.967-980, 1978.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: Internacional - A |
| Biblioteca(s): Embrapa Agrobiologia. |
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| 139. | | PESSANHA, G. G.; FRANCO, A. A.; DOBEREINER, J.; GROSZMANN, A.; BRITTO, D. P. P. de S. Correlação negativa da nodulação com a produção de feijão (Phaseolus vulgaris) em solos onde nitrogênio não é fator limitante. Pesquisa Agropecuária Brasileira, Rio de Janeiro, v. 7, p. 49-56, 1972. (Agronomia, 5). Título em inglês: Negative correlation of nodulation and grain production of beans (Phaseolus vulgaris) in soils where nitrogen is not limiting factor of plant growth.| Biblioteca(s): Embrapa Unidades Centrais. |
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| 140. | | BALDANI, J. I.; BALDANI, V. L. D.; SELDIN, L.; DOBEREINER, J. Characterization of Herbaspirillum seropedicae gen. nov., sp. nov., a root-associated nitrogen-fixing bacterium. International Journal of Systematic Bacteriology, Washington, v. 36, p. 86-93, 1986.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: Internacional - A |
| Biblioteca(s): Embrapa Agrobiologia. |
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| Registros recuperados : 197 | |
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