Sequencing the air to identify plant pathogens before they decimate crops

LEGGETT_E23CASE

Airborne crop pathogens pose a serious threat to food security and are responsible for devastating loss of yield. Early detection can enable farmers to take targeted action to reduce losses. In wheat, fungal diseases alone are estimated to cause losses averaging 21% (>160 million tonnes), with three cereal rusts amongst the most damaging. Yellow rust, caused by P. striiformis, is a constant threat to UK wheat production.

All current pathogen detection regimes for yellow rust rely on analysis post plant damage. In this project, however, we will deploy a state-of-the-art nanopore sequencing-based diagnostic to detect and monitor yellow rust pathogens present within captured air samples. Crucially, we hope to be able to demonstrate the ability to distinguish different genotypes/pathotypes. Such an approach would allow much earlier, more targeted treatment regimes.

The project is a collaboration between scientists at the Earlham Institute, John Innes Centre, the Natural History Museum, London, and the breeding company Elsoms Wheat. The research team combines expertise in metagenomics, bioinformatics, sequencing technology and crop pathogens. It would suit a student who is excited about carrying out both wet lab work and data analysis/bioinformatics. Training will be provided in all areas.

References

1. Leggett RM, Alcon-Giner C, Heavens D, Caim S, Brook TC, Kujawska M, Martin S, Hoyles L, Clarke P, Hall LJ, Clark MD (2020). Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics. Nature Microbiology 5:430–442.

2. Radhakrishnan et al. (2019). MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens. BMC biology 17(1):1-17.

3. Hales B, Steed A, Giovannelli V, Burt C, Lemmens M, Molnar-Lang M, Nicholson P (2020). Type II Fusarium head blight susceptibility conferred by a region on wheat chromosome 4D. Journal of experimental botany 71:4703- 4714.