Understanding evolution of fungicide resistance in wheat blast field populations in Brazil; can we learn lessons for future disease management?

Some diseases are becoming very difficult to control due to lack of host resistance and limited availability of crop protection products. Resistance, tighter regulations and a slowing pipeline of new products are reducing the range of available chemical classes. This has lead to a greater dependence of compounds with fewer modes of action and, subsequently, increases the selective pressure for further cases of resistance. In order to increase the shelf life of new and currently available actives, evolution-smart integrated pest management strategies are needed.
This project will focus on the plant pathogen Pyricularia graminis-tritici (Pygt), the causal agent of wheat blast, an important fungal disease in Brazil that is very difficult to control, with several groups of fungicides (e.g. sterol demethylase, quinone outside and succinate dehydrogenase inhibitors) having become ineffective. Wheat blast has been a major disease across central and southern Brazil and was first described in Paraná State in 1985. Following the emergence of wheat blast in Bangladesh in 2016, it has further spread into India in 2017. These Asian strains are the same as that of Brazil due to contaminated seed import, and the disease is expected to move into Pakistan, South East Asia and Africa and is expected to impact food security, welfare and economic growth of millions of undernourished people. To improve disease control, a better understanding of the epidemiology, the fungicide sensitivity status and disease management strategies are needed. In this project we will focus on all three aspects using the lastest spore trapping technology, fungicide pheno- and genotyping assays as well as a fungicide target protein expression system, enabling to investigate the impact of target mutations on enzyme function and fungicide binding. These tools are generic and can be applied for other plant pathogens.

This proposal is a submission under BBSRC-FAPESP joint-priming awards for antimicrobial resistance. Resistance to chemical agents used in agriculture to control pests, weeds and pathogens is a threat to effective crop protection and therefore to food security. Some disease are becoming very difficult to control due to lack of host resistance and limited availability of crop protection products. Resistance, tighter regulations and a slowing pipeline of new products are reducing the range of chemical classes available, and greater dependence on fewer modes of action increases the selective pressure for further cases of resistance. In order to increase the shelf life of new and currently available actives, evolution-smart integrated pest management strategies are needed. Strategies based on different dose rates, alternations and mixtures of fungicides have been advocated to reduce the selection of resistance. However, debate continues as to which strategies are most effective and there is a need for more empirical data on the fundamental evolutionary processes underlying the selection of resistance.

Chemical control of wheat blast (Pyricularia graminis-tritici (Pygt)) is currently dependent on three different modes of action, the azoles, QoI and SDHI fungicides. In vitro fungicide sensitivity assays has revealed different levels of resistance to all three groups. In order to rationalise fungicides inputs (e.g. choice, timing, dose-rate, spray number and mixing/alternation) and to test anti-resistance strategies aimed to delay evolution and spread of resistance to these three groups of fungicides and to future new actives entering the market, high throughput monitoring tools, enabling quantitative measurement of pathogen levels and detection of fungicide resistant alleles, in combination with disease forecasting are needed. The main objectives of this pump-prime project are: 1, to improve our understanding of wheat blast epidemics; 2, to investigate current fungicide sensitivity status to azoles, QoIs and SDHIs of Pygt populations in different geographic areas in Brazil and identify fungicide resistance mechanisms and 3, to develop of a yeast-based heterologous expression system for high throughput screening of different CYP51 variants to allow us to investigate functional constraints on introduced cyp51 mutations through complementation assays.

The research outcomes, regarding data, assays and tools, can also be used in follow-up research on other fungicides and/or pathogens (second stage project). A yeast expression system can also be developed for succinate dehydrogenase expression studies of different Sdh variants from other pathogens, such as Phakopsora pachyrhizi (Asian soybean rust) for which SDHI resistance has already been reported in Brazil. New DNA markers (genetic alterations linked with fungicide resistance) can be used for quantitative detection of fungicide resistant alleles in aerosols and infected leaf samples to evaluate resistance management strategies in field trials. The new high volume cyclone will be further developed into an automated spore trap that can remotely extract DNA and test samples with isothermal DNA amplification for semi-quantitative detection of pathogens; this equipment is also able to beam this data and measured weather variables directly to end users. This tool can also used to quantify fungicide resistant alleles and/or spore levels of other diseases in Brazil, for example citrus black spot (Phyllosticta citricarpa), which would improve forecasting and optimising disease management strategies benefitting growers (lower production costs), consumers (food safety, less residues) and the environment (less pesticides).