Skip to main content
SpringerLink
Log in

Current Challenges and Genomic Advances Toward the Development of Coffee Genotypes Resistant to Biotic Stress

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

Abstract

Coffee (Coffea spp.) is an important agricultural world commodity. Biotic stresses caused by pests or phytopathogens can affect not only the coffee production, but also the grain quality. They interfere with physiological processes affecting plant growth and development, and damaging different plant organs and tissues, such as leaves, roots, and fruits. The use of chemicals to control diseases and pests directly affects coffee cultivation sustainability and are often inefficient. This scenario could worsen with the rapid insurgence of new and/or more aggressive pathogens and pests as a result of the world climate change. Thus, coffee breeding with a focus on the development of resistant cultivars is the best strategy to control these biotic stresses. In this context, biotechnological tools can help the coffee breeding in a persuasive way. Advances in genomic editing techniques, such as CRISPR, are capable of introducing punctual modifications in the plant genome. As an alternative to the use of chemicals, the sequence-specific gene silencing via RNA interference (RNAi) holds a great promise for effective management of agricultural pests. The emergence of high-throughput sequencing technology has allowed unprecedented advances in genomic and transcriptomic data. The genomic and transcriptomic coffee data can now be used to identify a large number of genes and molecular markers that determine coffee resistance to pathogens and pests. The identification of these genes helps to elucidate plant pathogen interactions, as well as can be targets for genome editing. The implementation of molecular markers, through assisted selection, can help accelerate breeding programs and pyrimidize resistance genes. In addition, the genomic and transcriptomic data of pathogens and pests are useful to identified targets for RNAi approaches. In this review, we address the research in modern genetics and molecular biology related to the main biotic stresses of coffee plants and its implications for coffee breeding.

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 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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

Similar content being viewed by others

References

  • ACGC—Arabica Coffee Genome Consortium (2014) Towards a better understanding of the Coffea arabica genome structure. In: 25th international conference on Coffee Science (ASIC). Cogito, Armenia, pp 42–45

    Google Scholar 

  • Adugna G, Jefuka C, Teferi D, Abate S (2012) New record and outbreaks of bacterial blight of coffee (Pseudomonas syringae) in southern Ethiopia: impact of climate change scenarios. In: 24th international conference on coffee science. San José, Costa Rica, p 85

    Google Scholar 

  • Albuquerque EVS, Petitot A, Joseane P, Grossi-de-Sa MF, Fernandez D (2017) Early responses of coffee immunity-related genes to root-knot nematode infection. Physiol Mol Plant Pathol 100:142–150

    Article  CAS  Google Scholar 

  • Alkimim ER, Caixeta ET, Sousa TV, Pereira AA, de Oliveira ACB et al (2017) Marker-assisted selection provides arabica coffee with genes from other Coffea species targeting on multiple resistance to rust and coffee berry disease. Mol Breed 37:6

    Article  Google Scholar 

  • Almeida DP, Castro ISL, Mendes TAO, Alves DR, Barka GD et al (2021) Receptor-like kinase (Rlk) as a candidate gene conferring resistance to Hemileia vastatrix in coffee. Sci Agri 78(6):e20200023

    Article  Google Scholar 

  • Amaral JF, Teixeira C, Pinheiro ED (1956) A bactéria causadora da mancha-aureolada do cafeeiro. Arquivo do Instituto Biológico, São Paulo, Brazil, vol 23, pp 151–155

    Google Scholar 

  • Amorim L, Rezende JAM, Bergamin FA, Camargo LEA (2016) Doenças do cafeeiro. In: Zambolin L (ed) Manual de fitopatologiadoenças das plantas cultivadas. Agronômica Ceres, Ouro Fino, Brazil, pp 193–213

    Google Scholar 

  • Andersen EJ, Ali S, Byamukama E, Yen Y, Nepal MP (2018) Disease resistance mechanisms in plants. Genes 9(7):339

    Article  PubMed Central  Google Scholar 

  • Andreazi E, Sera GH, Faria RT, Sera T, Bastista Fonseca IC et al (2015) Behavior of ‘IPR 100’ and ‘Apoatã IAC 2258’ coffee cultivars under different infestation levels of Meloidogyne paranaensis inoculum. Aust J Crop Sci 9(11):1069–1074

    Google Scholar 

  • Anthony F, Topart P, Martinez A, Silva M, Nicole M (2005) Hypersensitive-like reaction conferred by the Mex-1 resistance gene against Meloidogyne exigua in coffee. Plant Pathol 54(4):476–482

    Article  CAS  Google Scholar 

  • Anthony F, Topart P, Astorga C, Anzueto F, Bertrand B (2003) La resistencia genética de Coffea spp. a Meloidogyne paranaensis: identificación y utilización para lacaficulturalatino-americana. Manejo integr. plagas agroecología, vol 67, pp 5–12

    Google Scholar 

  • Anzueto F, Bertrand B, Sarah JL, Eskes AB, Decazy B (2001) Resistance to Meloidogyne incognita in Ethiopian Coffea arabica accessions. Euphytica 118(1):1–8

    Article  Google Scholar 

  • Aribi J, Ribière W, Villain L, Anthony F (2018) Screening of wild coffee (Coffea spp.) for resistance to Meloidogyne incognita race 1. Nematropica 48(1):5–14

    Google Scholar 

  • Ariyoshi C, Sant’ana GC, Sera GH, Rodrigues LMR, Nogueira LM et al (2019) Estudo de associação genômica ampla para interação de Coffea arabica L. e Pseudomonas syringae pv. garcae. In: X Simpósio de Pesquisa dos Cafés do Brasil. Vitória, Brasil. ISSN:1984-9249

    Google Scholar 

  • Avelino J, Allinne C, Cerda R, Willocquet L, Savary S (2018) Multiple-disease system in coffee: from crop loss assessment to sustainable management. Annu Rev Phytopathol 56:611–635

    Article  CAS  PubMed  Google Scholar 

  • Barbosa AE, Albuquerque ÉV, Silva MC, Souza DS, 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):44

    Google Scholar 

  • Barka GD, Caixeta ET, Ferreira SS, Zambolim L (2020) In silico guided structural and functional analysis of genes with potential involvement in resistance to coffee leaf rust: a functional marker based approach. PLoS ONE 15(7):e0222747

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bartoli C, Roux F (2017) Genome-wide association studies in plant pathosystems: toward an ecological genomics approach. Front Plant Sci 8:763

    Article  PubMed  PubMed Central  Google Scholar 

  • Barton CR, Adams TL, Zarowitz MA (1991) Stable transformation of foreign DNA into Coffea arabica plants. In: 14th international conference on Coffee Science (ASIC), San Francisco, USA, pp 460–464

    Google Scholar 

  • Bawin Y, Ruttink T, Staelens A, Haegeman A, Stoffelen P et al (2020) Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica. J Syst Evol 59(5):953–9631

    Article  Google Scholar 

  • Bertrand B, Anthony F (2008) Genetics of resistance to root-knot nematodes (Meloidogyne spp.) and breeding. In: Souza RM (ed) Plant-parasitic nematodes of coffee. Springer, Dordrecht, Netherlands, pp 165–190

    Google Scholar 

  • Bettencourt AJ (1973) Considerações gerais sobre o ‘Híbrido de Timor’. Circular No. 23 - Instituto Agronômico de Campinas, Campinas – Brazil, p 20

    Google Scholar 

  • Boller T, Felix G (2009) A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annu Rev Plant Biol 60:379–406

    Article  CAS  PubMed  Google Scholar 

  • Boyd LA, Ridout C, O’Sullivan DM, Leach JE, Leung H (2013) Plant pathogen interactions: disease resistance in modern agriculture. Trends Genet 29(4):233–240

    Article  CAS  PubMed  Google Scholar 

  • Brandalise M, Severino FE, Maluf MP, Maia IG (2009) The promoter of a gene encoding an isoflavone reductase-like protein in coffee (Coffea arabica) drives a stress-responsive expression in leaves. Plant Cell Rep 28:1699–1708

    Article  CAS  PubMed  Google Scholar 

  • 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 Tissue Organ Cult 134:383–394

    Article  CAS  Google Scholar 

  • Cação SMB, Silva NV, Domingues DS, Vieira LGE, Diniz LEC et al (2013) Construction and characterization of a BAC library from the Coffea arabica genotype Timor Hybrid CIFC 832/2. Genetica 141:217–226

    Article  PubMed  Google Scholar 

  • Cacas J, Petitot AS, Bernier L, Estevan J, Conejero G et al (2011) Identification and characterization of the non-race specific disease resistance 1 (NDR1) orthologous protein in coffee. BMC Plant Biol 11:144

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cagliari D, Dias NP, Galdeano DM, dos Santos EÁ, Smagghe G et al (2019) Management of pest insects and plant diseases by non-transformative RNAi. Front Plant Sci 10:1319

    Article  PubMed  PubMed Central  Google Scholar 

  • Capucho AS, Zambolim EM, Freitas RL, Haddad F, Caixeta ET et al (2012) Identification of race XXXIII of Hemileia vastatrix on Coffea arabica Catimor derivatives in Brazil. Australas Plant Dis Notes 7:189–191

    Article  Google Scholar 

  • Cardoso DC, Martinati JC, Giachetto PF, Vidal RO, Carazzolle MF et al (2014) Large-scale analysis of differential gene expression in coffee genotypes resistant and susceptible to leaf miner–toward the identification of candidate genes for marker-assisted selection. BMC Genomics 15(1):1–21

    Article  Google Scholar 

  • Castro-Moretti FR, Cocuron JC, Vega FE, Alonso AP (2020) differential metabolic responses caused by the most important insect pest of coffee worldwide, the coffee berry borer (Hypothenemus hampei). J Agric Food Chem 68(8):2597–2605

    Google Scholar 

  • Chagné D, Vanderzande S, Kirk C, Profitt N, Weskett R et al (2019) Validation of SNP markers for fruit quality and disease resistance loci in apple (Malus x domesticaBorkh.) using the OpenArray® platform. Hortic Res 6(1):1–16

    Google Scholar 

  • Chen Z (2002) Morphocultural and pathogenic comparisons between Colletotrichum kahawae and C. gloeosporioides isolated from coffee berries. Lisboa, Instituto Superior de Agronomia da Universidade Técnica de Lisboa, Portugal, PhD thesis, p 163

    Google Scholar 

  • Claudianos C, Ranson H, Johnson RM, Biswas S, Schuler MA et al (2006) A deficit of detoxification enzymes: pesticide sensitivity and environmental response in the honeybee. Insect Mol Biol 15(5):615–636

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Coll N, Epple P, Dangl J (2011) Programmed cell death in the plant immune system. Cell Death Differ 18(8):1247–1256

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cristancho MA, Botero-Rozo DO, Giraldo W, Tabima J, Riaño-Pachón DM et al (2014) Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales. Front Plant Sci 5:594

    Article  PubMed  PubMed Central  Google Scholar 

  • Cui L, Hanika K, Visser RGF, Bai Y (2020) Improving pathogen resistance by exploiting plant susceptibility genes in coffee (Coffea spp.). Agronomy 10(12):1928

    Google Scholar 

  • Curi SM, Carvalho A, Moraes FRP, Monaco LC, Arruda HV (1970) Novas fontes de resistência genética de Coffea no controle do nematoide do cafeeiro, Meloidogyne exigua. O Biológico 36(10):293–295

    Google Scholar 

  • Dantas J, Motta I, Vidal L, Bílio J, Pupe JM et al (2020) A comprehensive review of the coffee leaf miner Leucoptera coffeella (Lepidoptera: Lyonetiidae), with special regard to neotropical impacts, pest manag control. Preprints 2020100629

    Google Scholar 

  • Davis AP, Govaerts R, Bridson DM, Stoffelen P (2006) Annotated taxonomic conspectus of the genus Coffea (Rubiaceae). Bot J Linn Soc 152:465–512

    Article  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(4):357–377

    Article  Google Scholar 

  • De Filippis LF (2017) Plant bioinformatics: next generation sequencing approaches. In: Hakeem K, Malik A, Vardar-Sukan F, Ozturk M (eds) Plant bioinformatics. Springer, Cham, Switzerland, pp 1–106

    Google Scholar 

  • De Guglielmo-Cróquer Z, Altosaar I, Zaidi M, Menéndez-Yuffá A (2010) Transformation of coffee (Coffea arabica L. cv. Catimor) with the cry1ac gene by biolistic, without the use of markers. Braz J Biol 70(2):387

    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(6201):1181–1184

    Article  CAS  PubMed  Google Scholar 

  • Diniz I, Figueiredo A, Loureiro A, Batista D, Azinheira H et al (2017) A first insight into the involvement of phytohormones pathways in coffee resistance and susceptibility to Colletotrichum kahawae. PLoS ONE 12(5):e0178159

    Article  PubMed  PubMed Central  Google Scholar 

  • Diola V, Brito GG, Caixeta ET, Pereira LFP, Loureiro M (2013) A new set of differentially expressed signaling genes is early expressed in coffee leaf rust race II incompatible interaction. FunctIntegr Genom 13:379–389

    CAS  Google Scholar 

  • Diola V, Brito GG, Caixeta ET, Maciel-Zambolim E, Sakiyama NS et al (2011) High-density genetic mapping for coffee leaf rust resistance. Tree Genet Genomes 7:1199–1208

    Google Scholar 

  • Dubberstein D, Rodrigues WP, Semedo JN, Rodrigues AP, Pais IP et al (2018) Mitigation of the negative impact of warming on the coffee crop: the role of increased air (CO2) and management strategies. In: Srinivasarao CH, Shanker AK, Shanker C (eds) Climate resilient agriculture—strategies and perspectives. IntechOpen, London, England, pp 57–85

    Google Scholar 

  • Dumont ES, Gassner A, Agaba G, Nansamba R, Sinclair F (2019) The utility of farmer ranking of tree attributes for selecting companion trees in coffee production systems. Agrofor Syst 93:1469–1483

    Article  Google Scholar 

  • FAO—Food and Agriculture Organization of the United Nations (2015) Statistical Pocketbook Coffee (2015). Available at: http://www.fao.org/3/a-i4985e.pdf. Accessed 8 June 2020. FAO, Rome, Italy

  • FAO—Food and Agriculture Organization (1968) Coffee mission to Ethiopia 1964–65. FAO, Rome, Italy

    Google Scholar 

  • Fatobene BJR, Andrade VT, Aloise GS, Silvarolla MB, Goncalves W et al (2017) Wild Coffea arabica resistant to Meloidogyne paranaensis and genetic parameters for resistance. Euphytica 213(8):1–9

    Article  Google Scholar 

  • Fazuoli LC, Lordello RRA (1978) Fontes de resistência em espécies de café a Meloidogyne exigua. NematolBras 3:49–52

    Google Scholar 

  • Fernandez D, Tisserant E, Talhinhas P, Azinheira H, Vieira A et al (2012) 454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant-rust interaction. Mol Plant Pathol 13(1):17–37

    Article  CAS  PubMed  Google Scholar 

  • Fernandez D, Santos P, Agostini C, Bon MC, Petitot AS et al (2004) Coffee (Coffea arabica L.) genes early expressed during infection by the rust fungus (Hemileia vastatrix). Mol Plant Patho 5(6):527–536

    Google Scholar 

  • Figueiredo A, Loureiro A, Batista D, Monteiro F, Várzea V et al (2013) Validation of reference genes for normalization of qPCR gene expression data from Coffea spp. hypocotyls inoculated with Colletotrichum kahawae. BMC Res Notes 6(1):388

    Google Scholar 

  • Florez JC, Mofatto LS, Freitas-Lopes RL, Ferreira SS, Zambolim EM et al (2017) High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection. Plant Mol Biol 95(6):607–623

    Article  CAS  PubMed  Google Scholar 

  • Gichuru EK, Agwanda CO, Combes MC, Mutitu EW, Ngugi ECK et al (2008) Identification of molecular markers linked to a gene conferring resistance to coffee berry disease (Colletotrichum kahawae) in Coffea arabica. Plant Pathol 57:1117–1124

    Article  CAS  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 Sudan. Euphytica 216:86

    Article  CAS  Google Scholar 

  • Gimase JM, Thagana WM, Omondi CO, Cheserek J, Gichuru EK (2021) Genetic relationship and the occurrence of multiple gene resistance to coffee berry disease (Colletotrichum Kahawae, Waller Bridge) within selected Coffea arabica Varieties in Kenya. Afr J Plant Sci 15(1):39–48

    Article  Google Scholar 

  • Girotto L, Ivamoto-Suzuki ST, Oliveira FF, Ariyoshi C, Santos TB et al (2019) Caracterização de promotores de Coffea spp. via transformação genética em planta modelo. In: X Simpósio de Pesquisa dos Cafés do Brasil. Vitória,Brazil. ISSN: 1984-9249

    Google Scholar 

  • Gonçalves W, de Lima MMA, Fazuoli LC (1988) Resistência do cafeeiro a nematóides: III., avaliação da resistência de espécies de Coffea ede híbridos interespecíficos a Meloidogyne incognita raça 3. NematolBras 12:47–54

    Google Scholar 

  • Grbić M, Van Leeuwen T, Clark RM, Rombauts S, Rouzé P et al (2011) The genome of Tetranychusurticae reveals herbivorous pest adaptations. Nature 479(7374):487–492

    Article  PubMed  PubMed Central  Google Scholar 

  • Guerreiro-Filho O, Denolf P, Peferoen M, Eskes AB, Frutos R (1998) Susceptibility of the coffee leaf miner (Perileucoptera spp.) to Bacillus thuringiensis delta-endotoxins: a model for transgenic perennial crops resistant to endocarpic insects. Current Microbiol 36:175–179

    Article  CAS  Google Scholar 

  • Guyot R, Hamon P, Couturon E, Raharimalala N, Rakotomalala JJ et al (2020) WCSdb: a database of wild Coffea species. Database 00:1–6

    Google Scholar 

  • Herrera JC, Alvarado G, Cortina H, Combes MC, Romero G et al (2009) Genetic analysis of partial resistance to coffee leaf rust (Hemileia vastatrix Berk et Br.) introgressed into the cultivated Coffea arabica L. from the diploid C. canephora species. Euphytica 167:57–67

    Article  Google Scholar 

  • Hindorf H, Omondi CO (2011) A review of three major fungal diseases of Coffea arabica L. in the rainforests of Ethiopia and progress in breeding for resistance in Kenya. J Adv Res2(2):109–120

    Google Scholar 

  • Holderbaum MM, Ito DS, Santiago DC, Shigueoka LH, Fernandes LE et al (2020) Arabica coffee accessions originated from Ethiopia with resistance to nematode Meloidogyne paranaensis. Aust J Crop Sci 14(08):1209–1213

    Article  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 (2019) Historical Data on the Global Coffee Trade (2020). http://www.ico.org/new_historical.asp. Accessed 8 June 2020. ICO, London, England

  • Idárraga SM, Castro AM, Macea EP, Gaitán AL, Rivera LF et al (2012) Sequences and transcriptional analysis of Coffea arabica var. Caturra and Coffea liberica plant responses to coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae: Scolytinae) attack. J Plant Interact 7(1):56–70

    Google Scholar 

  • Infante F (2018) Pest management strategies against the coffee berry borer (Coleoptera: Curculionidae: Scolytinae). J Agric Food Chem 66(21):5275–5280

    Article  CAS  PubMed  Google Scholar 

  • Ito DS, Sera T, Sera GH, Del Grossi L, Kanayama FS (2008) Resistance to bacterial blight in arabica coffee cultivars. Crop Breed Appl Biotechnol 8(2):99–1103

    Article  Google Scholar 

  • James C (2018) Executive summary-global status of commercialized biotech/GM crops. In: International service for the acquisition of agri-biotech applications (ISAAA), NY, EUA

    Google Scholar 

  • Jones JDG, Dangl JL (2006) The plant immune system. Nature 444:323–329

    Article  CAS  PubMed  Google Scholar 

  • Krishnan S, Ranker TA, Davis AP, Rakotomalala JJ (2015) Current status of coffee genetic resources: implications for conservation—case study in Madagascar. Acta Hort 1101:15–19

    Article  Google Scholar 

  • Kumar V, Madhava Naidu M, Ravishankar GA (2006) Developments in coffee biotechnology—in vitro plant propagation and crop improvement. Plant Cell Tiss Org 87(1):49–65

    Google Scholar 

  • Lashermes P, Hueber Y, Combes MC, Severac D, Dereeper A (2016) Inter-genomic DNA exchanges and homeologous gene silencing shaped the nascent allopolyploid coffee genome (Coffea arabica L.). Genes, Genomes, Genetics 6(9): 2937–2948

    Google Scholar 

  • Lemos S, Fonçatti LF, Guyot R, Paschoal AR, Domingues DS (2020) Genome-wide screening and characterization of noncoding RNAs in Coffea canephora. Non-coding RNA 6(3):39

    Google Scholar 

  • Leroy T, Henry AM, Royer M, Altosaar I, Frutos R et al (2000) Genetically modified coffee plants expressing the Bacillus thuringiensis cry1Ac gene for resistance to leaf miner. Plant Cell Rep 19(4):382–389

    Article  CAS  PubMed  Google Scholar 

  • Maciel KW, Destefano SAL, Beriam LOS, Almeida IMG, Patricio FRA et al (2018) Bacterial halo blight of coffee crop: aggressiveness and genetic diversity of strains. Bragantia 77(1):96–106

    Article  Google Scholar 

  • Maghuly F, Jankowicz-Cieslak J, Bado S (2020) Improving coffee species for pathogen resistance. CAB Reviews 15(9):1–18

    Google Scholar 

  • Maluf MP (2008) Tools for the development of engineered Meloidogyne-resistant coffee cultivars. In: Souza RM (ed) Plant-parasitic nematodes of coffee. Springer, Dordrecht, Netherlands, pp 191–205

    Google Scholar 

  • Matielo JB, Almeida SR, da Silva MB, Ferreira IB (2015) Siriema AS1, cultivar de cafeeiro com resistência à ferrugem e ao bicho mineiro. In: IX Simpósio de Pesquisa dos Cafés do Brasil. Curitiba, Brasil

    Google Scholar 

  • Melese K (2016) The role of biotechnology on coffee plant propagation: a current topics paper. J Biol Agric Healthcare 6(5):13–19

    Google Scholar 

  • Méndez-López I, Basurto-Rios R, Ibarra JE (2003) Bacillus thuringiensis serovar israelensis is highly toxic to the coffee berry borer, Hypothenemus hampeiFerr. (Coleoptera: Scolytidae). FEMS Microbiol Lett 226:73–77

    Google Scholar 

  • Merot-L’anthoene V, Tournebize R, Darracq O, Rattina V, Lepelley M et al (2019) Development and evaluation of a genome-wide coffee 8.5 K SNP array and its application for high density genetic mapping and for investigating the origin of Coffea arabica L. Plant Biotechnol J 17(7):1418–1430

    Google Scholar 

  • Mishra MK, Slater A (2012) Recent advances in the genetic transformation of coffee. Biotechnol Res Intl 2012:580857

    Article  CAS  Google Scholar 

  • Mohan SK, Cardoso RML, Paiva MA (1978) Resistência em germoplasma de Coffea ao crestamento bacteriano incitado por Pseudomonas garcae. Pesqui Agropecu Bras 13:53–64

    Google Scholar 

  • Mondego JMC, Guerreiro-Filho O, Bengtson MH, Drummond RD, Felix JM et al (2005) Isolation and characterization of Coffea genes induced during coffee leaf miner (Leucoptera coffeella) infestation. Plant Sci 169(2):351–360

    Google Scholar 

  • Muniz MFD, Campos VP, Moita AW, Gonçalves W, Almeida MRA et al (2009) Reaction of coffee genotypes to different populations of Meloidogyne spp.: detection of a naturally virulent M. exigua population. Trop plant Pathol 34(6):370–378

    Google Scholar 

  • Naidoo S, Slippers B, Plett JM, Coles D, Oates CN (2019) The road to resistance in forest trees. Front Plant Sci 10:273

    Google Scholar 

  • Navarro L, Zipfel C, Rowland O, Keller I, Robatzek S et al (2004) The transcriptional innate immune response to flg22. Interplay and overlap with Avr gene-dependent defense responses and bacterial pathogenesis. Plant Physiol 135(2):1113–1128

    Google Scholar 

  • Navarro-Escalante L, Hernandez-Hernandez EM, Nuñez J, Acevedo FE, Berrio A et al (2021) A coffee berry borer (Hypothenemus hampei) genome assembly reveals a reduced chemosensory receptor gene repertoire and male-specific genome sequences. Sci Rep 11:4900

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • NIH-National Human Genome Research Institute (2020) DNA sequencing costs: data. https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Costs-Data. Accessed 3 mar 2021. NIH, Bethesda, EUA

  • Noir S, Anthony F, Bertrand B, Combes MC, Lashermes P (2003) Identification of a major gene (Mex-1) from Coffea canephora conferring resistance to Meloidogyne exigua in Coffea arabica. Plant Pathol 52:97–103

    Article  CAS  Google Scholar 

  • Noriega DD, Arias PL, Barbosa HR, Arraes FBM, Ossa GA et al (2019) Transcriptome and gene expression analysis of three developmental stages of the coffee berry borer, Hypothenemus hampei. Sci Rep 9:12804

    Article  PubMed  PubMed Central  Google Scholar 

  • Noronha-Wagner M, Bettencourt AJ (1967) Genetic study of resistance of Coffea sp. to leaf rust. I. Identification and behaviour of four factors conditioning disease reaction in Coffea arabica to twelve physiologic races of Hemileia vastatrix. Can J Bot 45(11):2021–2031

    Google Scholar 

  • Oakeshott JG, Home I, Sutherland TD, Russell RJ (2003) The genomics of insecticide resistance. Genome Biol 4:202

    Google Scholar 

  • Oliveira GF, Nascimento ACC, Nascimento M, Sant’Anna IdC, Romero JV et al (2021) Quantile regression in genomic selection for oligogenic traits in autogamous plants: a simulation study. PLoS One 16(1): e0243666

    Google Scholar 

  • Orozco FJ, Schieder D (1982) Aislamiento y cultivo de protoplastos a partir de hojas de café. Cenicafé 33(4):129–136

    Google Scholar 

  • Patrício FRA, de Oliveira EG (2013) Alterações desafios do manejo no controle de doenças do café. Visão Agrícola 12:4

    Google Scholar 

  • Pereira AA, Baião AC (2015) Cultivares. In: Sakiyama N, Martinez H, Tomaz M, Borém A (eds) Café arábica do plantio à colheita. FUNEP, Viçosa, pp 24–45

    Google Scholar 

  • Perthuis B, Pradon JL, Montagnon C, Dufour M, Leroy T (2005) Stable resistance against the leaf miner Leucoptera coffeella expressed by genetically transformed Coffea canephora in a pluriannual field experiment in French Guiana. Euphytica 144(3):321–329

    Article  Google Scholar 

  • Pestana KN, Capucho AS, Caixeta ET, de Almeida DP, Zambolim EM et al (2015). Inheritance study and linkage mapping of resistance loci to Hemileia vastatrix in Híbrido de Timor UFV 443-03. Tree Genet Genomes 11:72

    Google Scholar 

  • Porto BN, Caixeta ET, Mathioni SM, Vidigal PMP, Zambolim L et al (2019) Genome sequencing and transcript analysis of Hemileia vastatrix reveal expression dynamics of candidate effectors dependent on host compatibility. PLoS One 14(4):e0215598

    Google Scholar 

  • Prakash NS, Marques DV, Varzea VMO, Silva MC, Combes MC et al (2004) Introgression molecular analysis of a leaf rust resistance gene from Coffea liberica into Coffea arabica L. Theor Appl Genet 109(6):1311–1317

    Google Scholar 

  • Ramos AH, Shavdia LD (1976) A die-back of coffee in Kenya. Plant Dis 60:831–835

    Google Scholar 

  • Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA et al (2013) Genome engineering using the CRISPR-Cas9 system. Nat Protoc 8(11):2281–2308

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ranson H, Claudianos C, Ortelli F, Abgrall C, Hemingway J et al (2002) Evolution of supergene families associated with insecticide resistance. Science 298(5591):179–181

    Article  CAS  PubMed  Google Scholar 

  • Ribas AF, Dechamp E, Champion A, Bertrand B, Combes M 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 

  • Rodrigues CJ, Bettencourt AJ, Rijo L (1975) Races of the pathogen and resistance to coffee rust. Annu Rev Phytopathol 13:49–70

    Article  Google Scholar 

  • Romero G, Vásquez LM, Lashermes P, Herrera JC (2014) Identification of a major QTL for adult plant resistance to coffee leaf rust (Hemileia vastatrix) in the natural Timor hybrid (Coffea arabica x C. canephora). Plant Breed 133:121–129

    Article  CAS  Google Scholar 

  • Salgado SML, Resende MLV, Campos VP (2005) Reprodução de Meloidogyne exigua em cultivares de cafeeiros resistentes e suscetíveis. Fitopatol Bras 30(4):413–415

    Article  Google Scholar 

  • Sander JD, Joung JK (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32(4):347–355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sanders M (2019) Breeding for coffee leaf rust resilience in Coffea sp. Nat Sci Educ 48:190102

    Article  Google Scholar 

  • Sant’ana GC, Pereira LF, 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 8:465

    Google Scholar 

  • Saucet SB, Van Ghelder C, Abad P, Duval H, Esmenjaud D (2016) Resistance to root-knot nematodes Meloidogyne spp. in woody plants. New Phytol 211:41–56

    Article  CAS  PubMed  Google Scholar 

  • Savary S, Willocquet L, Pethybridge SJ, Esker P, McRoberts N et al (2019) The global burden of pathogens and pests on major food crops. Nat Ecol Evol 3(3):430–439

    Article  PubMed  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 10:4642

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sera GH, Sera T, de Azevedo JA, da Matas JS, Ribeiro-Filho C et al (2006) Porta-enxertos de café robusta resistentes aos nematoides Meloidogyne paranaenses e M. incognita raças 1 e 2. Semina Cienc Agrar 27:171–184

    Article  Google Scholar 

  • Sera GH, Sera T, Ito DS, Ribeiro-Filho C, Villacorta A et al (2010) Coffee berry borer resistance in coffee genotypes. Braz Arch Biol Technol 53(2):261–268

    Article  Google Scholar 

  • Sera GH, Sera T, Fazuoli LC (2017) IPR 102—Dwarf arabica coffee cultivar with resistance to bacterial halo blight. Crop Breed Appl Biotechnol 17:403–407

    Article  Google Scholar 

  • Setotaw TA, Caixeta ET, Pereira AA, Baião de Oliveira AC, Cruz CD et al (2013) Coefficient of parentage in L. cultivars grown in brazil. Crop Sci 53:1237–1247

    Article  Google Scholar 

  • Setotaw TA, Caixeta ET, Zambolim EM, Sousa TV, Pereira AA et al (2020) Genome introgression of híbrido de timor and its potential to develop high cup quality C. Arabica cultivars. J Agric Sci 12(4):64

    Google Scholar 

  • Shigueoka LH, Sera T, Fonseca ICB, Andreazi E, Carducci FC et al (2017) Coffea arabica lines with resistance to nematode Meloidogyne paranaensis derived from crossings with IPR 100. Aust J Crop Sci 11:1203–1209

    Article  CAS  Google Scholar 

  • Silva MC, Nicole M, Guerra-Guimarães L, Rodrigues CJ Jr (2002) Hypersensitive cell death and post-haustorial defense responses arrest the orange rust (Hemileia vastatrix) growth in resistant coffee leaves. Physiol Mol Plant Pathol 60:169–183

    Article  CAS  Google Scholar 

  • Silva MC, Várzea V, Guerra-Guimarães L, Azinheira HG, Fernandez D et al (2006) Coffee resistance to the main diseases: leaf rust and coffee berry disease. Braz J Plant Physiol 18(1):119–147

    Article  CAS  Google Scholar 

  • Silva MC, Guerra-Guimarães L, Loureiro A, Nicole MR (2008) Involvement of peroxidases in the coffee resistance to orange rust (Hemileia vastatrix). Physiol Mol Plant Pathol 72(1):29–38

    Article  CAS  Google Scholar 

  • Silva RA, Zambolim L, Castro ISL, Rodrigues HS, Cruz CD et al (2018) The Híbrido de Timor germplasm: identification of molecular diversity and resistance sources to coffee berry disease and leaf rust. Euphytica 214(9):153

    Article  Google Scholar 

  • Silva GN, Nascimento M, Sant’Anna IdC, Cruz CD, Caixeta ET et al (2017) Artificial neural networks compared with Bayesian generalized linear regression for leaf rust resistance prediction in Arabica coffee. Pesq Agropec Bras 52(3):186–193

    Google Scholar 

  • Silva AG, Ariyoshi C, Shigueoka LH, Carducci FC, Pereira CTM et al (2019) Seleção assistida por marcadores associados ao gene SH3 de resistência à ferrugem alaranjada em genótipos de café. In: X Simpósio de Pesquisa dos Cafés do Brasil. Vitória, Brazil. ISSN: 1984-9249

    Google Scholar 

  • Silvestrini M, Junqueira MG, Favarin AC, Guerreiro-Filho O, Maluf MP et al (2007) Genetic diversity and structure of Ethiopian, Yemen and Brazilian Coffea arabica L. accessions using microsatellites markers. Genet Resour Crop Evol 54(6):1367–1379

    Google Scholar 

  • Sousa TV, Caixeta ET, Alkimim ER, Oliveira ACB, Pereira AA et al (2019) Early selection enabled by the implementation of genomic selection in Coffea arabica breeding. Front Plant Sci 9:1934

    Article  PubMed  PubMed Central  Google Scholar 

  • Spiral J, Pétiard V (1991) Protoplast culture and regeneration in Coffea species. In: 17th international conference on coffee science (ASIC). San Francisco, EUA, pp 383–391

    Google Scholar 

  • Strode C, Wondji CS, David JP, Hawkes NJ, Lumjuan N et al (2008) Genomic analysis of detoxification genes in the mosquito Aedes aegypti. Insect Biochem Mol Biol 38(1):113–123

    Article  CAS  PubMed  Google Scholar 

  • Talhinhas P, Batista D, Diniz I, Vieira A, Silva DN et al (2017) The coffee leaf rust pathogen Hemileia vastatrix: one and a half centuries around the tropics. Mol Plant Pathol 18(8):1039–1051

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tao Y, Xie Z, Chen W, Glazebrook J, Chang H et al (2003) Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae. Plant Cell 15(2):317–330

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • USDA—United States Department of Agriculture (2020) Production, supply and distribution. https://apps.fas.usda.gov/psdonline/circulars/coffee.pdf. Accessed 30 June 2020

  • 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. Intl J Mol Sci 20(21):5334

    Google Scholar 

  • van Boxtel J, Berthouly M, Carasco C, Dufuor M, Eskes A (1995) Transient expression of β-glucoronidase following biolistic delivery of foreign DNA into coffee tissue. Plant Cell Rep 14:748–752

    Article  PubMed  Google Scholar 

  • van der Vossen HAM (2009) The cup quality of disease-resistant cultivars of Arabica coffee (Coffea arabica). Expl Agri 45:323–332

    Article  Google Scholar 

  • van der Vossen HAM, Walyaro DJ (1980) Breeding for resistance to coffee berry disease in Coffee arabica II. Inheritance of resisitance. Euphytica 29:777–791

    Article  Google Scholar 

  • van der Vossen HAM, Walyaro DJ (2009) Additional evidence for oligogenic inheritance of durable host resistance to coffee berry disease (Colletotrichum kahawae) in arabica coffee (Coffea arabica L.). Euphytica 165:105–111

    Article  Google Scholar 

  • Várzea VMP, Marques DV (2005) Population variability of Hemileia vastatrix vs. coffee durable resistance. In: Zambolim L, Zambolim E, Várzea VMP (eds) Durable resistance to coffee leaf rust. UFV, Viçosa, Brazil, pp 53–74

    Google Scholar 

  • Vega FE, Brown SM, Chen H, Shen E, Nair MB et al (2015) Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei. Sci Rep 5:12525

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ventura JA, Costa H, Lima LDM (2017) Manejo de pragas do café conilon. In: Ferrão RG, da Fonseca AFA, Ferrão MAG, de Muner LH (eds) Café Conilon, 2nd edn. Incaper, Vitória, Brazil

    Google Scholar 

  • Villain L, Salgado SML and Trinh PQ (2018) Nematode parasites of coffee and cocoa. In: Sikora RA, Coyne D, Hallmann J, Timper P (eds) Plant parasitic nematodes in subtropical and tropical agriculture, 3rd edn. CABI, Boston, EUA, pp 536–583

    Google Scholar 

  • Villalta-Villalobos J, Rojas-Lorz L, Valdez-Melara MF, Arrieta-Espinoza G, Pereira LFP et al (2016) Use of biotechnological tools for crop improvement of coffee (Coffea arabica L.) varieties against coffee berry borer (CBB). In: 26th international conference on coffee science (ASIC). Kunming, China, p 21

    Google Scholar 

  • Willis JH (2010) Structural cuticular proteins from arthropods: annotation, nomenclature, and sequence characteristics in the genomics era. Insect Biochem Mol Biol 40:189–204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wolt JD, Wang K, Yang B (2016) The regulatory status of genome-edited crops. Plant Biotechnol J 14(2):510–518

    Article  CAS  PubMed  Google Scholar 

  • Xuehui B, Lihong Z, Yongliang H, Guanghai J, Jinhong L, Zhang H (2013) Isolation and identification of the pathogen of coffee bacterial blight disease. Chin J Trop Crop 34:738–742

    Google Scholar 

  • Zambolim L, Caixeta ET (2021) An overview of physiological specialization of coffee leaf rus—new designation of pathotypes. Intl J Curr Res 13(1):15479–15490

    Google Scholar 

  • Zambolim L, Vale FXR, Maciel-Zambolim E (2005) Doenças do cafeeiro (Coffea arabica e C. canephora). In: Kimati H, Amorim L, Rezende JAM, Bergamin Filho A, Camargo LEA (eds) Manual de Fitopatologia 2rd ed. Agronômica Ceres, São Paulo, Brazil, pp 165–180

    Google Scholar 

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

    Google Scholar 

  • Zhang H, Chu Y, Dang P, Tang Y, Clevenger JP et al (2020) Identification of QTLs for resistance to leaf spots in cultivated peanut (Arachis hypogaea L.) through GWAS analysis. Theor Appl Genet 133:2051–2061

    Google Scholar 

  • Zhong GY (2001) Genetic issues and pitfalls in transgenic plant breeding. Euphytica 118:137–144

    Article  CAS  Google Scholar 

  • Zipfel C, Rathjen JP (2008) Plant Immunity: AvrPto targets the frontline. Curr Biol 18:218–220

    Article  Google Scholar 

  • Ziska LH, Bradley BA, Wallace RD, Bargeron CT, LaForest JH et al (2018) Climate change, carbon dioxide, and pest biology, managing the future: coffee as a case study.Agronomy 8(8):152

    Google Scholar 

  • Zoccoli DM, Takatsu A, Uesugi CH (2011) Ocorrência de mancha aureolada em cafeeiros na região do triângulo mineiro e alto paranaíba. Bragantia 70(4):843–849

    Article  Google Scholar 

  • Zong N, Xiang T, Zou Y, Chai J, Zhou JM (2008) Blocking and triggering of plant immunity by Pseudomonas syringae effector AvrPto. Plant Signal Behav 3(8):583–585

    Google Scholar 

Download references

Acknowledgements

This research was funded by the Fundação de Amparo à Pesquisa e Inovação do Espírito Santo. L.F.P. Pereira and E.T. Caixeta received research support from Consórcio Pesquisa Café, INCT Café and FAPEMIG. This study was partially financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil (CAPES) throughout scholarships for C. Ariyoshi, F.F. Oliveira, A.G. Silva. Fellowships from the Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil (CNPq) to E.T. Caixeta, L.F.P. Pereira and F.L. Partellli are also greatly acknowledged.

Author information

Authors and Affiliations

  1. Biological Science Center, State University of Londrina, Londrina, Paraná, 86057-970, Brazil

    Caroline Ariyoshi, Fernanda Freitas de Oliveira, Angelita Garbossi da Silva & Suzana Tiemi Ivamoto-Suzuki

  2. Area of Genetic Improvement and Plant Propagation, Paraná Rural Development Institute, Londrina, Paraná, 86047-902, Brazil

    Caroline Ariyoshi, Fernanda Freitas de Oliveira, Luciana Harumi Shigueoka, Angelita Garbossi da Silva, Suzana Tiemi Ivamoto-Suzuki, Gustavo Hiroshi Sera & Luiz Filipe Protasio Pereira

  3. School of Biology, University of Costa Rica, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica

    Andres Gatica Arias & Jimmy Villalta-Villalobos

  4. Institute of Applied Biotechnology to Agriculture, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil

    Eveline Teixeira Caixeta

  5. Empresa Brasileira de Pesquisa Agropecuária (Embrapa Café), Brasília, Distrito Federal, 70770-901, Brazil

    Eveline Teixeira Caixeta & Luiz Filipe Protasio Pereira

  6. Department of Agronomy, Center of Agricultural Sciences and Engineering, Federal University of Espírito Santo, Alegre, Espírito Santo, 29500-000, Brazil

    Matheus Ricardo da Rocha & Willian Bucker Moraes

  7. Center of North of Espírito Santo, Federal University of Espírito Santo, São Mateus, Espírito Santo, 29933-515, Brazil

    Fábio Luiz Partelli

Authors
  1. Caroline Ariyoshi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Fernanda Freitas de Oliveira
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Luciana Harumi Shigueoka
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Angelita Garbossi da Silva
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Andres Gatica Arias
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jimmy Villalta-Villalobos
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Suzana Tiemi Ivamoto-Suzuki
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Gustavo Hiroshi Sera
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Eveline Teixeira Caixeta
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Matheus Ricardo da Rocha
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Willian Bucker Moraes
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Fábio Luiz Partelli
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Luiz Filipe Protasio Pereira
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Fábio Luiz Partelli or Luiz Filipe Protasio Pereira .

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

Ariyoshi, C. et al. (2022). Current Challenges and Genomic Advances Toward the Development of Coffee Genotypes Resistant to Biotic Stress. In: Kole, C. (eds) Genomic Designing for Biotic Stress Resistant Technical Crops. Springer, Cham. https://doi.org/10.1007/978-3-031-09293-0_4

Download citation

Publish with us

Policies and ethics

Search

Navigation