Screening for costs of disease resistance caused by stomatal dysfunction

Lead Research Organisation: University of Nottingham
Department Name: Sch of Biosciences


Wheat varieties combining high yield and good resistance against three of the main foliar diseases in the UK (Septoria tritici blotch, yellow rust and brown rust) have proved elusive. There is now significant evidence in the scientific literature that some disease resistance genes, introduced into varieties by conventional plant breeding, impose a yield penalty on the crop. Hence, breeding for disease resistance creates 'yield drag' which slows the rate of yield improvement. This acts as a disincentive for breeders to focus efforts on selection for resistance, so most commercially popular, high yielding wheat varieties are susceptible to foliar diseases. The result of this is that fungicides are routinely used to control important foliar diseases. Dependence on fungicides is associated with high input costs for the grower and strong pressure for the disease-causing pathogens to develop insensitivity to the fungicides used, reducing the number of fungicides that remain effective. The project proposed here will test important disease resistance genes for their effects on attainable yield. This is difficult to achieve in plant breeding programmes currently, because: (i) there are large numbers of genes to test, (ii) without careful experimentation, measurements of the yield loss caused by each gene are hidden by the yield benefit they provide via disease control, and (iii) testing requires production of wheat lines that differ for presence or absence of the resistance gene but are otherwise highly similar. This is important in order to rule out any effects on yield caused by other differences between the resistant and susceptible wheat lines. It would be useful to be able to select resistance genes which provide the benefit of disease control, without an associated yield cost. Recently, evidence has accumulated that the deleterious effects on yield may be caused by disease resistance responses in the cells of the leaf surface disrupting the function of adjacent stomata. Stomata are pores in the leaf surface that normally open during the day (to allow CO2 to enter the leaf for photosynthesis) and close at night (to prevent unnecessary water loss when the leaf is not photosynthesising). As a result of the stomatal dysfunction caused by the resistance response, they may fail to open fully during the day or fail to shut properly at night. The project proposed here will test the idea that measurements of stomatal function can be used to screen resistance genes, to identify those which are, or are not, likely to have deleterious effects on yield. This would allow wheat breeders to focus on introducing genes which are effective against foliar diseases and benign in their effects on the plant.

Technical Summary

Recent evidence published from controlled environment (CE) studies demonstrates that host resistance responses to challenge by avirulent fungal plant pathogens can cause dysfunction of stomata adjacent to attempted infection sites. Subsequent field experiments, using near-isogenic lines (NILs) differing for presence/absence of resistance genes, have shown that the effects seen in the CE studies also occur in the field and suggest that stomatal dysfunction occurs with a wider range of cereal pathosystems and resistance genes than previously studied. The work proposed here will test the hypothesis that the yield 'cost' associated with certain resistance genes is caused by stomatal dysfunction. Plant breeders are supporting the project, as they require techniques to allow them to characterise novel resistance genes/QTL for the likelihood of an associated yield penalty, to inform decisions about introgression into their breeding material. If the hypothesis is supported, then stomatal conductance measurements could act as an indicator for physiological cost. Alternatively, such costs may be found to be associated with certain types of resistance response which can be characterised by microscopy (termed, microphenotyping). The specific objectives of the proposed LINK project are to: 1. Screen key disease resistance genes for yield costs. 2. Characterise disease resistance genes which contrast for presence or absence of yield cost for effects on stomatal function. 3. Relate stomatal dysfunction at a leaf level to impacts on radiation use efficiency at a canopy level and grain yield. 4. Test stomatal conductance as an indicator of yield potential in the light-limited environment of the UK. 5. Test improved porometry methods to increase screening throughput. The objectives will be addressed by a combination of CE experiments, field trials and microphenotyping, on NILs and lines from mapping populations of wheat, which contrast for key resistance genes.

Planned Impact

Improving crop yield for a given level of crop inputs (principally: land, fertiliser, water and fossil fuel) benefits productivity and reduces environmental impact per tonne of grain. If 'defeated' major genes are found to carry a yield penalty, then selecting against them in plant breeding programmes will increase the rate of yield improvement, without affecting disease control. If currently important resistance genes/QTL are found to carry a yield cost then decisions will need to be made about the trade-off between yield and disease resistance (and hence the degree of dependence on fungicides), until they can be replaced by alternative sources of resistance with lower yield costs. The work will ultimately lead to wheat varieties which combine high yield and good disease resistance. Disease resistance is likely to be more important in future if the availability of effective fungicides is constrained by: (i) revised legislation regulating the approval and use of crop protection products, and (ii) evolution of insensitivity in pathogen populations to the remaining available modes of action. Improving the disease resistance of varieties offers the best prospect for reducing dependence on fungicides and minimising the selective pressure placed on pathogen populations for fungicide insensitivity. Therefore resistant varieties benefit growers by maintaining disease control options, as well as reducing the level of inputs required. High yielding varieties will be crucial to ensure grain production meets projected rising demand and to minimise pressure for land use change and maintain food security. Conversion of grassland and semi-natural vegetation into arable production has adverse consequences for biodiversity and for greenhouse gas emissions from carbon sequestered in soil. Thus, high yielding varieties result in benefits for the wider society.
Description Key findings:

1. Quantification of yield penalties associated with septoria, yellow rust and brown rust resistance genes

- Significant yield penalties associated with septoria, yellow rust and brown rust resistance genes (including genes recently identified and those which are already widely used within UK breeding programmes) were observed during the course of this project.
- Costs of resistance associated with the disease resistance genes tested in wheat caused yield losses of between 0.3 - 1.0 t/ha. Such losses could have a serious impact on wheat productivity in the absence of pathogen challenge, particularly if this scale of yield impact accumulates for genes targeted against each of a number of key diseases.
- Stacking multiple septoria resistance QTL did not incur a yield cost that was significantly greater than a variety containing a single QTL. This finding needs to be corroborated with other populations and QTL, before being considered as generally true.
- Not all rust resistance genes exhibit a yield cost in the absence of disease. It should therefore be feasible for breeders to increase variety yield, by prioritising the most effective disease resistance genes based on their productivity in both the presence and absence of pathogen challenge.

2. Quantification of yield penalties associated with 'defeated' resistance genes widely distributed in current UK wheat varieties

- Prior to the work the brown rust resistance gene Lr37 was considered 'defeated' by virulent strains in the UK. Lr37 exhibited significant yield costs in the absence of disease, when tested in three genetic backgrounds.
- Brown rust races dominant in the UK have changed in recent years and Lr37 appears to be effective against current UK brown rust races and even with a modest epidemic the yield benefit can outweigh the cost.
- For continued yield improvement in the UK, wheat breeders should identify key resistance genes/QTL which do, or do not, exhibit yield costs in the absence of challenge, and review deleterious yield losses against effectiveness of resistance regularly, in order to prioritise the most efficient resistance in future breeding programmes.

3. Identification and optimisation of methods to screen future resistance for yield penalties, e.g. stomatal dysfunction, metabolic flux

- No evidence was found to suggest that septoria tritici blotch induces stomatal dysfunction in wheat in controlled environment conditions or that stomatal dysfunction plays a role in yield losses associated with septoria resistance genes in field conditions.
- Yield losses associated with septoria resistance QTL could be successfully quantified by measuring grain yield, grains/m2, grains/ear, healthy area duration (HAD) and pre-anthesis radiation use efficiency (RUE). However, such methods are labour intensive and costly and would therefore not be suitable to identify costs of resistance in early pre-breeding programmes. An alternative, less labour intensive approach, could be to use high-throughput spectral reflectance (NDVI) as an indicator of GAI, in order to calculate HAD.
- Controlled environment studies concluded that brown rust challenge can induce stomatal dysfunction in wheat.
Exploitation Route Results on how stomatal conductance at a leaf level relates to crop growth and yield in the UK have led new measurement
methodologies for analysing and interpreting stomatal conductance data from the field - in relation to fluctuating environmental variables. The methods are of interest to crop physiology researchers and will be disseminated via appropriate plant physiology journals.

The project findings should also assist wheat breeders to select varieties which combine high yield and good disease resistance. Improving the disease resistance of varieties offers the best prospect for reducing dependence on fungicides and minimizing the selective pressure placed on pathogen populations for fungicide insensitivity. High yielding varieties will be crucial to ensure grain production meets projected rising demand and to minimize pressure for land use change and maintain food security.
Sectors Agriculture, Food and Drink,Environment

Description Project results showed it is possible to prioritise resistance genes in breeding programmes, by selecting high productivity in the presence and absence of disease. A significant decrease in stomatal conductance and yield was associated with several Lr brown rust resistance genes (inc. Lr37), in the presence or absence of pathogen challenge. In addition, metabolic analysis identified a number of Lr genes, including Lr37, as being associated with significant metabolic changes even in the absence of challenge. Detection of changes in host metabolism (from which changes in stomatal conductance may result) could prove a useful pre-breeding technique to screen for resistance genes which are at risk of exhibiting deleterious yield effects. There was also indirect evidence from field trials suggesting that certain fungicides may ameliorate physiological costs of resistance responses, where spore germination is reduced. This information has been deployed by the breeding companies in the project consortium, RAGT Seeds Ltd and Limagrain UK Ltd in their breeding programmes.
First Year Of Impact 2014
Sector Agriculture, Food and Drink,Environment
Description TSB Agri Tech Catalyst Exploiting novel canopy sensors for improved disease management, variety selection and resilience in wheat
Amount £417,292 (GBP)
Funding ID TS/M002217/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2014 
End 02/2018
Title Database quantifying yield penalties associated with defeated resistance genes which are widely distributed in current UK wheat varieties, 
Description Field experiments quantify yield, biomass and water-use efficiency effects associated with brown rust, yellow rust and septoria resistance genes. 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Information of impacts of disease resistance genes were delivered to industrial partners RAGT Seeds, Limagrain and Syngenta Seeds and ADAS 
Description Partnership with INRA Grignon and Agro Paris Tech 
Organisation French National Institute of Agricultural Research
Country France 
Sector Academic/University 
PI Contribution Co Supervision of PhD student Francois Collin who is jointly Registered at University of Nottingham and Agro Paris Tech
Collaborator Contribution Co supervision of the above Phd Studentship of Francois Collin at University of Nottingham jointly registered by Nottingham and Agro Paris Tech
Impact PhD Studentship still in 1st year , studentship registered at Nottingham in September 2014
Start Year 2013