Screening for costs of disease resistance caused by stomatal dysfunction

Lead Research Organisation: John Innes Centre
Department Name: Crop Genetics


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.


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Description Wheat varieties combining the highest yields and good resistance against septoria and rusts have proven elusive. There is significant evidence that some disease resistance genes impose a yield penalty. 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, resulting in continued fungicide dependence, high input costs and strong pressure for fungicide insensitivity. It would be useful to be able to select effective resistance genes, without a yield cost. The aim of this project was to identify resistance genes or QTL which do, or do not, exhibit a yield penalty and develop methods to minimise 'yield drag' associated with breeding for disease resistance. Specifically four deliverables were addressed. (1) Quantify yield penalties associated with resistance genes/QTL effective against Zymoseptoria tritici (septoria tritici blotch), Puccinia striiformis (yellow rust) and Puccinia triticina (brown rust); (2) Quantify yield penalties associated with 'defeated' resistance genes/QTL; (3) Identify/optimise methods to screen future resistance genes/QTL for yield penalties; (4) Assess scope for using fungicides to ameliorate deleterious effects of host resistance responses. Significant yield costs associated with genetic resistance to septoria tritici blotch, yellow rust and brown rust were identified. Yield penalties were found to range between 0.3 - 1 t/ha depending on the resistance gene/QTL and genetic background of the variety. Significant yield costs could be quantified by the measurement of yield, healthy area duration of the crop canopy (HAD) and pre-anthesis radiation use efficiency (RUE). Lr37, a 'defeated' brown rust resistance gene exhibited yield losses in the absence of disease in three genetic backgrounds. Lines containing three septoria resistance QTL did not exhibit significantly greater yield losses than lines containing a single QTL, suggesting that 'stacking' of septoria resistance QTL within a variety may not increase yield costs. Not all resistance genes or QTL tested exhibited deleterious yield effects. It should therefore be 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) tested in the Thatcher background, 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 in some cases) could prove a useful pre-breeding technique to screen for resistance genes which are at risk of exhibiting deleterious yield effects. There was indirect evidence from field trials suggesting that certain fungicides may ameliorate physiological costs of resistance responses, where spore germination is reduced.
Exploitation Route 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 disease resistance genes in wheat can cause 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 does incur a significant cost of resistance, however, the yield cost does not appear to be 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.
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.

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.

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.

Controlled environment studies concluded that brown rust challenge can induce stomatal dysfunction in wheat.

Significant stomatal dysfunction was identified in all of the Thatcher NILs carrying Lr brown rust resistance genes in the presence of challenge, when compared to the recurrent parent.

In addition, three NILs (Lr20, Lr34 and Lr37) exhibited significantly lower stomatal conductance than Thatcher in the absence of disease, suggesting that these Lr genes are constitutively expressed.

Metabolomic analysis of Lr10, Lr34 and Lr37 NILs identified a significant accumulation of metabolites linked to the tricarboxylic acid (TCA) cycle and core phenylpropanoid pathway; a source of defence related phenolic compounds. Such changes in metabolic flux may demonstrate a specific cost of resistance in the form of allocation costs, which may also impact stomatal opening and could help explain yield losses associated with Lr37 in field trials.

Metabolomic analysis of key defence and energy metabolism compounds combined with stomatal conductance measurements, could potentially be an effective technique for identifying costs of resistance in pre-breeding programmes.

Fungicides can suppress yellow rust germination and infection in susceptible lines to levels similar to resistant wheat lines.

Yield increases associated with fungicide treatment are predominantly associated with increased healthy area duration of the crop canopy.

Certain fungicides can significantly improve 'leaf greening' and photosynthetic rate of the crop canopy.

However, certain fungicides can increase auto fluorescence and localised cell death, associated with elicitation of plant defence mechanisms.

Certain fungicides can significantly and consistently lower stomatal conductance.

To conclude, it appears that fungicide treatments can exert direct physiological effects on the host, many of which are considered to be beneficial to yield. However, it remains unclear whether these physiological responses can directly ameliorate the effects of costs of resistance.
Sectors Agriculture, Food and Drink,Environment

Description The findings are of use to plant breeders in designing programmes for breeding simultaneously for increased yield and higher disease resistance. The ways in which plant breeding companies exploit the results of research such as this are normally confidential but it is expected that it will enable them to optimise their choice of germplasm and to modify their variety trialling methods.
First Year Of Impact 2015
Sector Agriculture, Food and Drink,Environment
Impact Types Economic