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Strategies to revise agrosystems and breeding to control Fusarium wilt of banana


The recent emergence of the fungus Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), the deadly strain that causes Fusarium wilt of banana, has put the banana production chain for export under threat. Here, we propose research priorities and complementary strategies and challenges for effective and efficient mitigation management of Fusarium wilt. Our strategies include diversifying the agrosystems to increase crop resilience, as well as using precision breeding approaches to rapidly assess and introduce disease-resistance genes to develop stable and complete Foc resistance in commercial banana cultivars.

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Fig. 1: Two contrasting banana cropping systems.

Rony Swennen.

Fig. 2: Targeted genome editing of banana using CRISPR-Cas9.

Yasmín Zorrilla-Fontanesi.

Fig. 3: Integrated view of the proposed strategies for Fusarium wilt mitigation management in banana.


  1. García-Bastidas, F. et al. First report of Fusarium wilt tropical race 4 in Cavendish bananas caused by Fusarium odoratissimum in Colombia. Plant Dis. 104, 994 (2020).

    Article  Google Scholar 

  2. FAOSTAT Crops (Food and Agriculture Organization of the United Nations, 2020);

  3. Varma, V. & Bebber, D. P. Climate change impacts on banana yields around the world. Nat. Clim. Change 9, 752–757 (2019).

    Article  ADS  Google Scholar 

  4. Simmonds, N. W. & Shepherd, K. The taxonomy and origins of the cultivated bananas. J. Linn. Soc. Bot. 55, 302–312 (1955).

    Article  Google Scholar 

  5. Gold, C. S., Kiggundu, A., Abera, A. M. K. & Karamura, D. Diversity, distribution and farmer preference of Musa cultivars in Uganda. Exp. Agric. 38, 39–50 (2002).

    Article  Google Scholar 

  6. Gambart, C. et al. Impact and opportunities of agroecological intensification strategies on farm performance: a case study of banana-based systems in central and south-western Uganda. Front. Sustain. Food Syst. 23, 87 (2020).

    Article  Google Scholar 

  7. Wielemaker, F. in Achieving Sustainable Cultivation of Bananas. Volume 1: Cultivation Techniques (eds Kema, G. H. J. & Drenth, A.) Ch. 15 (Burleigh Dodds Science Publishing, 2018).

  8. Ordonez, N. et al. Worse comes to worst: bananas and Panama disease—when plant and pathogen clones meet. PLOS Pathog. 11, e1005197 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. Ndayihanzamaso, P. et al. The development of a multiplex PCR assay for the detection of Fusarium oxysporum f. sp. cubense lineage VI strains in East and Central Africa. Eur. J. Plant Pathol. (2020).

  10. Soluri, J. Accounting for taste: export bananas, mass markets, and Panama disease. Environ. Hist. 7, 386–410 (2002).

    Article  Google Scholar 

  11. Stover, R. H. Disease management strategies and the survival of the banana industry. Annu. Rev. Phytopathol. 24, 83–91 (1986).

    Article  Google Scholar 

  12. Bubici, G., Kaushal, M., Prigigallo, M. I., Gómez-Lama Cabanás, C. & Mercado-Blanco, J. Biological control agents against Fusarium wilt of banana. Front. Microbiol. 10, 616 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Kaushal, M., Mahuku, G. & Swennen, R. Metagenomic insights of the root colonizing microbiome associated with symptomatic and non-symptomatic bananas in Fusarium wilt infected fields. Plants. 9, 263 (2020).

    Article  CAS  PubMed Central  Google Scholar 

  14. Mollot, G., Tixier, P., Lescourret, F., Quilici, S. & Duyck, P. F. New primary resource increases predation on a pest in a banana agroecosystem. Agric. For. Entomol. 14, 317–323 (2012).

    Article  Google Scholar 

  15. Djigal, D. et al. Cover crops alter the soil nematode food web in banana agroecosystems. Soil Biol. Biochem. 48, 142–150 (2012).

    Article  CAS  Google Scholar 

  16. Karangwa, P. et al. Genetic Diversity of Fusarium oxysporum f. sp. cubense in East and Central Africa. Plant Dis. 102, 552–560 (2018).

    Article  CAS  PubMed  Google Scholar 

  17. Jassogne, L. et al. in Banana Systems in the Humid Highlands of Sub-Saharan Africa (eds Blomme, G. et al.) 144–149 (CABI, 2013).

  18. Norgrove, L. & Hauser, S. Yield of plantain under different tree densities and ‘slash and mulch’ versus ‘slash and burn’ management in a agrisilvicultural system in southern Cameroon. Field Crops Res. 78, 185–195 (2002).

    Article  Google Scholar 

  19. Zhu, Y. et al. Genetic diversity and disease control in rice. Nature 406, 718–722 (2000).

    Article  ADS  CAS  PubMed  Google Scholar 

  20. Deltour, P. et al. Disease suppressiveness to Fusarium wilt of banana in an agroforestry system: influence of soil characteristics and plant community. Agric. Ecosyst. Environ. 239, 173–181 (2017).

    Article  Google Scholar 

  21. Zhu, S. & Morel, J.-B. Molecular mechanisms underlying microbial disease control in intercropping. Mol. Plant Microbe Interact. 32, 20–24 (2019).

    Article  CAS  PubMed  Google Scholar 

  22. Wei, Z. et al. Initial soil microbiome composition and functioning predetermine future plant health. Sci. Adv. 5, eaaw0759 (2019).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  23. Yu, K., Pieterse, C. M. J., Bakker, P. A. H. M. & Berendsen, R. L. Beneficial microbes going underground of root immunity. Plant Cell Environ. 42, 2860–2870 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Morella, N. M. et al. Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection. Proc. Natl Acad. Sci. USA 117, 1148–1159 (2020).

    Article  CAS  PubMed  Google Scholar 

  25. Wille, L., Messmer, M. M., Studer, B. & Hohmann, P. Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes. Plant Cell Environ. 42, 20–40 (2019).

    Article  CAS  PubMed  Google Scholar 

  26. Christelová, P. et al. Molecular and cytological characterization of the global Musa germplasm collection provides insights into the treasure of banana diversity. Biodivers. Conserv. 26, 801–824 (2016).

    Article  Google Scholar 

  27. Ortiz, R. & Swennen, R. From crossbreeding to biotechnology-facilitated improvement of banana and plantain. Biotechnol. Adv. 32, 158–169 (2014).

    Article  CAS  PubMed  Google Scholar 

  28. Zuo, C. et al. Germplasm screening of Musa spp. for resistance to Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4). Eur. J. Plant Pathol. 151, 723–734 (2018).

    Article  Google Scholar 

  29. Chen, Y. F. et al. Fusarium wilt-resistant lines of Brazil banana (Musa spp., AAA) obtained by EMS-induced mutation in a micro-cross-section cultural system. Plant Pathol. 62, 112–119 (2013).

    Article  CAS  Google Scholar 

  30. Dale, J. et al. Transgenic Cavendish bananas with resistance to Fusarium wilt tropical race 4. Nat. Commun. 8, 1496 (2017).

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  31. McFadden, B. R. The unknowns and possible implications of mandatory labeling. Trends Biotechnol. 35, 1–3 (2017).

    Article  CAS  PubMed  Google Scholar 

  32. Cheng, K., Wang, Y., Zhang, R., Zhang, H. & Gao, C. CRISPR/Cas genome editing and precision plant breeding in agriculture. Annu. Rev. Plant Biol. 70, 667–697 (2019).

    Article  CAS  Google Scholar 

  33. Zaidi, S. S. -E. -A. et al. New plant breeding technologies for food security. Science 363, 1390–1391 (2019).

    Article  ADS  CAS  PubMed  Google Scholar 

  34. Zhang, Y., Pribil, M., Palmgren, M. & Gao, C. A CRISPR way for accelerating improvement of food crops. Nat. Food 1, 200–205 (2020).

    Article  CAS  Google Scholar 

  35. Ntui, V. O., Tripathi, J. N. & Tripathi, L. Robust CRISPR/Cas9 mediated genome editing tool for banana and plantain (Musa spp.). Curr. Plant Biol. 21, 100128 (2020).

    Article  Google Scholar 

  36. Shao, X. et al. Using CRISPR/Cas9 genome editing system to create MaGA20ox2 gene-modified semi-dwarf banana. Plant Biotechnol. J. 18, 17–19 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  37. Kaur, N. et al. CRISPR/Cas9-mediated efficient editing in phytoene desaturase (PDS) demonstrates precise manipulation in banana cv. Rasthali genome. Funct. Integr. Genomics 18, 89–99 (2018).

    Article  CAS  PubMed  Google Scholar 

  38. Naim, F. et al. Gene editing the phytoene desaturase alleles of Cavendish banana using CRISPR/Cas9. Transgenic Res. 27, 451–460 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Klimyuk, V. I. et al. A chromodomain protein encoded by the Arabidopsis CAO gene is a plant-specific component of the chloroplast signal recognition particle pathway that is involved in LHCP targeting. Plant Cell 11, 87–99 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Zhang, Y., Malzahn, A. A., Sretenovic, S. & Qi, Y. The emerging and uncultivated potential of CRISPR technology in plant science. Nat. Plants 5, 778–794 (2019).

    Article  PubMed  Google Scholar 

  41. Strosse, H. et al. Development of embryogenic cell suspensions from shoot meristematic tissue in bananas and plantains (Musa spp.). Plant Sci. 170, 104–112

  42. Escalant, J. V. & Teisson, C. Somatic embryogenesis and plants from immature zygotic embryos of species Musa acuminata and Musa balbisiana. Plant Cell Rep. 7, 181–186 (1989).

    Google Scholar 

  43. Kelliher, T. et al. One-step genome editing of elite crop germplasm during haploid induction. Nat. Biotechnol. 37, 287–292 (2019).

    Article  CAS  PubMed  Google Scholar 

  44. Jacquier, N. M. A. et al. Puzzling out plant reproduction by haploid induction for innovations in plant breeding. Nat. Plants 6, 610–619 (2020).

    Article  PubMed  Google Scholar 

  45. Veillet, F. et al. Transgene-free genome editing in tomato and potato plants using Agrobacterium-mediated delivery of a CRISPR / Cas9 cytidine base editor. Int. J. Mol. Sci. 20, 402 (2019).

    Article  PubMed Central  CAS  Google Scholar 

  46. Demirer, G. S. et al. High aspect ratio nanomaterials enable delivery of functional genetic material without DNA integration in mature plants. Nat. Nanotechnol. 14, 456–464 (2019).

    Article  ADS  CAS  PubMed  Google Scholar 

  47. Svitashev, S. et al. Genome editing in maize directed by CRISPR-Cas9 ribonucleoprotein complexes. Nat. Commun. 16, 13274 (2016).

    Article  ADS  CAS  Google Scholar 

  48. Zhang, Y. et al. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nat. Commun. 7, 12617 (2016).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  49. Woo, J. W. et al. DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nat. Biotechnol. 33, 1162–1164 (2015).

    Article  CAS  PubMed  Google Scholar 

  50. Sági, L. et al. Genetic transformation of banana and plantain (Musa spp.) via particle bombardment. Nat. Biotechnol. 13, 481–485 (1995).

    Article  Google Scholar 

  51. Sági, L., Remy, S., Panis, B., Swennen, R. & Volckaert, G. Transient gene expression in electroporated banana (Musa spp., cv. ‘Bluggoe’, ABB group) protoplasts isolated from regenerable embryogenetic cell suspensions. Plant Cell Rep. 13, 262–266 (1994).

    Article  PubMed  Google Scholar 

  52. Oh, T. J. et al. Genomic changes associated with somaclonal variation in banana (Musa spp.). Physiol. Plant. 129, 766–74 (2007).

    Article  CAS  Google Scholar 

  53. Lowe, K. et al. Morphogenic regulators Baby boom and Wuschel improve monocot transformation. Plant Cell 28, 1998–2015 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Panis, B., Withers, L. & De Langhe, E. Cryopreservation of Musa suspension cultures and subsequent regeneration of plants. Cryo Lett. 11, 337–350 (1990).

    Google Scholar 

  55. Ghosh, S. et al. Speed breeding in growth chambers and glasshouses for crop breeding and model plant research. Nat. Protoc. 13, 2944–2963 (2018).

    Article  CAS  PubMed  Google Scholar 

  56. Arinaitwe, I. K. et al. Evaluation of banana germplasm and genetic analysis of an F1 population for resistance to Fusarium oxysporum f. sp. cubense race 1. Euphytica 215, 175 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  57. Sun, J. et al. Comparative transcriptome analysis reveals resistance-related genes and pathways in Musa acuminata banana ‘Guijiao 9’ in response to Fusarium wilt. Plant Physiol. Biochem. 141, 83–94 (2019).

    Article  CAS  PubMed  Google Scholar 

  58. Zhang, L. et al. Transcriptomic analysis of resistant and susceptible banana corms in response to infection by Fusarium oxysporum f. sp. cubense tropical race 4. Sci. Rep. 9, 8199 (2019).

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  59. Li, C. et al. Analysis of banana transcriptome and global gene expression profiles in banana roots in response to infection by race 1 and tropical race 4 of Fusarium oxysporum f. sp. cubense. BMC Genom. 14, 851 (2013).

    Article  CAS  Google Scholar 

  60. Chatterjee, M. et al. Analysis of root proteome unravels differential molecular responses during compatible and incompatible interaction between chickpea (Cicer arietinum L.) and Fusarium oxysporum f. sp. ciceri Race1 (Foc1). BMC Genom. 15, 949 (2015).

    Article  CAS  Google Scholar 

  61. Shen, Y. & Diener, A. C. Arabidopsis thaliana RESISTANCE TO FUSARIUM OXYSPORUM 2 implicates tyrosine-sulfated peptide signaling in susceptibility and resistance to root infection. PLOS Genet. 9, e1003525 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. D’Hont, A., Denoeud, F. & Aury, J. et al. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488, 213–217 (2012).

    Article  ADS  PubMed  CAS  Google Scholar 

  63. Côte, F. et al. Agro-ecological intensification in banana and plantain (Musa spp.): an approach to develop more sustainable cropping systems for both smallholder farmers and large-scale commercial producers. Acta Hortic. 879, 457–463 (2010).

    Article  Google Scholar 

  64. Tixier, P., Malezieux, E. & Dorel, M. SIMBA-POP: a cohort population model for long-term simulation of banana crop harvest. Ecol. Model. 180, 407–417 (2004).

    Article  Google Scholar 

  65. Carvajal-Yepes, M. et al. A global surveillance system for crop diseases. Science 364, 1237–1239 (2019).

    Article  ADS  CAS  PubMed  Google Scholar 

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This work was supported by the Horizon 2020 Project ‘Microbial Uptakes for Sustainable Management of Major Banana Pests and Diseases’ (MUSA; grant agreement ID 727624). The authors also thank all donors who supported this work through their contributions to the CGIAR Fund (, and in particular to the CGIAR Research Program on Roots, Tubers and Bananas (RTB-CRP).

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R.S., H.V. and Y.Z.-F. led the writing of the paper. L.P., B.P. and S.S. contributed to the critical reading of the manuscript, and provided suggestions and contributed to the writing of specific sections. Y.Z.-F. composed Figs. 1, 2 and 3. S.S. composed Supplementary Fig. 1. R.S. and H.V. initiated and coordinated the manuscript.

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Correspondence to Hervé Vanderschuren or Rony Swennen.

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Zorrilla-Fontanesi, Y., Pauwels, L., Panis, B. et al. Strategies to revise agrosystems and breeding to control Fusarium wilt of banana. Nat Food 1, 599–604 (2020).

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