Mobile And Real-time PLant disEase (MARPLE) diagnostics for strain-level identification of complex fungal pathogens

Authors: RADHAKRISHNAN, GURU - John Innes Center; COOK, NICOLA - John Innes Center; BUENO-SANCHO, VANESSA - John Innes Center; LEWIS, CLARE - John Innes Center; PERSOONS, ANTOINE - John Innes Center; MITIKU, ABEL - Ethiopian Institute Of Agricultural Research; HEATON, MATTHEW - John Innes Center; DAVEY, PHOEBE - John Innes Center; ABEYO, BEKELE - International Maize & Wheat Improvement Center (CIMMYT); ALEMAYEHU, YOSEPH - International Maize & Wheat Improvement Center (CIMMYT); BADEBO, AYELE - International Maize & Wheat Improvement Center (CIMMYT); BARNETT, MARLA - Limagrain Cereal Seeds; BRYANT, RUTH - Limagrain Cereal Seeds; CHATELAIN, JERON - Limagrain Cereal Seeds; Chen, Xianming; DONG, SUOMENG - Nanjing Agricultural University; HENRIKSSON, TINA - Lantmännen; HOLDGATE, SARAH - National Institute Of Agricultural Botany (NIAB); JUSTESEN, ANNEMARIE - Aarhus University; KALOUS, JAY - Limagrain Cereal Seeds; KANG, ZHENSHENG - Northwest Agricultural & Forestry University; LACZNY, SZYMON - Basf Plant Science Llc; LEGOFF, JEAN-PAUL - Centre De Recherche Sur Les Macromolécules Végétales (CERMAV); RICHARDS, TRACY - Limagrain Cereal Seeds; RANDHAWA, HARPINDER - Agriculture And Agri-Food Canada; THACH, TINE - Aarhus University; WANG, MEINAN - Washington State University; HOVMOLLER, MOGENS - Aarhus University; HODSON, DAVID - International Maize & Wheat Improvement Center (CIMMYT); SAUNDERS, DIANE - John Innes Center

Submitted to: BioMed Central Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/12/2019
Publication Date: 8/13/2019
Citation: Radhakrishnan, G.V., Cook, N., Bueno-Sancho, V., Lewis, C.M., Persoons, A., Mitiku, A.D., Heaton, M., Davey, P., Abeyo, B., Alemayehu, Y., Badebo, A., Barnett, M., Bryant, R., Chatelain, J., Chen, X., Dong, S., Henriksson, T., Holdgate, S., Justesen, A.F., Kalous, J., Kang, Z., Laczny, S., Legoff, J., Richards, T., Randhawa, H.S., Thach, T., Wang, M., Hovmoller, M.S., Hodson, D.P., Saunders, D.G. 2019. Mobile And Real-time PLant disEase (MARPLE) diagnostics for strain-level identification of complex fungal pathogens. Genome Biology. Volume 17, Article 65. https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0684-y.
DOI: https://doi.org/10.1186/s12915-019-0684-y

Interpretive Summary: Effective disease management depends on timely and accurate diagnosis to guide control measures. We developed a portable, genomics-based, point-of-care approach specifically tailored for identifying individual strains of complex fungal plant pathogens. Using targeted sequencing, we overcame limitations associated with the sheer size of fungal genomes and their frequent obligately biotrophic nature. This new method called Mobile And Real-time PLant disEase (MARPLE) diagnostics enables rapid identification of both newly emergent strains and those with specific properties such as fungicide resistance. We developed the method and demonstrated its usefulness using a global collection of wheat stripe rust samples. Generating results within 48 hour of field sampling, this new strategy has far-reaching implications for tracking plant health threats.

Technical Abstract: Effective disease management depends on timely and accurate diagnosis to guide control measures. We developed a portable, genomics-based, point-of-care approach specifically tailored for identifying individual strains of complex fungal plant pathogens. Using targeted sequencing, we overcame limitations associated with the sheer size of fungal genomes and their frequent obligately biotrophic nature. This new method called Mobile And Real-time PLant disEase (MARPLE) diagnostics enables rapid identification of both newly emergent strains and those with specific properties such as fungicide resistance. Generating results within 48 h of field sampling, this new strategy has far-reaching implications for tracking plant health threats.