Gene Expression in Coffee

Marraccini, Pierre

doi:10.1007/124_2020_42

Cited by 4 publications

(3 citation statements)

References 253 publications

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“…In conclusion, the C. arabica genome exhibits little, if any, subgenome expression dominance, while individual genes demonstrate fine-scale expression partitioning by subgenome, as expected. Importantly, dominance was observed within specialized metabolic pathways contributing to coffee aromatic quality, consistent with earlier studies on these and other gene families 64-67 . These studies suggest that subgenome dominance, while averaging out equally in a global sense, follows a mosaic pattern in C. arabica wherein different sub-processes are locally dominated by each of the subgenomes.…”

Section: Resultssupporting

confidence: 89%

The genome and population genomics of allopolyploidCoffea arabicareveal the diversification history of modern coffee cultivars

Salojärvi,

Rambani,

et al. 2023

Preprint

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Coffea arabica, an allotetraploid hybrid ofC. eugenioidesandC. canephora, is the source of approximately 60% of coffee products worldwide. Cultivated accessions have undergone several population bottlenecks resulting in low genetic diversity. We present chromosome-level assemblies of a di-haploidC. arabicaaccession and modern representatives of its diploid progenitors,C. eugenioidesandC. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, which show a mosaic pattern of dominance, similar to other polyploid crop species. Resequencing of 39 wild and cultivated accessions suggests a founding polyploidy event ∼610,000 years ago, followed by several subsequent bottlenecks, including a population split ∼30.5 kya and a period of migration between Arabica populations until ∼8.9 kya. Analysis of lines historically introgressed withC. canephorahighlights loci that may contribute to their superior pathogen resistance and lay the groundwork for future genomics-based breeding ofC. arabica.

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Section: Resultssupporting

confidence: 89%

The genome and population genomics of allopolyploidCoffea arabicareveal the diversification history of modern coffee cultivars

Salojärvi,

Rambani,

et al. 2023

Preprint

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“…Physiological studies on the relationship between drought tolerance and gene expression have led to the identification of more than 80 CGs in both C. canephora (Marraccini et al, 2011(Marraccini et al, , 2012Vieira et al, 2013;Vinecky et al, 2012) and C. arabica (Freire et al, 2013;Mofatto et al, 2016). Additional genes that are assumed to play a key role in plant responses to abiotic stress have also been identified (Marraccini, 2020), such as those involved in the ABA biosynthetic pathway (Costa, 2014;Cotta, 2017;Simkin et al, 2008), cell protection and detoxification (Hinniger et al, 2006;Santos & Mazzafera, 2012;Thioune et al, 2017Thioune et al, , 2020, and aquaporins biosynthesis (Miniussi et al, 2015;Santos & Mazzafera, 2013). Other genes are involved in carotenoid/phenylpropanoid (Lepelley et al, 2012;Simkin et al, 2010), caffeine (Denoeud et al, 2014) and sugar (Geromel et al, 2006;Privat et al, 2008) biosynthetic pathways, or they encode transcription factors (Alves, 2015;Alves et al, 2017Alves et al, , 2018Thioune et al, 2017Thioune et al, , 2020Torres et al, 2019).…”

Section: Climate Change Is Predicted To Have Marked Negative Impacts Onmentioning

confidence: 99%

Adaptive potential of Coffea canephora from Uganda in response to climate change

et al. 2022

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Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programmes.To this end, landscape genomics is a useful approach for assessing putative adaptations to future climatic conditions, especially in long-lived species such as trees. We conducted a population genomics study of 207 Coffea canephora trees from seven forests along different climate gradients in Uganda. For this, we sequenced 323 candidate genes involved in key metabolic and defence pathways in coffee. Seventy-one single nucleotide polymorphisms (SNPs) were found to be significantly associated with bioclimatic variables, and were thereby considered as putatively adaptive loci. These SNPs were linked to key candidate genes, including transcription factors, like DREB-like and MYB family genes controlling plant responses to abiotic stresses, as well as other genes of organoleptic interest, such as the DXMT gene involved in caffeine biosynthesis and a putative pest repellent. These climate-associated genetic markers were used to compute genetic offsets, predicting population responses to future climatic conditions based on local climate change forecasts. Using these measures of maladaptation to future conditions, substantial levels of genetic differentiation between present and future diversity were estimated for all populations and scenarios considered. The populations from the forests Zoka and Budongo, in the northernmost zone of Uganda, appeared to have the lowest genetic offsets under all predicted climate change patterns, while populations from Kalangala and Mabira, in the Lake Victoria region, exhibited the highest genetic offsets. The potential of these findings in terms of ex situ conservation strategies are discussed.

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“…The bean biochemical composition (and their associated cup quality) variation observed in shaded vs. FS cultivated coffee plants has been attributed to greater expression of genes involved in important metabolic pathways (de Castro and Marraccini, 2006;Cheng et al, 2020). For example, the elevated sucrose level observed in lower canopy (LC) beans compared to the upper canopy (UC) beans is likely the result of increased expression of a battery of genes (such as SPS1, SPS2.2, SUS2.1, CIN, VIN1, and VINI.2), previously reported to play a key role in coffee bean sugar metabolism (Geromel et al, 2006;Privat et al, 2008;Joët et al, 2009;Marraccini, 2020). Another example of this is the elevated expression of RD22 (a gene involved in plant responses to stress as reported by Yamaguchi-Shinozaki and Shinozaki, 1993) in beans from LC compared to UC, suggesting that the continued bean growth until the red stage in LC was facilitated by a stronger dehydration resistance and less chlorophyll degradation.…”

Section: Shade Effects On Coffee Bean Biochemical Compositionmentioning

confidence: 99%

Shaded-Coffee: A Nature-Based Strategy for Coffee Production Under Climate Change? A Review

Koutouleas

Sarzynski

Bordeaux³

et al. 2022

Front. Sustain. Food Syst.

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Coffee is deemed to be a high-risk crop in light of upcoming climate changes. Agroforestry practices have been proposed as a nature-based strategy for coffee farmers to mitigate and adapt to future climates. However, with agroforestry systems comes shade, a highly contentious factor for coffee production in terms of potential yield reduction, as well as additional management needs and interactions between shade trees and pest and disease. In this review, we summarize recent research relating to the effects of shade on (i) farmers' use and perceptions, (ii) the coffee microenvironment, (iii) pest and disease incidence, (iv) carbon assimilation and phenology of coffee plants, (v) coffee quality attributes (evaluated by coffee bean size, biochemical compounds, and cup quality tests), (vi) breeding of new Arabica coffee F1 hybrids and Robusta clones for future agroforestry systems, and (vii) coffee production under climate change. Through this work, we begin to decipher whether shaded systems are a feasible strategy to improve the coffee crop sustainability in anticipation of challenging climate conditions. Further research is proposed for developing new coffee varieties adapted to agroforestry systems (exhibiting traits suitable for climate stressors), refining extension tools by selecting locally-adapted shade trees species and developing policy and economic incentives enabling the adoption of sustainable agroforestry practices.

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Gene Expression in Coffee

Cited by 4 publications

References 253 publications

The genome and population genomics of allopolyploidCoffea arabicareveal the diversification history of modern coffee cultivars

The genome and population genomics of allopolyploidCoffea arabicareveal the diversification history of modern coffee cultivars

Adaptive potential of Coffea canephora from Uganda in response to climate change

Shaded-Coffee: A Nature-Based Strategy for Coffee Production Under Climate Change? A Review

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