Pathogen Detection and Microbiome Analysis of Infected Wheat Using a Portable DNA Sequencer

Abstract

Fungal diseases of plants are responsible for major losses in agriculture, highlighting the need for rapid and accurate identification of plant pathogens. Disease outcomes are often defined not only by the main pathogen but are influenced by diverse microbial communities known as the microbiome at sites of infection. Here we present the first use of whole genome shot-gun sequencing with a portable DNA sequencing device as a method for the detection of fungal pathogens from wheat(Triticum aestivum)in a standard molecular biology laboratory. The data revealed that our method is robust and applicable to the diagnosis of fungal diseases including wheat stripe rust (caused byPuccinia striiformisf. sp.tritici),septoria tritici blotch (caused byZymoseptoria tritici)and yellow leaf spot (caused byPyrenophora tritici repentis).We also identified the bacterial genusPseudomonasco-present withPucciniaandZymoseptoriabut notPyrenophorainfections. One limitation of the method is the over-representation of redundant wheat genome sequences from samples. This could be addressed by long-range amplicon-based sequencing approaches in future studies, which specifically target non-host organisms. Our work outlines a new approach for detection of a broad range of plant pathogens and associated microbes using a portable sequencer in a standard laboratory, providing the basis for future development of an on-site disease monitoring system.

Genetic modification to improve disease resistance in crops

“…A third trend is the miniaturisation of sequencing technologies. Pathogen detection and analyses of the microbiome with a portable DNA sequencer has already successfully been executed (Hu et al, 2019). By the time that most solutions developed today will reach the field, such real-time monitoring of pathogen populations in the field will be possible and likely standardised enough to be performed by growers or agronomists.…”