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

BMC Biology. 2019;17(1):1-17 DOI 10.1186/s12915-019-0684-y

 

Journal Homepage

Journal Title: BMC Biology

ISSN: 1741-7007 (Online)

Publisher: BMC

LCC Subject Category: Science: Biology (General)

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML

 

AUTHORS

Guru V. Radhakrishnan (John Innes Centre, Norwich Research Park)
Nicola M. Cook (John Innes Centre, Norwich Research Park)
Vanessa Bueno-Sancho (John Innes Centre, Norwich Research Park)
Clare M. Lewis (John Innes Centre, Norwich Research Park)
Antoine Persoons (John Innes Centre, Norwich Research Park)
Abel Debebe Mitiku (Ethiopian Institute of Agricultural Research)
Matthew Heaton (John Innes Centre, Norwich Research Park)
Phoebe E. Davey (John Innes Centre, Norwich Research Park)
Bekele Abeyo (International Maize and Wheat Improvement Center (CIMMYT))
Yoseph Alemayehu (International Maize and Wheat Improvement Center (CIMMYT))
Ayele Badebo (International Maize and Wheat Improvement Center (CIMMYT))
Marla Barnett (Limagrain Cereal Seeds)
Ruth Bryant (RAGT Seeds Ltd)
Jeron Chatelain (Limagrain Cereal Seeds)
Xianming Chen (USDA-ARS and Department of Plant Pathology, Washington State University)
Suomeng Dong (Nanjing Agricultural University)
Tina Henriksson (Lantmännen Lantbruk)
Sarah Holdgate (NIAB)
Annemarie F. Justesen (Aarhus University Flakkebjerg)
Jay Kalous (Limagrain Cereal Seeds)
Zhensheng Kang (State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University)
Szymon Laczny (BASF Poland)
Jean-Paul Legoff (RAGT 2n, Centre de Recherche de Druelle)
Driecus Lesch (Sensako)
Tracy Richards (Limagrain Cereal Seeds)
Harpinder S. Randhawa (Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre)
Tine Thach (Aarhus University Flakkebjerg)
Meinan Wang (USDA-ARS and Department of Plant Pathology, Washington State University)
Mogens S. Hovmøller (Aarhus University Flakkebjerg)
David P. Hodson (International Maize and Wheat Improvement Center (CIMMYT))
Diane G. O. Saunders (John Innes Centre, Norwich Research Park)

EDITORIAL INFORMATION

Peer review

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Instructions for authors

Time From Submission to Publication: 9 weeks

 

Abstract | Full Text

Abstract 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.