MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

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  • Guru Radhakrishnan, John Innes Ctr, BBSRC John Innes Center
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  • Nicola M. Cook, John Innes Ctr, BBSRC John Innes Center
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  • Vanessa Bueno-Sancho, John Innes Ctr, BBSRC John Innes Center
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  • Clare M. Lewis, John Innes Ctr, BBSRC John Innes Center
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  • Antoine Persoons, John Innes Ctr, BBSRC John Innes Center
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  • Abel Debebe Mitiku, Ethiopian Inst Agr Res, Ethiopian Institute of Agricultural Research (EIAR)
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  • Matthew Heaton, John Innes Ctr, BBSRC John Innes Center
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  • Phoebe E. Davey, John Innes Ctr, BBSRC John Innes Center
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  • Bekele Abeyo, Int Maize & Wheat Improvement Ctr CIMMYT
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  • Yoseph Alemayehu, Int Maize & Wheat Improvement Ctr CIMMYT
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  • Ayele Badebo, Int Maize & Wheat Improvement Ctr CIMMYT
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  • Marla Barnett, Limagrain Cereal Seeds
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  • Ruth Bryant, RAGT Seeds Ltd
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  • Jeron Chatelain, Limagrain Cereal Seeds
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  • Xianming Chen, Washington State Univ, Washington State University, Dept Plant Pathol
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  • Suomeng Dong, Nanjing Agr Univ, Nanjing Agricultural University, Dept Entomol
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  • Tina Henriksson, Lantmannen Lantbruk
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  • Sarah Holdgate, NIAB
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  • Annemarie F. Justesen
  • Jay Kalous, Limagrain Cereal Seeds
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  • Zhensheng Kang, Northwest A&F Univ, Northwest A&F University - China, Coll Plant Protect
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  • Szymon Laczny, BASF Poland
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  • Jean-Paul Legoff, RAGT 2n, Ctr Rech Druelle
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  • Driecus Lesch, Sensako
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  • Tracy Richards, Limagrain Cereal Seeds
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  • Harpinder S. Randhawa, Agr & Agrifood Canada, Agriculture & Agri Food Canada, Lethbridge Res & Dev Ctr
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  • Tine Thach
  • Meinan Wang, Washington State Univ, Washington State University, Dept Plant Pathol
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  • Mogens S. Hovmoller
  • David P. Hodson, Int Maize & Wheat Improvement Ctr CIMMYT
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  • Diane G. O. Saunders, John Innes Ctr, BBSRC John Innes Center

Background Effective disease management depends on timely and accurate diagnosis to guide control measures. The capacity to distinguish between individuals in a pathogen population with specific properties such as fungicide resistance, toxin production and virulence profiles is often essential to inform disease management approaches. The genomics revolution has led to technologies that can rapidly produce high-resolution genotypic information to define individual variants of a pathogen species. However, their application to complex fungal pathogens has remained limited due to the frequent inability to culture these pathogens in the absence of their host and their large genome sizes. Results Here, we describe the development of Mobile And Real-time PLant disEase (MARPLE) diagnostics, a portable, genomics-based, point-of-care approach specifically tailored to identify individual strains of complex fungal plant pathogens. We used targeted sequencing to overcome limitations associated with the size of fungal genomes and their often obligately biotrophic nature. Focusing on the wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici (Pst), we demonstrate that our approach can be used to rapidly define individual strains, assign strains to distinct genetic lineages that have been shown to correlate tightly with their virulence profiles and monitor genes of importance. Conclusions MARPLE diagnostics enables rapid identification of individual pathogen strains and has the potential to monitor those with specific properties such as fungicide resistance directly from field-collected infected plant tissue in situ. Generating results within 48 h of field sampling, this new strategy has far-reaching implications for tracking plant health threats.

Original languageEnglish
Article number65
JournalBMC Biology
Volume17
Issue1
Number of pages17
ISSN1741-7007
DOIs
Publication statusPublished - Aug 2019

    Research areas

  • Pathogen surveillance, Genomics, Point of care, Disease diagnostics, Wheat rust, Nanopore sequencing, RUST, WHEAT, RESISTANCE, RACES

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