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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

Expression profiles of genes up-regulated under drought conditions. Gene expression was analysed in plagiotropic buds of Rubi (RUB) and IAPAR59 (I59) cultivars of C. arabica grown under control (white isobars) and drought (black isobars) conditions. The gene names are indicated in the histograms. Transcript abundances were normalized using the expression of the CaUBQ10 gene as the endogenous control. Results are expressed using RUB-C as the reference sample (Relative expression = 1). Values of three technical replications are presented as mean ± SD (bar)
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Fig4: Expression profiles of genes up-regulated under drought conditions. Gene expression was analysed in plagiotropic buds of Rubi (RUB) and IAPAR59 (I59) cultivars of C. arabica grown under control (white isobars) and drought (black isobars) conditions. The gene names are indicated in the histograms. Transcript abundances were normalized using the expression of the CaUBQ10 gene as the endogenous control. Results are expressed using RUB-C as the reference sample (Relative expression = 1). Values of three technical replications are presented as mean ± SD (bar)

Mentions: Twenty-five genes showing up-regulated expression profiles under drought conditions, mainly in IAPAR59 and to a lesser extent in Rubi, were identified (Fig. 4). This was observed for CaSTK1 which encodes a putative oxidative stress response serine/threonine protein kinase with 87 % identity with a predicted protein of Populus trichocarpa (XP_002299433). In that case, expression of this gene was highly induced by drought in the DT cultivar IAPAR59. Similar profiles were also observed for the CaSAMT1 gene encoding a putative S-adenosyl-L-methionine-dependent methyltransferase and the orphan genes CaUNK2 and CaUNK3. The latter gene had no open reading frame but presented high identity (e-value 2E-45) with the SGN-U637447 contig and also with various coffee ESTs mainly found in C. canephora cherries at early developmental stages (data not shown).Fig. 4


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)

Expression profiles of genes up-regulated under drought conditions. Gene expression was analysed in plagiotropic buds of Rubi (RUB) and IAPAR59 (I59) cultivars of C. arabica grown under control (white isobars) and drought (black isobars) conditions. The gene names are indicated in the histograms. Transcript abundances were normalized using the expression of the CaUBQ10 gene as the endogenous control. Results are expressed using RUB-C as the reference sample (Relative expression = 1). Values of three technical replications are presented as mean ± SD (bar)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4837521&req=5

Fig4: Expression profiles of genes up-regulated under drought conditions. Gene expression was analysed in plagiotropic buds of Rubi (RUB) and IAPAR59 (I59) cultivars of C. arabica grown under control (white isobars) and drought (black isobars) conditions. The gene names are indicated in the histograms. Transcript abundances were normalized using the expression of the CaUBQ10 gene as the endogenous control. Results are expressed using RUB-C as the reference sample (Relative expression = 1). Values of three technical replications are presented as mean ± SD (bar)
Mentions: Twenty-five genes showing up-regulated expression profiles under drought conditions, mainly in IAPAR59 and to a lesser extent in Rubi, were identified (Fig. 4). This was observed for CaSTK1 which encodes a putative oxidative stress response serine/threonine protein kinase with 87 % identity with a predicted protein of Populus trichocarpa (XP_002299433). In that case, expression of this gene was highly induced by drought in the DT cultivar IAPAR59. Similar profiles were also observed for the CaSAMT1 gene encoding a putative S-adenosyl-L-methionine-dependent methyltransferase and the orphan genes CaUNK2 and CaUNK3. The latter gene had no open reading frame but presented high identity (e-value 2E-45) with the SGN-U637447 contig and also with various coffee ESTs mainly found in C. canephora cherries at early developmental stages (data not shown).Fig. 4

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