ArticleBMC plant biology2016
Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars.
Article in BMC plant biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 63 citations in OpenAlex.
- Transcriptomic Analysis of Osmotic Stress-Tolerant Somatic Embryos ofInternational journal of molecular sciences · 2025Article
- Stress resilience inFrontiers in plant science · 2025Article
- The Identification and Characterization of WOX Family Genes inInternational journal of molecular sciences · 2024Article
- Genome-wide analysis and identification of Carotenoid Cleavage Oxygenase (CCO) gene family in coffee (coffee arabica) under abiotic stress.BMC genomic data · 2024Article
- Genome-Wide Association Study of Rice Diversity Panel Reveals New QTLs for Tolerance to Water Deficit Under the Egyptian Conditions.Rice (New York, N.Y.) · 2024Article
- Transcriptomic Data Analysis Using the Galaxy Platform: Coffee (Coffea arabica L.) Flowers as Example.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Effects of drought stress on photosynthetic physiological characteristics, leaf microstructure, and related gene expression of yellow horn.Plant signaling & behavior · 2023Article
- Plants' Response to Abiotic Stress: Mechanisms and Strategies.International journal of molecular sciences · 2023Review
- The Lost and Found: Unraveling the Functions of Orphan Genes.Journal of developmental biology · 2023Review
- Transcriptome and carotenoid profiling of different varieties ofPlant diversity · 2022Article
- Identification and differential analysis of noncoding RNAs in response to drought inFrontiers in plant science · 2022Article
- Non-Coding RNAs in Response to Drought Stress.International journal of molecular sciences · 2021Review
- Photochemical efficiency correlated with candidate gene expression promote coffee drought tolerance.Scientific reports · 2021Article
- Modern Approaches for Transcriptome Analyses in Plants.Advances in experimental medicine and biology · 2021Article
- Elevated Temperatures Impose Transcriptional Constraints and Elicit Intraspecific Differences Between Coffee Genotypes.Frontiers in plant science · 2020Article
- Transcript and metabolic adjustments triggered by drought in Ilex paraguariensis leaves.Planta · 2019Article
- An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses.Functional & integrative genomics · 2019Article
- Identification of charcoal rot resistance QTLs in sorghum using association and in silico analyses.Journal of applied genetics · 2018Article
- Coffee Somatic Embryogenesis: How Did Research, Experience Gained and Innovations Promote the Commercial Propagation of Elite Clones From the Two Cultivated Species?Frontiers in plant science · 2018Review
- High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection.Plant molecular biology · 2017Article
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Authors and funding
18 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDrought 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.
resultsPyrosequencing 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.
conclusionsThe 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.
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