Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars

Mofatto, Luciana Souto; Carneiro, F. de A.; Vieira, Natália Gomes; Duarte, Karoline Estefani; Vidal, Ramón; Alekcevetch, Jean Carlos; Cotta, Michelle G.; Verdeil, Jean‐Luc; Lapeyre-Montes, Fabienne; Lartaud, Marc; Leroy, Thierry; Bellis, Fabien De; Pot, David; Rodrigues, Gustavo Costa; Carazzolle, Marcelo Falsarella; Pereira, Gonçalo Amarante Guimarães; Andrade, Alan Carvalho; Marraccini, Pierre

doi:10.1186/s12870-016-0777-5

Cited by 53 publications

(35 citation statements)

References 75 publications

(98 reference statements)

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“…DEGs encoding wax transporters showed variable expression patterns: while lipid transfer proteins (LTPs) were repressed, non-specific lipid transfer proteins (nLTPs) and ABC (ATP-binding cassette) transporters were mostly activated. Based on these findings, we suggest that although drought negatively affected LTPs, the other transporters may play an important role in wax accumulation, and thus enhance the rigidity of the plant, as reported in coffee plants undergoing drought stress (Mofatto et al, 2016). …”

Section: Discussionsupporting

confidence: 71%

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

et al. 2016

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Prunus persica L. Batsch, or peach, is one of the most important crops and it is widely established in irrigated arid and semi-arid regions. However, due to variations in the climate and the increased aridity, drought has become a major constraint, causing crop losses worldwide. The use of drought-tolerant rootstocks in modern fruit production appears to be a useful method of alleviating water deficit problems. However, the transcriptomic variation and the major molecular mechanisms that underlie the adaptation of drought-tolerant rootstocks to water shortage remain unclear. Hence, in this study, high-throughput sequencing (RNA-seq) was performed to assess the transcriptomic changes and the key genes involved in the response to drought in root tissues (GF677 rootstock) and leaf tissues (graft, var. Catherina) subjected to 16 days of drought stress. In total, 12 RNA libraries were constructed and sequenced. This generated a total of 315 M raw reads from both tissues, which allowed the assembly of 22,079 and 17,854 genes associated with the root and leaf tissues, respectively. Subsets of 500 differentially expressed genes (DEGs) in roots and 236 in leaves were identified and functionally annotated with 56 gene ontology (GO) terms and 99 metabolic pathways, which were mostly associated with aminobenzoate degradation and phenylpropanoid biosynthesis. The GO analysis highlighted the biological functions that were exclusive to the root tissue, such as “locomotion,” “hormone metabolic process,” and “detection of stimulus,” indicating the stress-buffering role of the GF677 rootstock. Furthermore, the complex regulatory network involved in the drought response was revealed, involving proteins that are associated with signaling transduction, transcription and hormone regulation, redox homeostasis, and frontline barriers. We identified two poorly characterized genes in P. persica: growth-regulating factor 5 (GRF5), which may be involved in cellular expansion, and AtHB12, which may be involved in root elongation. The reliability of the RNA-seq experiment was validated by analyzing the expression patterns of 34 DEGs potentially involved in drought tolerance using quantitative reverse transcription polymerase chain reaction. The transcriptomic resources generated in this study provide a broad characterization of the acclimation of P. persica to drought, shedding light on the major molecular responses to the most important environmental stressor.

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Section: Discussionsupporting

confidence: 71%

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

et al. 2016

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“…Leaf and fruit transcriptome analysis of Coffea eugenioides produced 36,935 contigs using Illumina HiSeq platform (Yuyama et al 2016). Also Mofatto et al (2016) obtained a total of 41,512 contigs from C. arabica transcriptome, comparing the molecular responses to drought in two commercial cultivars using 454-pyrosequencing and Sanger platforms. The expression profiles (read counts) in all libraries were submitted for PCA analysis in order to evaluate the intrinsic variation between libraries.…”

Section: Read Quality Filtering Mapping and Assemblymentioning

confidence: 99%

High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection

et al. 2017

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We provide a transcriptional profile of coffee rust interaction and identified putative up regulated resistant genes Coffee rust disease, caused by the fungus Hemileia vastatrix, is one of the major diseases in coffee throughout the world. The use of resistant cultivars is considered to be the most effective control strategy for this disease. To identify candidate genes related to different mechanism defense in coffee, we present a time-course comparative gene expression profile of Caturra (susceptible) and Híbrido de Timor (HdT, resistant) in response to H. vastatrix race XXXIII infection. The main objectives were to obtain a global overview of transcriptome in both interaction, compatible and incompatible, and, specially, analyze up-regulated HdT specific genes with inducible resistant and defense signaling pathways. Using both Coffea canephora as a reference genome and de novo assembly, we obtained 43,159 transcripts. At early infection events (12 and 24 h after infection), HdT responded to the attack of H. vastatrix with a larger number of up-regulated genes than Caturra, which was related to prehaustorial resistance. The genes found in HdT at early hours were involved in receptor-like kinases, response ion fluxes, production of reactive oxygen species, protein phosphorylation, ethylene biosynthesis and callose deposition. We selected 13 up-regulated HdT-exclusive genes to validate by real-time qPCR, which most of them confirmed their higher expression in HdT than in Caturra at early stage of infection. These genes have the potential to assist the development of new coffee rust control strategies. Collectively, our results provide understanding of expression profiles in coffee-H. vastatrix interaction over a time course in susceptible and resistant coffee plants.

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“…High elevation improves the quality of the bean and potential cup quality due to delay in ripening brought about by cooler weather associated with higher altitudes, and the inherent characteristics of acidity, aroma and bold bean can develop fully (Mangal, 2007). Above 23°C, fruit development and ripening are accelerated, leading to loss of quality; below 18°C, growth is depressed (Mofatto, 2016).…”

Section: Impact Of Climate Change On Coffee Qualitymentioning

confidence: 99%

“…Increased drought and sunshine can induce the premature ripening of the beans, with sufficient quality loss as well as the yield (Mofatto, 2016). Water availability has also been found to affect the maintenance of maximum photosynthetic rates, high fruit set levels, and fruit size.…”

Section: Impact Of Climate Change On Coffee Qualitymentioning

confidence: 99%

Climate Change Effect on Coffee Yield and Quality: A Review

2019

International Journal of Forestry and Horticulture

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Coffee is one of the most widely drunk beverages in the world, and is a very important source of foreign exchange income for many countries. More than 125 million people in the coffee growing areas worldwide derive their income directly or indirectly from its products (Lashermes et al., 2011; Mishra and Slater, 2012). It ranks second after oil in international trade and has created several million jobs in the producer and consumer countries where more than nine million tons of green beans are produced annually (ICO, 2016). In the world, Brazil is the leading coffee producer and exporter country followed by Vietnam, Colombia, Indonesia and Ethiopia (ICO, 2016). The genus Coffea comprises nearly 124 well identified species; however, Coffea arabica L. and Coffea canephora P. are the two commercially important species (Davis et al., 2006; Gray et al., 2013). Predominately, Arabica coffee represents 70% of global coffee production and Caniphora (Robusta) represents about 30% (Damatta and Ramalho, 2006; Davis et al., 2012). The production and productive of both species are largely dependent on the climate for attain high yields and quality (Killeen and Harper, 2016). The effect of climate variation on natural systems has begun as one of the most critical issues of humankind (Jaramillo et al., 2009). Many finding proof that weather alteration is hastening at ample quicker stride than earlier that leading to irreversible changes in major earth systems and ecosystems (ITC, 2010). Important factors that play a role for climate change are, rising fossil fuel burning and land use changes are continuing to emit, and increasing quantities of greenhouse gases into the Earth's atmosphere. The rising greenhouse gases [carbon dioxide (CO2), methane (CH4) and nitrogen dioxide (N2O)] in the atmosphere can increase the amount of heat from the sun withheld in the Earth's atmosphere, that would normally be radiated back into space (Vergara, 2014). Carbon dioxide (CO2) and methane (CH4) are the most greenhouse gases that influence global climate through emissions (Masters et al., 2009). Climate change is transforming ecosystems on an extraordinary scale, at an extraordinary pace. The main characteristics of climate change are increases in average global temperature (global warming); changes in cloud cover and precipitation particularly over land; melting of ice caps and glaciers and reduced snow cover; and raise in ocean temperatures and ocean acidity due to seawater absorbing heat and carbon dioxide from the atmosphere (IEH, 2012). Changing climatic conditions and rising global temperatures pose one of the most significant threats to world coffee production. According to Killeen and Harper (2016) both the productivity and quality of Arabica and Robusta coffee largely depend on the climate suitability, especially the precipitation and air Abstract: Climate changes are alarming the world by hampering agriculture and its products. Coffee production is highly dependent on a regular sequence of weather events. Alteration in precipitation pa...

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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

Cited by 53 publications

References 75 publications

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection

Climate Change Effect on Coffee Yield and Quality: A Review

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