A strategy for broad root disease resistance in barley

Increasing crop yield to feed the world is a major challenge of our century but it is hampered by diseases caused by filamentous plant pathogens. A particular challenge are diseases caused by root pathogens because several different fungi with similar infection strategies can lead to root rots. The arms race between pathogen and plant demands constant adjustment of crop germplasm to tackle emerging pathogen races with new virulence features. But specific resistance genes against root rotting pathogens are not known. In addition, resistance gene deployment by use of transgenic approaches has encountered significant opposition from the public.
A viable alternative is quantitative disease resistance based on manipulation of infection-critical host processes since it has a higher probability for durability and potentially may affect multiple different root pathogens. The innovative aspect of this proposal is to explore a newly discovered mechanism that is universally required for root access in monocot and dicot plants without impacting growth, development and seed yield traits as well as plant interactions with symbiotic fungi.

Barley is the fourth most cereal cultivated globally and pivotal to the UK economy. It is also an excellent experimental model with a fully sequenced diploid genome and extensive information on its shoot disease resistance and root microbiota. Our work has revealed that inactivation of a SCAR gene encoding a protein component of the conserved SCAR/WAVE complex involved in localised cell trafficking at root tips can alter cell walls and renders roots of barley resistant to a filamentous pathogen while having no detrimental impact on growth, development and seed yield.

Building on this knowledge and resource we can now address whether scar-mutant mediated barley root resistance extends towards Uk relevant filamentous root rot pathogens (oomycetes and fungi). We have already generated the required barley germplasm but require funding support to carry out a thorough characterisation of the infection process as well as infection studies with UK-relevant pathogens under ideal and stressed conditions. Importantly, we also want to examine the capacity of this germplasm to shape root associated microbiota and test its competence for fungal symbiosis.

Upon completion of the proposed experiments we will have a good understanding whether previously unexplored barley SCAR proteins control filamentous pathogen colonisation processes. We will know whether individual SCAR genes impact on root infections and whether they are required for fungal symbiosis. We will also have obtained important information on the impact of SCAR protein removal and on the plant's interaction with its soil environment. This will allow us to recommend a specific SCAR gene as promising target for non-transgenic mutagenesis breeding to achieve broad resilience against filamentous pathogens in cereals and to recruit industrial partners to develop a EU market-compatible final germplasm in barley varieties of economic relevance.

We propose to test whether barley with CRISPR/Cas9-inactivated SCAR genes display a quantitative resistance to hemibiotrophic and necrotrophic filamentous pathogens while maintaining fungal symbiosis. We have identified SCAR-C as prime candidate conferring quantitative resistance to the experimental model oomycete Phytophthora palmivora. We have furthermore generated barley lines inactivated in individual SCAR-A, B, C genes as well as crosses between scar-b x scar-c mutants. All individual barley scar mutant lines have been characterised for their growth, development and seed yield using macroscopic and microscopic imaging.
We will carry out an extensive characterisation of the scar-b and scar-c mutant lines with our well established barley root pathogen Phytophthora palmivora which allows tracing the pathogen as well as the symptom extent. In addition, we will employ several UK relevant fungal and oomycete barley root rot pathogens with hemibiotrophic and necrotrophic lifestyles. Moreover, we will test the impact of deleting SCAR genes on the formation of beneficial arbuscular mycorrhizal symbiosis and carry out infections under agriculturally relevant nutrient limiting or nutrient rich conditions and during drought stress known to enhance fungal diseases. Barley lines with altered infection phenotypes will be subjected to root system analysis and soil microbiota studies.
Upon completion we anticipate the identification of a line that is significantly more resistant to UK relevant root pathogens. Our comparisons of scar mutation mediated resistance to field-relevant accessions and medium-resistant accessions from prior work will demonstrate how much stronger this engineered resistance is compared to natural variation. This material will serve as proof-of-concept to initiate future work for mutagenesis-based breeding efforts to implement the trait into barley varieties of interest for the industry.