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Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars.

Mofatto LS, Carneiro Fde A, Vieira NG, Duarte KE, Vidal RO, Alekcevetch JC, Cotta MG, Verdeil JL, Lapeyre-Montes F, Lartaud M, Leroy T, De Bellis F, Pot D, Rodrigues GC, Carazzolle MF, Pereira GA, Andrade AC, Marraccini P - BMC Plant Biol. (2016)

Bottom Line: Genetic diversity for drought tolerance exists within the coffee genus.This may have been related to the thicker cuticle observed on the abaxial leaf surface in IAPAR59 compared to Rubi.The identification of these genes should help advance our understanding of the genetic determinism of drought tolerance in coffee.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Genômica e Expressão (LGE), Departamento de Genética e Evolução, Instituto de Biologia/UNICAMP, Cidade Universitária Zeferino Vaz, 13083-970, Campinas, SP, Brazil.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

Gene ontology (GO) enrichment analysis on a list of differentially expressed genes up- and down-regulated under four conditions. The calculation of fold change was based on the ratio of: (a) I59-D/I59-C; (b) RUB-D/RUB-C; (c) RUB-C/I59-C; and (d) RUB-D/I59-D. The Y axis indicates the number of genes normalized by the total number of genes used in each comparison from each library. Cultivars (RUB: Rubi and I59: IAPAR59) of C. arabica and treatments (C: control and D: drought) are indicated
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Fig3: Gene ontology (GO) enrichment analysis on a list of differentially expressed genes up- and down-regulated under four conditions. The calculation of fold change was based on the ratio of: (a) I59-D/I59-C; (b) RUB-D/RUB-C; (c) RUB-C/I59-C; and (d) RUB-D/I59-D. The Y axis indicates the number of genes normalized by the total number of genes used in each comparison from each library. Cultivars (RUB: Rubi and I59: IAPAR59) of C. arabica and treatments (C: control and D: drought) are indicated

Mentions: The results of the gene ontology (GO) enrichment analysis are shown in Fig. 3 and all GO enrichment data are listed in Additional file 1: Tables S1 and Additional file 3: Table S2. For IAPAR59, the comparison of drought and control conditions (I59-D/I59-C) identified over-represented GO terms characterized by up-regulated genes involved in expression (gALL_c3501) and translation (gALL_c2033, gALL_c4461, gALL_c6492) processes and in the generation of precursor metabolites and energy (gALL_c921, gALL_c4013, gALL_c4540). For Rubi, a comparison of the RUB-D/RUB-C libraries revealed an over-representation of the following GO terms which were up-regulated: protein metabolic process (gALL_c2021, gALL_c3355), response to stress (gALL_rep_c33197/CaHSP3) and response to abiotic stimulus (gALL_rep_c32771/CaELIP3, gALL_c2829, gALL_rep_c32766). When comparing both cultivars under drought conditions (RUB-D/I59-D), GO terms were identified related to increased enrichment of tropism for up-regulated genes (gALL_c1270, gALL_c1524, gALL_c1864) and photosynthesis for down-regulated genes (gALL_c27215, gALL_rep_c34074, gALL_rep_c34746). Under the control conditions (RUB-C/I59-C), proteins of translational machinery were identified for up-regulated genes (gALL_c3061, gALL_c16674, gALL_c19094) and photosynthesis for down-regulated genes (gALL_rep_c34074, gALL_rep_c37283, gALL_rep_c50892).Fig. 3


Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars.

Mofatto LS, Carneiro Fde A, Vieira NG, Duarte KE, Vidal RO, Alekcevetch JC, Cotta MG, Verdeil JL, Lapeyre-Montes F, Lartaud M, Leroy T, De Bellis F, Pot D, Rodrigues GC, Carazzolle MF, Pereira GA, Andrade AC, Marraccini P - BMC Plant Biol. (2016)

Gene ontology (GO) enrichment analysis on a list of differentially expressed genes up- and down-regulated under four conditions. The calculation of fold change was based on the ratio of: (a) I59-D/I59-C; (b) RUB-D/RUB-C; (c) RUB-C/I59-C; and (d) RUB-D/I59-D. The Y axis indicates the number of genes normalized by the total number of genes used in each comparison from each library. Cultivars (RUB: Rubi and I59: IAPAR59) of C. arabica and treatments (C: control and D: drought) are indicated
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4837521&req=5

Fig3: Gene ontology (GO) enrichment analysis on a list of differentially expressed genes up- and down-regulated under four conditions. The calculation of fold change was based on the ratio of: (a) I59-D/I59-C; (b) RUB-D/RUB-C; (c) RUB-C/I59-C; and (d) RUB-D/I59-D. The Y axis indicates the number of genes normalized by the total number of genes used in each comparison from each library. Cultivars (RUB: Rubi and I59: IAPAR59) of C. arabica and treatments (C: control and D: drought) are indicated
Mentions: The results of the gene ontology (GO) enrichment analysis are shown in Fig. 3 and all GO enrichment data are listed in Additional file 1: Tables S1 and Additional file 3: Table S2. For IAPAR59, the comparison of drought and control conditions (I59-D/I59-C) identified over-represented GO terms characterized by up-regulated genes involved in expression (gALL_c3501) and translation (gALL_c2033, gALL_c4461, gALL_c6492) processes and in the generation of precursor metabolites and energy (gALL_c921, gALL_c4013, gALL_c4540). For Rubi, a comparison of the RUB-D/RUB-C libraries revealed an over-representation of the following GO terms which were up-regulated: protein metabolic process (gALL_c2021, gALL_c3355), response to stress (gALL_rep_c33197/CaHSP3) and response to abiotic stimulus (gALL_rep_c32771/CaELIP3, gALL_c2829, gALL_rep_c32766). When comparing both cultivars under drought conditions (RUB-D/I59-D), GO terms were identified related to increased enrichment of tropism for up-regulated genes (gALL_c1270, gALL_c1524, gALL_c1864) and photosynthesis for down-regulated genes (gALL_c27215, gALL_rep_c34074, gALL_rep_c34746). Under the control conditions (RUB-C/I59-C), proteins of translational machinery were identified for up-regulated genes (gALL_c3061, gALL_c16674, gALL_c19094) and photosynthesis for down-regulated genes (gALL_rep_c34074, gALL_rep_c37283, gALL_rep_c50892).Fig. 3

Bottom Line: Genetic diversity for drought tolerance exists within the coffee genus.This may have been related to the thicker cuticle observed on the abaxial leaf surface in IAPAR59 compared to Rubi.The identification of these genes should help advance our understanding of the genetic determinism of drought tolerance in coffee.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Genômica e Expressão (LGE), Departamento de Genética e Evolução, Instituto de Biologia/UNICAMP, Cidade Universitária Zeferino Vaz, 13083-970, Campinas, SP, Brazil.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus