Fungal effectors as activators of novel resistances in cereals

This is a joint project between the James Hutton Institute (JHI, formerly SCRI) and Rothamsted Research (RRes) that focuses on the "Combating pests and diseases" research challenge highlighted by the industrial members of the Crop Improvement Research Club (CIRC). It is addressing one of the highlighted areas for the second CIRC call: Crop protection. Two teams with complementary expertise in different areas of plant science will combine efforts in exploiting pathogen genome sequence. We aim to advance fundamental understanding of plant immune responses and identify novel sources of resistance to the most economically important barley fungal pathogen Rhynchosporium commune (Rc), formerly known as R. secalis.
Rc can cause yield losses of up to 40% and reduce grain quality. Populations of Rc can change rapidly, defeating new barley resistance (R) genes and fungicides after just a few seasons of their widespread commercial use. New EU regulations may lead to loss of the most effective triazole fungicides, making Rc control even more problematic.
All pathogens trigger non-host resistance (NHR) in plants. Successful pathogens can suppress or manipulate NHR by secretion of small proteins called 'effectors'. Once a pathogen has suppressed NHR, plants deploy a second layer of defence in the form of R proteins. R proteins detect certain pathogen effectors, termed 'avirulence' (Avr) proteins, and activate resistance responses. Pathogens can avoid recognition by some of the R proteins by losing either the expression or function of a non-essential (redundant) effector with no apparent cost to pathogen fitness. Both of these strategies have been deployed by Rc, mutating or eliminating AvrRrs1, to completely overcome Rrs1-mediated resistance in under 10 years.
We aim to understand redundancy within Rc effectors. R proteins recognising non-essential effectors are not durable. Therefore breeding should aim to target introgression of R genes recognising essential effectors that are less variable in pathogen populations. This effector type has been found for other fungal and oomycete plant pathogens.
Rc genome sequencing has provided a unique opportunity to identify the putative effector repertoire. Comparison of genome sequences of 9 Rc strains that are able to overcome different R genes will allow rapid prediction of candidate effectors that are less variable in Rc populations, and therefore are more likely to be indispensable. RNA sequencing of Rc germinated conidia and barley leaves infected with Rc provides important information about predicted effectors expressed during the onset of infection. Expression of less variable candidate Rc effectors will be assessed throughout the infection. Based on expression profiles, degree of conservation between the strains, and the ability to induce cell death in one or more barley genotype, 25 predicted effectors will be chosen for targeted gene disruption to identify those essential for fungal pathogenicity.
The RRes team has recently developed an efficient system for screening barley germplasm for recognition of Rc effectors. It is based on systemic expression of Rc small secreted proteins in barley leaves using a plant virus as a delivery vector. This method can be extended to other cereals, including wheat, and their pathogens. The extensive JHI collection of barley cultivars, landraces and mapping populations will be screened to (1) identify novel sources of distinct and potentially durable resistances to Rc, which can be combined to increase the durability of resistance, and (2) characterise resistance already present in current breeding material. This will have direct positive impact on Rc disease resistance breeding programmes. Deployment of this resistance will stably increase yield and quality of new barley cultivars, while reducing fungicide use, greenhouse gas emissions and environmental pollution.

Recent sequencing of the Rhynchosporium commune (Rc) genome has provided a unique opportunity to identify and catalogue the putative effector repertoire mediating interactions with its host barley. Comparison of genome sequences of 9 Rc strains representing different physiological races will allow rapid prediction of candidate effectors less variable in Rc populations. Deep RNA sequencing of germinated Rc conidia and barley epidermal strips at 3 days post inoculation with Rc provided important information about predicted effectors expressed during fungal conidia germination and onset of infection. Less variable candidate Rc effectors will be expression profiled using quantitative RT-PCR in pre-infection stages and at 8 time points during first 2 weeks after inoculation of barley seedlings with highly virulent local contemporary Rc isolate L2A. Based on expression profiles, variability between strains and recognition by barley germplasm, 25 predicted effectors will be chosen for targeted gene disruption to identify those essential for pathogenicity.
The RRes team has recently developed an efficient system for screening barley germplasm for recognition of Rc effectors, which can be extended to other cereals, including wheat, and their pathogens. This method is based on systemic expression of Rc small secreted proteins in barley leaves using Barley stripe mosaic virus (BSMV) as a vector. The extensive JHI collection of barley cultivars, landraces and mapping populations will be screened to (1) identify novel sources of distinct resistances to Rc, which can be used in gene pyramiding to increase the durability of resistance, and (2) characterise resistance already present in current breeding material. This will have direct positive impact on Rc disease resistance breeding programmes by providing rapid identification of new effective resistance sources.

Crop plant diseases are a major threat to global food security. Rhynchosporium commune (Rc), formerly R. secalis, is one of the most destructive pathogens of barley worldwide. It can cause yield losses of up to 40% and decrease grain quality, thus discounting prices for quality uses such as malting. Rc can complete its infection cycle asymptomatically, allowing the disease threat to remain hidden only to appear and cause crop damage when conditions favour the pathogen. Populations of Rc can change rapidly, defeating new barley resistance (R) genes and fungicides after just a few seasons of widespread commercial use. New EU regulations may lead to loss of the most effective triazole fungicides, making Rc control even more problematic.
This proposal aims to address the problems faced by existing control measures through exploitation of the Rc genome to seek largely conserved, essential pathogenicity factors that can be targeted for sustainable barley protection. This information will be used to identify novel sources of potentially durable resistance to Rc that can be used in barley breeding, and to characterise resistance already present in current breeding material.
A major output of the project is understanding redundancy within Rc effectors. Non-essential (redundant) effectors are readily lost by the pathogen, leading to lower durability of host R genes recognising these effectors. This new knowledge will have direct impact on disease resistance breeding programmes. R gene introgression should target genes recognising effectors that are less variable in pathogen populations and essential to pathogenic fitness. R genes recognising different effectors and/or alleles of the same effector can be combined to provide more durable resistance. Characterisation of R genes to Rc present in barley varieties currently grown in UK as well as in existing breeding material will help to predict durability of these genes.
Barley germplasm representing novel sources of resistance to Rc from outside the elite gene pool will provide a key resource for exploitation by breeders to control this destructive pathogen. Deployment of this resistance will stably increase yield and quality of new barley cultivars as well as help to eliminate seed-borne infection. It will also lead to reduction of fungicide use (in line with new EU regulations), greenhouse gas emissions, environmental pollution and farm costs.
Data from the deep RNA sequencing of bulk susceptible barley lines before and after inoculation with Rc will provide an invaluable resource for identification of barley genes involved in non-host resistance that are suppressed by Rc during infection.
Industry uptake of the knowledge from this research will be facilitated by the regular CIRC workshops as well as excellent links with breeders forged through the BBSRC LINK projects and the Technology Strategy board grant. Resources and communication will also be promoted through the UK Barley Network which will be developed to continue the collaboration of researchers, breeders, maltsters, brewers and distillers beyond the end of AGOUEB project. We will use the links with the plant breeding community in CIRC to ensure that our exploitation plan is relevant and feasible.

Transient expression of pathogen effectors
Methods for efficient transient expression of pathogen effectors in barley used in this project can be extended to other cereals including wheat to benefit scientists and breeders both in the UK and worldwide.

Rhynchosporium diagnostics to forecast and respond to population changes
The sequence analyses of putative effectors in diverse Rc strains will provide the means to characterise future changes in natural Rc populations. Knowledge of effector diversity within the population will become a new diagnostic tool. It will allow growers to deploy the most appropriate, and thus effective, resistances to sustain durable disease resistance in the face of a changing pathogen population.