Skip to main content
SpringerLink
Log in

Current Challenges and Genomic Advances Towards the Development Resilient Coffee Genotypes to Abiotic Stresses

  • Chapter
  • First Online:
Genomic Designing for Abiotic Stress Resistant Technical Crops

Abstract

Climate variability and change are among the major drivers of abiotic stresses and the concomitant vulnerability of agricultural production systems. With the advent of systems biology, the analysis of complex crop-environment interactions through integrated high-throughput approaches, such as genomics, transcriptomics, proteomics, metabolomics, lipidomics, and interactomics, is currently the most assertive strategy to unravel plant development, metabolism, and acclimation capabilities, and to implement genomics-assisted breeding programs towards the production of resilient crops. With the sequencing of the coffee reference genome, the last decade has seen a rapid worldwide progress in establishing genomic tools, entering a new era of coffee functional genomics. New genomic tools offer practical toolkits for high-throughput identification of genes and pathways that are key resources for improving the adaptability of coffee crop to the present and future climate change scenarios, using worldwide genetic resources of Coffea spp. In this review, we summarize the available coffee genomic resources and discuss their use in the development of new (hybrid) varieties with greater ability to cope with environmental abiotic constraints. To ensure sustainable coffee production, stress-tolerant varieties will be critical in maintaining the coffee bean yield and quality.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Acidri R, Sawai Y, Sugimoto Y, Handa T, Sasagawa D et al (2020) Exogenous kinetin promove the nonenzymatic antioxidant system and photosynthetic activity of coffee (Coffea arabica L.) plants under cold stress conditions. Plants 9:281

    Google Scholar 

  • Aglawe SB, Barbadikar KM, Mangrauthia SK, Madhav MS (2018) New breeding technique “genome editing” for crop improvement: applications, potentials and challenges. 3 Biotechnology 8:336

    Google Scholar 

  • Albuquerque EVS, Cunha WG, Barbosa AEAD, Costa PM, Texeira JB et al (2009) Transgenic coffee fruits from Coffea arabica genetically modified by bombardment. In Vitro Cell Dev Biol Plant 45:532–539

    Article  CAS  Google Scholar 

  • Alkimim ER, Caixeta ET, Sousa TV, Resende MDV, Silva FL et al (2020) Selective efficiency of genome-wide selection in Coffea canephora breeding. Tree Genet Genom 16:41

    Article  Google Scholar 

  • Alves GSC, Torres LF, Déchamp E, Breitler JC, Joët T et al (2017) Differential fine tuning of gene expression regulation in coffee leaves by CcDREB1D promoter haplotypes under water stress. J Exp Bot 68:3017–3031

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alves GSC, Torres LF, de Aquino SO, Reichel T, Freire LP et al (2018) Nucleotide diversity of the coding and promoter regions of DREB1D, a candidate gene for drought tolerance in Coffea species. Trop Plant Biol 11:31–48

    Article  CAS  Google Scholar 

  • Aria M, Cuccurullo C (2017) Bibliometrix: an R-tool for comprehensive science mapping analysis. J Informet 11:959–975

    Article  Google Scholar 

  • Avila RT, Almeida WL, Costa LC, Machado KLG, Barbosa ML et al (2020a) Elevated air [CO2] improves photosynthetic performance and alters biomass accumulation and partitioning in drought-stressed coffee plants. Environ Exp Bot 177:104137

    Article  CAS  Google Scholar 

  • Avila RT, Cardoso AA, Almeida WL (2020b) Coffee plants respond to drought and elevated [CO2] through changes in stomatal function, plant hydraulic conductance, and aquaporin expression. Environ Exp Bot 177:104148

    Article  CAS  Google Scholar 

  • Barbosa AEAD, Albuquerque EVS, Silva MCM, Souza DSL, Oliveira-Neto OB et al (2010) α-Amylase inhibitor-1 gene from Phaseolus vulgaris expressed in Coffea arabica plants inhibits α-amylases from the coffee berry borer pest. BMC Biotechnol 10:1–8

    Article  Google Scholar 

  • Batista-Santos P, Lidon FC, Fortunato A, Leitão AE, Lopes E et al (2011) The impact of cold on photosynthesis in genotypes of Coffea spp.—photosystem sensitivity, photoprotective mechanisms and gene expression. J Plant Physiol 168:792–806

    Article  CAS  PubMed  Google Scholar 

  • Baulcombe DC, Dean C (2014) Epigenetic regulation in plant responses to the environment. Cold Spring Harb Perspect Biol 6:a019471

    Article  PubMed  PubMed Central  Google Scholar 

  • Bawin Y, Ruttink T, Staelens A, Haegeman A, Stoffelen P et al (2020) Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica L. bioRxiv. https://doi.org/10.1101/2020.03.22.002337

  • Bennett MD, Leitch IJ (2011) Nuclear DNA amounts in angiosperms: targets, trends and tomorrow. Ann Bot 107:467–590

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berthaud J (1986) Les ressources genetiques pour l’amelioration des cafeires africains diploides. Orstom, Paris

    Google Scholar 

  • Bewg WP, Ci D, Tsai C-J (2018) Genome editing in trees: from multiple repair pathways to long-term stability. Front Plant Sci 9:1732

    Article  PubMed  PubMed Central  Google Scholar 

  • Bibi F, Barozai MYK, Din M (2017) Bioinformatics profiling and characterization of potential microRNAs and their targets in the genus Coffea. Turk J Agric For 41:191–200

    Article  CAS  Google Scholar 

  • Brasil (2018) Instrução Normativa Nº 16, DE 10 de Julho de 2018. Brasília, DF. http://www.in.gov.br/materia/-/asset_publisher/Kujrw0TZC2Mb/content/id/29493718/do1-2018-07-11-instrucao-normativa-n-16-de-10-de-julho-de-2018-29493696

  • Breitler JC, Dechamp E, Campa C, Rodrigues LAZ, Guyot R et al (2018) CRISPR/Cas9-mediated efficient targeted mutagenesis has the potential to accelerate the domestication of Coffea canephora. Plant Cell Tiss Org Cult 134:383–394

    Article  CAS  Google Scholar 

  • Bunn C, Läderach P, Rivera OO, Kirschke D (2015) A bitter cup: Climate change profile of global production of Arabica and Robusta coffee. Clim Change 129:89–101

    Article  Google Scholar 

  • Caixeta ET, Pestana KN, Pestana RKN (2015) Melhoramento do cafeeiro: ênfase na aplicação dos marcadores moleculares. In: Garcia GO, Reis EF, Lima JSS, Xaxier AC, Rodrigues WN (eds) Tópicos Especiais em produção vegetal V, Alegre, Brasil, pp 154–179

    Google Scholar 

  • Campos NA, Panis B, Carpentier SC (2017) Somatic embryogenesis in coffee: the evolution of biotechnology and the integration of omics technologies offer great opportunities. Front Plant Sci 8:1460

    Article  PubMed  PubMed Central  Google Scholar 

  • Camargo MBPD (2010) The impact of climatic variability and climate change on arabica coffee crop in Brazil. Bragantia, 69:239–247

    Google Scholar 

  • Carelli ML, Fahl JI, Ramalho JC (2006) Aspects of nitrogen metabolism in coffee plants. Theor Exp Plant Physiol (ex-Braz J Plant Physiol) 18(1):9–21

    Google Scholar 

  • Carneiro FA, De Aquino SO, Mattos NG, Valeriano JC, Carneiro WWJ et al (2019) Desenvolvimento e validação de uma plataforma de genotipagem em larga escala para Coffea canephora. In: X Simpósio de Pesquisa dos Cafés do Brasil, Vitória, Brasil

    Google Scholar 

  • Carvalho FG, Sera GH, Andreazi E, Sera T, Fonseca ICB et al (2017) Drought tolerance in seedlings of coffee genotypes carrying genes of different species. Coffee Sci 12:156–163

    Article  Google Scholar 

  • Cenci A, Combes MC, Lashermes P (2012) Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments. Plant Mol Biol 78:135–145

    Article  CAS  PubMed  Google Scholar 

  • Charr JC, Garavito A, Guyeux C, Crouzillat D, Descombes P et al (2020) Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee). Mol Phylogenet Evol 151:106906

    Article  PubMed  Google Scholar 

  • Charrier A, Berthaud J (1985) Botanical classification of coffee. In: Clifforf MN, Willson KC (eds) Coffee: botany, biochemistry, and production of beans and beverage. Croom Herm, Westport, London, pp 13–47

    Chapter  Google Scholar 

  • Chaves SS, Fernandes-Brum CN, Silva GFF, Ferrara-Barbosa BC, Paiva LV et al (2015) New insights on Coffea miRNAs: features and evolutionary conservation. Appl Biochem Biotechnol 177:879–908

    Article  CAS  PubMed  Google Scholar 

  • Chen X, Zhou DX (2013) Rice epigenomics and epigenetics: challenges and opportunities. Curr Opin Plant Biol 16:164–169

    Article  CAS  PubMed  Google Scholar 

  • Chen H, Hu B, Zhao L, Shi D, She Z et al (2019) Differential expression analysis of reference genes in pineapple (Ananas comosus L.) during reproductive development and response to abiotic stress, hormonal stimuli. Trop Plant Biol 12:67–77

    Article  CAS  Google Scholar 

  • Clarindo WR, Carvalho CR (2009) Comparison of the Coffea canephora and Coffea arabica karyotype based on chromosomal DNA content. Plant Cell Rep 28:73–81

    Article  CAS  PubMed  Google Scholar 

  • Clarindo WR, Carvalho CR, Caixeta ET, Koehler AD (2013) Following the track of “Híbrido de Timor” origin by cytogenetic and flow cytometry approaches. Genet Resour Crop Evol 60:2253–2259

    Article  Google Scholar 

  • Coffee Genome Hub (2020) Coffea canephora genoma—gene predictions. https://coffee-genome.org/coffeacanephora. Acessed 29 Oct 2020

  • Cruz F, Kalaoun S, Nobile P, Colombo C, Almeida J et al (2009) Evaluation of coffee reference genes for relative expression studies by quantitative real-time RT-PCR. Mol Breed 23:607–616

    Article  CAS  Google Scholar 

  • Cubry P, Musoli P, Legnaté H, Pot D, Bellis F et al (2008) Diversity in coffee assessed with SSR markers: structure of the genus Coffea and perspectives for breeding. Genome 51:50–63

    Article  CAS  PubMed  Google Scholar 

  • DaMatta FM, Ramalho JDC (2006) Impacts of drought and temperature stress on coffee. Braz J Plant Physiol 18:55–81

    Article  CAS  Google Scholar 

  • DaMatta FM, Ronchi CP, Maestri M, Barros RS (2010) Coffee: environment and crop physiology. In: DaMatta FM (ed) Ecophysiology of tropical tree crops. Nova Science Publishers, New York, pp 181–216

    Google Scholar 

  • DaMatta FM, Rahn E, Läderach P, Ghini R, Ramalho JC (2019) Why could the coffee crop endure climate change and global warming to a greater extent than previously estimated? Clim Change 152(1):167–178

    Article  CAS  Google Scholar 

  • Daniell H, Lin CS, Yu M, Chang WJ (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17:134

    Article  PubMed  PubMed Central  Google Scholar 

  • Dankowska A, Domagała A, Kowalewski W (2017) Quantification of Coffea arabica and Coffea canephora var. robusta concentration in blends by means of synchronous fluorescence and UV-Vis spectroscopies. Talanta 172:215–220

    Article  CAS  PubMed  Google Scholar 

  • Davis AP, Tosh J, Ruch N, Fay MF (2011) Growing coffee: Psilanthus (Rubiaceae) subsumed on the basis of molecular and morphological data implications for the size, morphology, distribution and evolutionary history of Coffea. Bot J Linn Soc 167:357–377

    Article  Google Scholar 

  • Davis AP, Chadburn H, Moat J, O’Sullivan R, Hargreaves S, Lughadha EN (2019) High extinction risk for wild coffee species and implications for coffee sector sustainability. Sci Adv 5:eaav3473

    Google Scholar 

  • Davis AP, Gargiulo R, Fay MF, Sarmu D, Haggar J (2020) Lost and found: Coffea stenophylla and C. affinis, the forgotten coffee crop species of West Africa. Front Plant Sci 11:616

    Google Scholar 

  • De Aquino SO, Carneiro FA, Rêgo ECS, Alves GSC, Andrade AC et al (2018) Functional analysis of different promoter haplotypes of the coffee (Coffea canephora) CcDREB1D gene through genetic transformation of Nicotiana tabacum. Plant Cell Tiss Org Cult 132:279–294

    Article  Google Scholar 

  • De Carvalho K, Bespalhok Filho JC, Dos Santos TB, Souza SGH, Vieira LGE et al (2013) Nitrogen starvation, salt and heat stress in coffee (Coffea arabica L.): identification and validation of new genes for qPCR normalization. Mol Biotechnol 53:315–325

    Article  PubMed  Google Scholar 

  • De Carvalho K, Petkowicz CLO, Nagashima GT, Bespalhok Filho JC, Vieira LGE et al (2014) Homeologous genes involved in mannitol synthesis reveal unequal contributions in response to abiotic stress in Coffea arabica. Mol Genet Genom 289:951–963

    Article  Google Scholar 

  • Demirel U, Morris WL, Ducreux LJ, Yavuz C, Asim A et al (2020) Physiological, biochemical, and transcriptional responses to single and combined abiotic stress in stress-tolerant and stress-sensitive potato genotypes. Front Plant Sci 11:169

    Article  PubMed  PubMed Central  Google Scholar 

  • Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R et al (2014) The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345:1181–1184

    Article  CAS  PubMed  Google Scholar 

  • Dereeper A, Bocs S, Rouard M, Guignon V, Ravel S et al (2015) The coffee genome hub: a resource for coffee genomes. Nucleic Acids Res 43:1028–1035

    Article  Google Scholar 

  • Van Deynze A, Hulse-Kemp Amanda C, Dario, Medrano JF (2017) Update on sequencing of the Coffea arabica variety, Geisha. In: Plant and animal genome conference, San Diego, California, pp 12–18

    Google Scholar 

  • Dong X, Jiang Y, Yang Y, Xiao Z, Bai X et al (2019) Identification and expression analysis of the NAC gene family in Coffea canephora. Agronomy 9:1–17

    Article  Google Scholar 

  • Dos Santos TB, Vieira LGE (2020) Involvement of the galactinol synthase gene in abiotic and biotic stress responses: a review on current knowledge. Plant Gene 24:100258

    Article  Google Scholar 

  • Dos Santos TB, Budzinski IGF, Marur CJ, Petkowicz CLO, Pereira LFP et al (2011) Expression of three galactinol synthase isoforms in Coffea arabica L. and accumulation of raffinose and stachyose in response to abiotic stresses. Plant Physiol Biochem 49:441–448

    Article  PubMed  Google Scholar 

  • Dos Santos TBD, Lima RBD, Nagashima GT, Petkowicz CLO, Carpentieri-Pípolo V et al (2015) Galactinol synthase transcriptional profile in two genotypes of Coffea canephora with contrasting tolerance to drought. Genet Mol Biol 38:182–190

    Article  PubMed  PubMed Central  Google Scholar 

  • Dos Santos TB, Soares JD, Lima JE, Silva JC, Ivamoto ST et al (2019) An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses. Funct Integr Genom 19:151–169

    Article  Google Scholar 

  • Dubberstein D, Lidon FC, Rodrigues AP, Semedo JN, Marques I et al (2020) Resilient and sensitive key points of the photosynthetic machinery of Coffea spp. to the single and superimposed exposure to severe drought and heat stresses. Front Plant Sci 11:1049

    Google Scholar 

  • Dussert S, Lashermes P, Anthony F, Montagnon C, Berthaud J, Noirot M, Hamon S (1999) Coffea Canephora. Diversité génétique des plantes tropicales cultivées, CIRAD, p 175

    Google Scholar 

  • Etienne H, Breton D, Breitler J-C, Bertrand B, Déchamp E et al (2018) Coffee somatic embryogenesis: how did research, experience gained and innovations promote the commercial propagation of elite clones from the two cultivated species? Front Plant Sci 9:1630

    Article  PubMed  PubMed Central  Google Scholar 

  • Ferrão RG, Fonseca AFA, Silveira JSM, Ferrão MAG, Bragança SM (2000) EMCAPA 8141—Robustão Capixaba, variedade clonal de café conilon tolerante à seca, desenvolvida para o estado do Espírito Santo. Ceres 273:555–560

    Google Scholar 

  • Ferrão RG, Moreira SO, Ferrão MAG, Riva EM, Arantes LO et al (2016) Genética e melhoramento: desenvolvimento e recomendação de cultivares com tolerância à seca para o Espírito Santo. Incaper em Rev 6:51–71

    Google Scholar 

  • Ferrão RG, De Muner LH, Da Fonseca AFA, Ferrão M (2019) Conilon coffee, 3rd edn. Vitória, Brazil, pp 1–974

    Google Scholar 

  • Fleta-Soriano E, Munné-Bosch S (2016) Stress memory and the inevitable effects of drought: a physiological perspective. Front Plant Sci 7:1–6

    Article  Google Scholar 

  • Fortunato A, Lidon FC, Batista-Santos P, Leitão AE, Pais IP et al (2010) Biochemical and molecular characterization of the antioxidative system of Coffea sp. under cold conditions in genotypes with contrasting tolerance. J Plant Physiol 167(5):333–342

    Google Scholar 

  • Galle A, Florez-Sarasa I, Aououad HE, Flexas J (2011) The Mediterranean evergreen Quercus ilex and the semi-deciduous Cistus albidus differ in their leaf gas exchange regulation and acclimation to repeated drought and re-watering cycles. J Exp Bot 62:5207–5216

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gallusci P, Dai Z, Génard M, Gauffretau A, Leblanc-Fournier N et al (2017) Epigenetics for plant improvement: current knowledge and modeling avenues. Trends Plant Sci 22:610–623

    Article  CAS  PubMed  Google Scholar 

  • Garavito A, Montagnon C, Guyot R, Bertrand B (2016) Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico. BMC Plant Biol 16:242–253

    Article  PubMed  PubMed Central  Google Scholar 

  • Garcia V, Ribas AF, Vieira LGE, dos Santos TB (2018) In silico analysis of the Dof transcription factor family in Coffea canephora. Coll Agrariae 14:99–111

    Article  Google Scholar 

  • Gimase JM, Thagana WM, Omondi CO, Cheserek JJ, Gichimu BM et al (2020) Genome-wide association study identify the genetic loci conferring resistance to Coffee Berry disease (Colletotrichum kahawae) in Coffea arabica var. Rume. Euphytica 46:47

    Google Scholar 

  • Gomez C, Dussert S, Hamon P, Hamon S, de Kochko A, Poncet V, (2009) Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities. BMC Evol Biol 9:167

    Google Scholar 

  • González L, González-Vilar M (2001) Determination of relative water content. In: Roger M (ed) Handbook of plant ecophysiology techniques. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 207–212

    Google Scholar 

  • Goulao LF, Fortunato AS, Ramalho JC (2012) Selection of reference genes for normalizing quantitative real-time PCR gene expression data with multiple variables in Coffea spp. Plant Mol Biol Rep 30:741–759

    Article  CAS  Google Scholar 

  • Guedes FAF, Nobres P, Rodrigues Ferreira DC, Menezes-Silva PE, Ribeiro-Alves M et al (2018) Transcriptional memory contributes to drought tolerance in coffee (Coffea canephora) plants. Environ Exp Bot 147:220–233

    Article  CAS  Google Scholar 

  • Guénin S, Mauriat M, Pelloux J, Van Wuytswinkel O, Bellini C, Gutierrez L (2009) Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of references. J Exp Bot 60:487–493

    Article  PubMed  Google Scholar 

  • Guyeux C, Charr JC, Tran HTM, Furtado A, Henry RJ, Crouzillat D, Guyot R, Hamon P (2019) Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species. PLoS One 14(6):e0216347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guyot R, Hamon P, Couturon E, Rakotomalala JJ, Raharimalala NE et al (2020) WCSdb: a database of Wild Coffea species. (Version V1). Zenodo. https://doi.org/10.5281/zenodo.3899717

  • Haile M, Kang WH (2018) Transcriptome profiling of the coffee (C. arabica L.) seedlings under salt stress condition. J Plant Biotechnol 45:45–54

    Article  Google Scholar 

  • Hauben M, Haesendonckx B, Standaert E, Van Der Kelen K, Azmi A et al (2009) Energy use efficiency is characterized by an epigenetic component that can be directed through artificial selection to increase yield. Proc Natl Acad Sci USA 106:20109–20114

    Google Scholar 

  • Herrera JC, Villegas AM, Garcia FA, Dereeper A, Combes MC et al (2014) Genomic relationships among different Timor hybrid (Coffea L.) accessions as revealed by SNP identification and RNA-seq analysis. In: Castillo LF, Cristancho M, Isaza G, Pinzón A, Corchado Rodríguez JM (eds) Advances in computational biology. Springer, Cham, pp 161–168

    Google Scholar 

  • Huang L, Wang X, Dong Y, Long Y, Hao C et al (2020) Resequencing 93 accessions of coffee unveils independent and parallel selection during Coffea species divergence. Plant Mol Biol 103:51–61

    Article  CAS  PubMed  Google Scholar 

  • ICO - International Coffee Organization (2020) Global coffee trade. http://www.ico.org/tradestatistics.asp. Accessed Aug 14 2020

  • Imbach P, Fung E, Hannah L, Navarro-Racines CE, Roubik DW et al (2017) Coupling of pollination services and coffee suitability under climate change. Proc Natl Acad Sci USA 114:10438–10442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kinoshita T, Seki M (2014) Epigenetic memory for stress response and adaptation in plants. Plant Cell Physiol 55:1859–1863

    Article  CAS  PubMed  Google Scholar 

  • Lashermes P, Combes MC, Robert J, Trouslot P, D’Hont A et al (1999) Molecular characterisation and origin of the Coffea arabica L. genome. Mol Gen Genet 261:259–266

    Article  CAS  PubMed  Google Scholar 

  • Lashermes P, Andrzejewski S, Bertrand B, Combes MC, Dussert S et al (2000) Molecular analysis of introgressive breeding in coffee (Coffea arabica L.). Theor Appl Genet 100:139–146

    Article  CAS  Google Scholar 

  • Lemos S, Fonçatti LF, Guyot R, Paschoal AR, Domingues DS (2020) Genome-wide screening and characterization of non-coding RNAs in Coffea canephora. Non-Coding RNA 6:39

    Article  CAS  PubMed Central  Google Scholar 

  • Long Y, Xia W, Li R, Wang J, Shao M et al (2011) Epigenetic QTL mapping in Brassica napus. Genetics 189:1093–1102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Loss-Morais G, Ferreira DC, Margis R, Alves-Ferreira M, Corrêa RL (2014) Identification of novel and conserved microRNAs in Coffea canephora and Coffea arabica. Genet Mol Biol 37:671–682

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marçal DMS, Avila RT, Quiroga-Rojas LF, de Souza RPB, Gomes Junior CC et al (2021) Elevated [CO2] benefits coffee growth and photosynthetic performance regardless of light availability. Plant Physiol Biochem 158:524–535

    Article  PubMed  Google Scholar 

  • Marie L, Abdallah C, Campa C, Courtel P, Bordeaux M et al (2020) G × E interactions on yield and quality in Coffea arabica: new F1 hybrids outperform American cultivars. Euphytica 216:78

    Article  CAS  Google Scholar 

  • Marques I, Fernandes I, David PHC, Paulo OS, Goulão LF et al (2020) Transcriptomic leaf profiling reveals differential responses of the two most traded coffee species to elevated [CO2]. Int J Mol Sci 21(23):9211

    Article  CAS  PubMed Central  Google Scholar 

  • Marraccini P, Vinecky F, Alves GSC, Ramos HJO, Elbelt E et al (2012) Differentially expressed genes and proteins upon drought acclimation in tolerant and sensitive genotypes of Coffea canephora. J Exp Bot 63:4191–4212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martinez HEP, de Souza BP, Caixeta ET, de Carvalho FP, Clemente JM, (2020) Water stress changes nitrate uptake and expression of some nitrogen related genes in coffee-plants (Coffea arabica L.). Sci Hort 267:109254

    Google Scholar 

  • Martins MQ, Rodrigues WP, Fortunato AS, Leitão AE, Rodrigues AP et al (2016) Protective response mechanisms to heat stress in interaction with high [CO2] conditions in Coffea spp. Front Plant Sci 29:947–964

    Google Scholar 

  • Martins LD, Tomaz MA, Lidon FC, DaMatta FM, Ramalho JC (2014) Combined effects of elevated [CO2] and high temperature on leaf mineral balance in Coffea spp. plants. Clim Change 126(3–4):365–379

    Google Scholar 

  • Martins MQ, Fortunato AS, Rodrigues WP, Partelli FL, Campostrini E et al (2017) Selection and validation of reference genes for accurate RT-qPCR data normalization in Coffea spp. under a climate changes context of interacting elevated [CO2] and temperature. Front Plant Sci 8:307

    Google Scholar 

  • Menezes-Silva PE, Sanglard LMPV, Ávila RT, Morais LE, Martins SCV et al (2017) Photosynthetic and metabolic acclimation to repeated drought events play key roles in drought tolerance in coffee. J Exp Bot 68:4309–4322

    Article  CAS  PubMed  Google Scholar 

  • Merot-L’anthoene V, Tournebize R, Darracq O, Rattina V, Lepelley M et al (2018) Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L. Plant Biotechnol J 17:1418–1430

    Article  Google Scholar 

  • Mhuantong W, Wichadakul D (2009) MicroPC (microPC): a comprehensive resource for predicting and comparing plant microRNAs. BMC Genom 10:366

    Article  Google Scholar 

  • Moat J, Gole TW, Davis AP (2019) Least concern to endangered: applying climate change projections profoundly influences the extinction risk assessment for wild Arabica coffee. Glob Change Biol 25:390–403

    Article  Google Scholar 

  • Mofatto LS, de Araújo CF, Vieira NG, Duarte KE, Vidal RO et al (2016) Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars. BMC Plant Biol 16:94

    Article  PubMed  PubMed Central  Google Scholar 

  • Montagnon C, Leroy T, Eskes AB (1998) Amélioration variétale de Coffea canephora; 1: Criteres et methodes de sélection. Mejora varietal de Coffea canephora, 1: Criterios y métodos de selecciónVarietal improvement of Coffea canephora, 1: Criteria and breeding methods. Plantations Recherche Développement (Francia) 5:18–33

    Google Scholar 

  • Montagnon C, Cubry P, Leroy T (2012) Coffee Coffea canephora Pierre genetic improvement: acquired knowledge, strategies and perspectives. Cahiers Agric 21:143–153

    Article  Google Scholar 

  • Mueller L, Strickler S, Domingues D, Pereira L, Andrade A et al (2015) Towards a better understanding of the Coffea arabica genome structure. In: Embrapa Café-Artigo em anais de congresso (ALICE). International Conference on Coffee Science, Udine, Cogito

    Google Scholar 

  • Musoli P, Cubry P, Aluka P, Billot C, Dufour M et al (2009) Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda. Genome 52:634–646

    Article  CAS  PubMed  Google Scholar 

  • NCBI - National Center for Biotechnology Information (2020) US, National Library of Medicine. Accessed 01 Sept 2020

    Google Scholar 

  • Nobres P, Patreze CM, Waltenberg FP, Correa MF, Tavano ECR et al (2016) Characterization of the promoter of the homeobox gene CaHB12 in Coffea arabica. Trop Plant Biol 9:50–62

    Article  CAS  Google Scholar 

  • Noirot M, Poncet V, Barre P, Hamon P, Hamon S, Kochko A (2003) Genome size variations in diploid African Coffea species. Ann Bot 92:709–714

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Noman A, Fahad S, Aqeel M, Ali U, Anwar S et al (2017) miRNAs: major modulators for crop growth and development under abiotic stresses. Biotechnol Lett 39:685–700

    Article  CAS  PubMed  Google Scholar 

  • Nowak MD, Davis AP, Anthony F, Yoder AD (2011) Expression and trans-specific polymorphism of self-incompatibility RNases in Coffea (Rubiaceae). PLoS One 6(6):e21019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oliveira RR, Ribeiro THC, Cardon CH, Fedenia L, Maia VA et al (2020) Elevated temperatures impose transcriptional constraints and elicit intraspecific differences between coffee genotypes. Front Plant Sci 11:1113

    Article  PubMed  PubMed Central  Google Scholar 

  • Osakabe Y, Kajitab S, Osakabea K (2011) Genetic engineering of woody plants: current and future targets in a stressful environment. Physiol Planta 142:105–117

    Article  CAS  Google Scholar 

  • Ovalle-Rivera O, Läderach P, Bunn C, Obersteiner M, Schroth G (2015) Projected shifts in Coffea arabica suitability among major global producing regions due to climate change. PLoS One 10:e0124155

    Article  PubMed  PubMed Central  Google Scholar 

  • Park J, Xi H, Kim Y, Heo KI, Nho M et al (2019) The complete chloroplast genome of cold hardiness individual of Coffea arabica L. (Rubiaceae). Mitochon DNA Part B 4:1083–1084

    Article  Google Scholar 

  • Parsell DA, Lindquist S (1993) The function of heat-shock proteins in stress tolerance: degradation and reactivation of damaged proteins. Annu Rev Genet 27:437–496

    Article  CAS  PubMed  Google Scholar 

  • Partelli FL, Vieira HD, Rodrigues APD, Pais I, Campostrini E et al (2010) Cold induced changes on sugar contents and respiratory enzyme activities in Coffee genotypes. Ciência Rural 40(4):781–786

    Article  CAS  Google Scholar 

  • Pérez-Pascual D, Jiménez-Guillen D, Villanueva-Alonzo H, Souza-Pereira R, Godoy-Hernández G et al (2018) Ectopic expression of the Coffea canephora SERK1 homolog-induced differential transcription of genes involved in auxin metabolism and in the developmental control of embryogenesis. Physiol Plant 163:530–551

    Article  PubMed  Google Scholar 

  • Prakash NS, Muniswamy B, Hanumantha BT, Sreenath HL, Sundaresha KD et al (2011) Marker assisted selection and breeding for leaf rust resistance in coffee (Coffea arabica L.) some recent leads. Indian J Genet P Br 71:185–189

    Google Scholar 

  • Rakocevic M, Batista ER, Pazianotto RAA, Scholz MBS, Souza GAR et al (2021) Leaf gas exchange and bean quality fluctuations over the whole-canopy vertical profile of arabic coffee cultivated under elevated CO2. Funct Plant Biol (in Press). https://doi.org/10.1071/FP20298

    Article  Google Scholar 

  • Ramalho JC, Pais IP, Leitão AE, Guerra M, Reboredo FH et al (2018a) Can elevated air [CO2] conditions mitigate the predicted warming impact on the quality of coffee bean? Front Plant Sci 9:287

    Article  PubMed  PubMed Central  Google Scholar 

  • Ramalho JC, Rodrigues AP, Lidon FC, Marques LMC, Leitão AE et al (2018b) Stress cross-response of the antioxidative system promoted by superimposed drought and cold conditions in Coffea spp. PLoS One 13(6):e0198694

    Article  PubMed  PubMed Central  Google Scholar 

  • Ramalho JC, Campos PS, Teixeira M, Nunes MA (1998) Nitrogen dependent changes in antioxidant systems and in fatty acid composition of chloroplast membranes from Coffea arabica L. plants submitted to high irradiance. Plant Sci 135(2):115–124

    Google Scholar 

  • Ramalho JC, Pons T, Groeneveld H, Azinheira HG, Nunes MA, (2000) Photosynthetic acclimation to high light conditions in mature leaves of Coffea arabica L.: role of xanthophylls, quenching mechanisms and nitrogen nutrition. Funct Plant Biol (ex- Aust J Plant Physiol) 27:43–51

    Google Scholar 

  • Ramalho JC, Fortunato AS, Goulao LF, Lidon FC (2013) Cold-induced changes in mineral content in leaves of Coffea spp. Identification of descriptors for tolerance assessment. Biol Plant 57(3):495–506

    Google Scholar 

  • Ramalho JC, DaMatta FM, Rodrigues AP, Scotti-Campos P, Pais I et al (2014) Cold impact and acclimation response of Coffea spp. plants. Theor Exp Plant Physiol 26(1):5–18

    Google Scholar 

  • Rao S, Balyan S, Jha S, Mathur S (2020) Novel insights into expansion and functional diversification of MIR169 family in tomato. Planta 25:55

    Article  Google Scholar 

  • Ribas AF, Dechamp E, Champion A, Bertrand B, Combes MC et al (2011) Agrobacterium-mediated genetic transformation of Coffea arabica (L.) is greatly enhanced by using established embryogenic callus cultures. BMC Plant Biol 11:92

    Google Scholar 

  • Rijo L (1974) Observações cariológicas no cafeeiro “Híbrido de Timor.” Port Acta Biol 8:157–168

    Google Scholar 

  • Rodrigues WP, Martins MQ, Fortunato AS, Rodrigues AP, Semedo JN et al (2016) Long-term elevated air [CO2] strengthens photosynthetic functioning and mitigates the impact of supra-optimal temperatures in tropical Coffea arabica and C. canephora species. Glob Change Biol 22:415–431

    Article  Google Scholar 

  • Sade N, Moshelion M (2017) Plant aquaporins and abiotic stress. In: Chaumont F, Tyerman SD (eds) Plant aquaporins. Springer, Cham, pp 185–206

    Google Scholar 

  • Sant’Ana GC, Pereira LFP, Pot D, Ivamoto ST, Domingues DS et al (2018) Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L. Sci Rep 8:1–12

    Google Scholar 

  • Scalabrin S, Toniutti L, Di Gaspero G, Scaglione D, Magris G et al (2020) A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm. Sci Rep 10:1–13

    Article  Google Scholar 

  • Scotti-Campos P, Pais IP, Ribeiro-Barros AI, Martins LD, Tomaz MA et al (2019) Lipid profile adjustments may contribute to warming acclimation and to heat impact mitigation by elevated [CO2] in Coffea spp. Environ Exp Bot 167:103856

    Article  CAS  Google Scholar 

  • Sengupta S, Mukherjee S, Basak P, Majumder AL (2015) Significance of galactinol and raffinose family oligosaccharide synthesis in plants. Front Plant Sci 6:656

    Article  PubMed  PubMed Central  Google Scholar 

  • Simkin AJ, Moreau H, Kuntz M, Pagny G, Lin C et al (2008) An investigation of carotenoid biosynthesis in Coffea canephora and Coffea arabica. J Plant Physiol 165:1087–1106

    Article  CAS  PubMed  Google Scholar 

  • Soltis DE, Soltis PS, Pires JC, Kovarik A, Tate JA, Mavrodiev E (2004) Recent and recurrent polyploidy in Tragopogon (Asteraceae): cytogenetic, genomic and genetic comparisons. Biol J Linn Soc 82:485–550

    Article  Google Scholar 

  • Stebbins GL Jr (1947) Types of polyploids: their classification and significance. Adv Genet 1:403–429

    Article  PubMed  Google Scholar 

  • Szcześniak MW, Deorowicz S, Gapskiak J, Kaczyński L, Makałowska I et al (2012) miRNEST database: an integrative approach in microRNA search and annotation. Nucleic Acids Res 40:198–204

    Article  Google Scholar 

  • Tan BC, Joseph LM, Deng WT, Liu L, Li QB et al (2003) Molecular characterization of the Arabidopsis 9-cis epoxycarotenoid dioxygenase gene family. Plant J 35:44–56

    Article  CAS  PubMed  Google Scholar 

  • Tang X, Zhang N, Si HJ, Urrea AC (2017) Selection and validation of reference genes for RT-qPCR analysis in potato under abiotic stress. Plant Methods 13:1–8

    Article  CAS  Google Scholar 

  • Thellin O, Zorzi W, Lakaye B, De Borman B, Coumans B et al (1999) Housekeeping genes as internal standards: use and limits. J Biotechnol 75:291–295

    Article  CAS  PubMed  Google Scholar 

  • Thioune EH, McCarthy J, Gallagher T, Osborne B (2017) A humidity shock leads to rapid, temperature dependent changes in coffee leaf physiology and gene expression. Tree Physiol 37:367–379

    CAS  PubMed  Google Scholar 

  • Thioune EH, Strickler S, Gallagher T, Charpagne A, Decombes P et al (2020) Temperature impacts the response of Coffea canephora to decreasing soil water availability. Trop Plant Biol 13:236–250

    Article  CAS  Google Scholar 

  • Torres LF, Reichel T, Déchamp E, de Aquino SO, Duarte KE et al (2019) Expression of DREB-like genes in Coffea canephora and C. arabica subjected to various types of abiotic stress. Trop Plant Biol 12:98–116

    Article  CAS  Google Scholar 

  • Valencia-Lozano E, Cabrera-Ponce JL, Gómez-Lim MA, Ibarra JE (2019) Development of an efficient protocol to obtain transgenic coffee, Coffea arabica L., expressing the Cry10Aa toxin of Bacillus thuringiensis. Int J Mol Sci 20:5334

    Google Scholar 

  • Van der Vossen H, Bertrand B, Charrier A (2015) Next generation variety development for sustainable production of arabica coffee (Coffea arabica L.): a review. Euphytica 204:243–256

    Article  Google Scholar 

  • Vats S, Kumawat S, Kumar V, Patil GB, Joshi T et al (2019) Genome editing in plants: exploration of technological advancements and challenges. Cells 8(11):1386

    Article  CAS  PubMed Central  Google Scholar 

  • Vidal RO, Mondego JMC, Pot D, Ambrósio AB, Andrade AC et al (2010) A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica. Plant Physiol 154:1053–1066

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vinecky F, Davrieux F, Mera AC, Alves GSC, Lavagnini G et al (2017) Controlled irrigation and nitrogen, phosphorous and potassium fertilization affect the biochemical composition and quality of Arabica coffee beans. J Agric Sci 155:902–918

    Article  CAS  Google Scholar 

  • Wu D, Bi C, Wang X, Xu Y, Ye Q et al (2017) The complete chloroplast genome sequence of an economic plant Coffea canephora. Mitochon DNA Part B 2:483–485

    Article  Google Scholar 

  • Yaguinuma DH, dos Santos TB, de Souza SGH, Vieira LGE, Ribas AF (2021) Genome-wide identification, evolution, and expression profile of aquaporin genes in Coffea canephora in response to water stress. Plant Mol Biol Rep 39:146–162

    Article  CAS  Google Scholar 

  • Yang Q, Chen Q, Zhu Y, Li T (2018) Identification of MdD of genes in apple and analysis of their response to biotic or abiotic stress. Funct Plant Biol 45:528–541

    Article  CAS  PubMed  Google Scholar 

  • Yu QY, Guyot R, de Kochko A, Byers A, Navajas-Pérez R et al (2011) Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea). Plant J 67:305–317

    Article  CAS  PubMed  Google Scholar 

  • Yuyama PM, Júnior OR, Ivamoto ST, Domingues DS, Carazzolle MF et al (2016) Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits. Mol Genet Genom 291:323–336

    Article  CAS  Google Scholar 

  • Zambolim L (2016) Current status and management of coffee leaf rust in Brazil. Trop Plant Pathol 41:1–8

    Article  Google Scholar 

  • Zeng A, Xu Y, Song L, Li J, Yan J (2020) Validation of suitable reference genes for qRT-PCR in cabbage (Brassica oleracea L.) under different abiotic stress experimental conditions. J Plant Biochem Biotechnol 4:1–12

    Google Scholar 

  • Zheng JY, Liu F, Zhu CH, Li X, Dai X et al (2019) Identification, expression, alternative splicing and functional analysis of pepper WRKY gene family in response to biotic and abiotic stresses. PLoS One 14:e0219775

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou Y, Tao J, Ahammed GJ, Li J, Yang Y (2019) Genome-wide identification and expression analysis of aquaporin gene family related to abiotic stress in watermelon. Genome 62:643–656

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This research was funded by the Fundação de Amparo à Pesquisa e Inovação do Espírito Santo (FAPES, grant number 84320893). Fellowships from the Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil (CNPq) to L. F. P. Pereira and F. L. Partellli are also greatly acknowledged. This work received funding support from national funds from Fundação para a Ciência e a Tecnologia, I.P. (FCT), Portugal, through the project PTDC/ASP-AGR/31257/2017, and the research units UIDB/00239/2020 (CEF), and UIDP/04035/2020 (GeoBioTec).

Author information

Authors and Affiliations

  1. Postgraduate Program in Agronomy, Universidade do Oeste Paulista (Unoeste), Rodovia Raposo Tavares Km 572, Limoeiro, Presidente Prudente, São Paulo, 19067-175, Brazil

    Tiago Benedito dos Santos & Alessandra Ferreira Ribas

  2. Universidade Federal do Espírito Santo (UFES), Alto Universitário S/N - Caixa Postal 16, Alegre, Espírito Santo, 29500-000, Brazil

    Marcia Flores da Silva Ferreira, Stefanie Cristina Oliveira & Iasmine Ramos Zaidan

  3. PlantStress and Biodiversity Lab, Forest Research Center (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, 2784-505 Oeiras, and Tapada da Ajuda, 1349-017, Lisboa, Portugal

    Isabel Marques, José Cochicho Ramalho & Ana I. Ribeiro-Barros

  4. Universidade Federal do Espírito Santo (UFES), Rod. Br 101, Km 60, Litorâneo, São Mateus, Espírito Santo, 29933-515, Brazil

    Marcos Góes Oliveira & Fábio Luiz Partelli

  5. Universidade Estadual da Região Tocantina do Maranhão (Uemasul), Avenida Brejo do Pinto, S/N, Estreito, Maranhão, 65975-000, Brazil

    Weverton Pereira Rodrigues

  6. Centre de coopération internationale en recherche agronomique pour le développement - Cirad: Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, 911 ave Agropolis BP 64501, Cedex 5, 34394, Montpellier, France

    Romain Guyot

  7. Department of Electronics and Automatization, Universidad Autónoma de Manizales (Uam), Manizales, Caldas, Colombia

    Romain Guyot

  8. Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516, Caparica, Portugal

    José Cochicho Ramalho & Ana I. Ribeiro-Barros

  9. Embrapa Café, Laboratório de Biotecnologia, AMG, IDR-IAPAR, Rod Celso Garcia Cid, Km 375, Londrina, Paraná, 86047-902, Brazil

    Luiz Filipe Protasio Pereira

Authors
  1. Tiago Benedito dos Santos
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marcia Flores da Silva Ferreira
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Isabel Marques
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Stefanie Cristina Oliveira
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Iasmine Ramos Zaidan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Marcos Góes Oliveira
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Weverton Pereira Rodrigues
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Alessandra Ferreira Ribas
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Romain Guyot
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. José Cochicho Ramalho
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Ana I. Ribeiro-Barros
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Luiz Filipe Protasio Pereira
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Fábio Luiz Partelli
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Fábio Luiz Partelli .

Editor information

Editors and Affiliations

  1. Raja Ramanna Fellow, Department of Atomic Energy, Government of India, ICAR-National Institute for Plant Biotechnology, New Delhi, India

    Chittaranjan Kole

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

dos Santos, T.B. et al. (2022). Current Challenges and Genomic Advances Towards the Development Resilient Coffee Genotypes to Abiotic Stresses. In: Kole, C. (eds) Genomic Designing for Abiotic Stress Resistant Technical Crops. Springer, Cham. https://doi.org/10.1007/978-3-031-05706-9_3

Download citation

Publish with us

Policies and ethics

Search

Navigation