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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

Predawn leaf water potentials (Ψpd) measured in plants of C. arabica. Rubi (RUB, triangle) and IAPAR59 (I59, square) cultivars were grown under control (C, open symbols) and drought (D, black symbols) conditions. Ψpd values (expressed in mega-Pascal, MPa) were measured once a week during the 2009 dry season (23-month-old plants) (a). The time scale is in days and months (dd/mm, from 20/05 to 02/10). Vertical bars are standard deviations (n = 9 leaves) and the dashed vertical line (20/08) represents the harvest point of plagiotropic buds for RNA extraction for 454 sequencing and leaves for microscopic analyses. bΨpd of Rubi and IAPAR59 plants (47-month-old plants) measured at the end of the 2011dry season. In this case, Ψpd values ranged from -0.1 to -0.2 MPa for the control conditions, but were below (< -4.0 MPa = severe drought) the range of use of a Scholander-type pressure chamber for drought conditions
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Fig2: Predawn leaf water potentials (Ψpd) measured in plants of C. arabica. Rubi (RUB, triangle) and IAPAR59 (I59, square) cultivars were grown under control (C, open symbols) and drought (D, black symbols) conditions. Ψpd values (expressed in mega-Pascal, MPa) were measured once a week during the 2009 dry season (23-month-old plants) (a). The time scale is in days and months (dd/mm, from 20/05 to 02/10). Vertical bars are standard deviations (n = 9 leaves) and the dashed vertical line (20/08) represents the harvest point of plagiotropic buds for RNA extraction for 454 sequencing and leaves for microscopic analyses. bΨpd of Rubi and IAPAR59 plants (47-month-old plants) measured at the end of the 2011dry season. In this case, Ψpd values ranged from -0.1 to -0.2 MPa for the control conditions, but were below (< -4.0 MPa = severe drought) the range of use of a Scholander-type pressure chamber for drought conditions

Mentions: In 2009, leaf predawn water potential (Ψpd) values were similar in the leaves of irrigated Rubi and IAPAR59 plants, ranging from -0.06 to -0.16 MPa (Fig. 2a). This confirmed the unstressed status of these plants which were considered as the control in our experiment. At the same time, the Ψpd values decreased gradually during the dry season in the leaves of Rubi and IAPAR59 under drought conditions reaching the lowest values at the end of the dry season (Fig. 2a). At that time, the less negative Ψpd values in IAPAR59 indicated that it had better access to soil water. The first rains then occurred and the Ψpd values of drought-stressed plants increased almost to those measured in irrigated plants, illustrating the complete recovery of stressed plants. In 2011, Ψpd was measured at the peak of the drought (end of dry season). Under drought conditions, both Rubi and IAPAR59 had similar Ψpd values that were more negative than those measured in 2009, indicating more severe drought stress in 2011 (Fig. 2b).Fig. 2


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)

Predawn leaf water potentials (Ψpd) measured in plants of C. arabica. Rubi (RUB, triangle) and IAPAR59 (I59, square) cultivars were grown under control (C, open symbols) and drought (D, black symbols) conditions. Ψpd values (expressed in mega-Pascal, MPa) were measured once a week during the 2009 dry season (23-month-old plants) (a). The time scale is in days and months (dd/mm, from 20/05 to 02/10). Vertical bars are standard deviations (n = 9 leaves) and the dashed vertical line (20/08) represents the harvest point of plagiotropic buds for RNA extraction for 454 sequencing and leaves for microscopic analyses. bΨpd of Rubi and IAPAR59 plants (47-month-old plants) measured at the end of the 2011dry season. In this case, Ψpd values ranged from -0.1 to -0.2 MPa for the control conditions, but were below (< -4.0 MPa = severe drought) the range of use of a Scholander-type pressure chamber for drought conditions
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Predawn leaf water potentials (Ψpd) measured in plants of C. arabica. Rubi (RUB, triangle) and IAPAR59 (I59, square) cultivars were grown under control (C, open symbols) and drought (D, black symbols) conditions. Ψpd values (expressed in mega-Pascal, MPa) were measured once a week during the 2009 dry season (23-month-old plants) (a). The time scale is in days and months (dd/mm, from 20/05 to 02/10). Vertical bars are standard deviations (n = 9 leaves) and the dashed vertical line (20/08) represents the harvest point of plagiotropic buds for RNA extraction for 454 sequencing and leaves for microscopic analyses. bΨpd of Rubi and IAPAR59 plants (47-month-old plants) measured at the end of the 2011dry season. In this case, Ψpd values ranged from -0.1 to -0.2 MPa for the control conditions, but were below (< -4.0 MPa = severe drought) the range of use of a Scholander-type pressure chamber for drought conditions
Mentions: In 2009, leaf predawn water potential (Ψpd) values were similar in the leaves of irrigated Rubi and IAPAR59 plants, ranging from -0.06 to -0.16 MPa (Fig. 2a). This confirmed the unstressed status of these plants which were considered as the control in our experiment. At the same time, the Ψpd values decreased gradually during the dry season in the leaves of Rubi and IAPAR59 under drought conditions reaching the lowest values at the end of the dry season (Fig. 2a). At that time, the less negative Ψpd values in IAPAR59 indicated that it had better access to soil water. The first rains then occurred and the Ψpd values of drought-stressed plants increased almost to those measured in irrigated plants, illustrating the complete recovery of stressed plants. In 2011, Ψpd was measured at the peak of the drought (end of dry season). Under drought conditions, both Rubi and IAPAR59 had similar Ψpd values that were more negative than those measured in 2009, indicating more severe drought stress in 2011 (Fig. 2b).Fig. 2

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