Limits...
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

Tissue dissection of plagiotropic buds. a The plagiotropic buds (including small leaves) were collected from plants during the 2011 dry season and used to extract RNA for qPCR expression analysis. b Meristem and leaf primordium dissected from plagiotropic buds harvested during the 2009 dry season and used to extract RNA for pyrosequencing. The dotted circles show the position of meristem and leaf primordium. The same scale (white bar = 1 mm) is used for both documents
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Tissue dissection of plagiotropic buds. a The plagiotropic buds (including small leaves) were collected from plants during the 2011 dry season and used to extract RNA for qPCR expression analysis. b Meristem and leaf primordium dissected from plagiotropic buds harvested during the 2009 dry season and used to extract RNA for pyrosequencing. The dotted circles show the position of meristem and leaf primordium. The same scale (white bar = 1 mm) is used for both documents

Mentions: For both cultivars and experiments, leaf predawn water potentials (Ψpd) were measured once a week during the 2009 dry season (from May to October) of (23-month-old plants) and only once in 2011 (at the end of the dry season) (47-month-old plants) using a Scholander-type pressure chamber (Plant Water Status Console, Model 3000 F01, Soil Moisture Equipment Corp, Santa Barbara, CA USA) in fully expanded leaves (8–15 cm long) from the third pair from the apex of plagiotropic branches located in the upper third of the plant canopy. For 454 sequencing, between 30 and 50 shoot apices were collected (between 10:00 and 11:00 am) from three different plants at the end of the dry season from Rubi and IAPAR59 under the control and drought conditions, and further dissected to isolate the shoot apex (Fig. 1b). For microscopic analyses, leaves identical to those used for Ψpd measurements were also collected from the same plants. At the end of the 2011 dry season, Ψpd were measured once for Rubi and IAPAR59 plants under control and drought treatments, and shoot apices were collected (Fig. 1a) for gene expression analyses (qPCR).Fig. 1


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)

Tissue dissection of plagiotropic buds. a The plagiotropic buds (including small leaves) were collected from plants during the 2011 dry season and used to extract RNA for qPCR expression analysis. b Meristem and leaf primordium dissected from plagiotropic buds harvested during the 2009 dry season and used to extract RNA for pyrosequencing. The dotted circles show the position of meristem and leaf primordium. The same scale (white bar = 1 mm) is used for both documents
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Tissue dissection of plagiotropic buds. a The plagiotropic buds (including small leaves) were collected from plants during the 2011 dry season and used to extract RNA for qPCR expression analysis. b Meristem and leaf primordium dissected from plagiotropic buds harvested during the 2009 dry season and used to extract RNA for pyrosequencing. The dotted circles show the position of meristem and leaf primordium. The same scale (white bar = 1 mm) is used for both documents
Mentions: For both cultivars and experiments, leaf predawn water potentials (Ψpd) were measured once a week during the 2009 dry season (from May to October) of (23-month-old plants) and only once in 2011 (at the end of the dry season) (47-month-old plants) using a Scholander-type pressure chamber (Plant Water Status Console, Model 3000 F01, Soil Moisture Equipment Corp, Santa Barbara, CA USA) in fully expanded leaves (8–15 cm long) from the third pair from the apex of plagiotropic branches located in the upper third of the plant canopy. For 454 sequencing, between 30 and 50 shoot apices were collected (between 10:00 and 11:00 am) from three different plants at the end of the dry season from Rubi and IAPAR59 under the control and drought conditions, and further dissected to isolate the shoot apex (Fig. 1b). For microscopic analyses, leaves identical to those used for Ψpd measurements were also collected from the same plants. At the end of the 2011 dry season, Ψpd were measured once for Rubi and IAPAR59 plants under control and drought treatments, and shoot apices were collected (Fig. 1a) for gene expression analyses (qPCR).Fig. 1

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