Coffea arabica
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA305756 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3223077.fastq.gz | Fastqsanger.gz | |||
| SRR3223157.fastq.gz | Fastqsanger.gz | |||
| SRR3223158.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:Understanding coffee quality
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Project description:The 'PUCE CAFÉ' project: A genome-wide 15K coffee microarray, a new tool to discover candidate genes correlated to quality traits
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Project description:Caffeine is a metabolite of great economic importance, especially in coffee, where it influences the sensorial and physiological impacts of the beverage. Caffeine metabolism in the Coffea species begins with the degradation of purine nucleotides through three specific N-methyltransferases: XMT, MXMT and DXMT. A comparative analysis was performed to clarify the molecular reasons behind differences in caffeine accumulation in two Coffea species, namely Coffea arabica and Coffea canephora var. robusta. Three different genes encoding N-methyltransferase were amplified in the doubled haploid Coffea canephora: CcXMT1, CcMXMT1 and CcDXMT. Six genes were amplified in the haploid Coffea arabica: CaXMT1, CaXMT2, CaMXMT1, CaMXMT2, CaDXMT1, and CaDXMT2. A complete phylogenic analysis was performed to identify specific key amino acids defining enzymatic function for each protein identified. Furthermore, a quantitative gene-expression analysis was conducted on leaves and on maturing coffee beans, simultaneously analyzing caffeine content. In the different varieties analyzed, caffeine accumulation is higher in leaves than in the coffee bean maturation period, higher in Robusta than in Arabica. In Robusta, CcXMT1 and CcDXMT gene expressions are predominant and transcriptional activity is higher in leaves than in maturing beans, and is highly correlated to caffeine accumulation. In Arabica, the CaXMT1 expression level is high in leaves and CaDXMT2 as well to a lesser extent, while global transcriptional activity is weak during bean maturation, suggesting that the transcriptional control of caffeine-related genes differs within different organs and between Arabica and Robusta. These findings indicate that caffeine accumulation in Coffea species has been modulated by a combination of differential transcriptional regulation and genome evolution.
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Project description:Coffea arabica: Variant analysis for caffeine and trigonelline content
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Project description:Epidemics of coffee leaf rust (CLR) lead to great yield losses and huge depreciation of coffee marketing values, if no control measures are applied. Societal expectations of a more sustainable coffee production are increasingly imposing the replacement of pesticide treatments by alternative solutions. A good protection strategy is to take advantage of the plant immune system by eliciting its constitutive defenses. Based on such concept, plant resistance inducers (PRIs) have been developed. The Greenforce CuCa formulation made by UFLA (Brazil) is, in addition to acibenzolar-S-methyl (ASM), showing promising results in the control of CLR (Hemileia vastatrix) in Coffea arabica. In order to improve our understanding of the molecular mechanisms of the PRIs, proteomic (2DE-MALDI/TOF/TOF-MS/MS), physiological (leaf gas-exchange) and biochemical (enzymatic) analyses of coffee leaves treated with Greenforce CuCa and ASM and inoculation with H. vastatrix were performed. Proteomic data showed metabolic adjustments mainly related with photosynthesis, protein metabolism and stress responses but, the proteins modulated by the two PRIs were different. Greenforce CuCa, on its own, increased photosynthesis and stomatal conductance, while ASM caused a decrease in these parameters. Upon H. vastratix infection, the Greenforce CuCa showed a higher protective effect on the leaf physiology than ASM. The enzymatic analyses indicated that Greenforce CuCa reinforces the redox homeostasis of the leaf, while ASM seems to increase the involvement of secondary metabolism. So, the PRIs prepare the plant to resist CLR but, inducing different defense mechanisms upon pathogen infection. The data also evidenced the existence of a link between the primary metabolism and defense responses. Furthermore, Greenforce CuCa emerged as a significant agent for CLR management. The identification of components of the plant primary metabolism, essential for plant growth and development that, simultaneously, participate in the plant defense responses can open new perspectives for plant breeding programs.
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Project description:Coffea arabica transcriptome under rust control and fruit thinning treatments
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Project description:The intermediate seed category was defined in the early 1990s using coffee (Coffea arabica) as a model. In contrast to orthodox seeds, intermediate seeds cannot survive complete drying, which is a major constraint for seed storage, for both biodiversity conservation and agricultural purposes. However, intermediate seeds are considerably more tolerant to drying than recalcitrant seeds, which are highly sensitive to desiccation. To gain insight into the mechanisms governing such differences, changes in desiccation tolerance (DT), hormone content and the transcriptome were analysed in developing coffee seeds. Acquisition of DT coincided with a dramatic transcriptional switch characterised by the repression of primary metabolism, photosynthesis and respiration, and the upregulation of genes coding for late embryogenesis abundant (LEA) proteins, heat shock proteins (HSP) and antioxidant enzymes. Analysis of heat-stable proteome in the mature coffee seed confirmed the accumulation of LEA proteins identified at the transcript level. Transcriptome analysis also suggests a major role for ABA and for the transcription factors CaHSFA9, CaDREB2G, CaANAC029, CaPLATZ and CaDOG-like in DT acquisition. The ability of CaHSFA9 and CaDREB2G to trigger HSP gene transcription was validated by Agrobacterium-mediated transformation of coffee somatic embryos.
2017-12-13 | GSE107949 | GEO