Wheat Association Genetics for Trait Advancement and Improvement of Lineages

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

Abstract

Diseases of crops present major threats to the security of food supplies throughout the world. In the UK, our more important crop, wheat, is challenged by several significant harmful organisms including fungi, viruses and insects. Food production which is environmentally and economically sustainable requires crop yields to be maintained despite attacks by these pathogens. The two main pillars of disease control in arable crops are pesticide applications and the cultivation of resistant varieties. New legislation by the European Union will prevent increasingly severe obstacles to the introduction and use of pesticides from 2014 onwards, especially after 2018. Improved disease resistance is an important objective for wheat breeding but will become even more crucial to project food production in the UK once the new EU regulations come fully into effect. Almost all research on plant diseases, whether of crops or model species, focuses on single diseases. In field conditions, however, it is normal for crops to be attacked by epidemics of several pests and parasites simultaneously. This proposal takes a novel approach to researching the genetics of resistances to multiple diseases and their impact on yield. A particularly important goal is to identify genes for resistance to one disease which neither reduce yield nor increase susceptibility to other, non-target diseases. We will achieve this aim using association genetics, an approach which has proved extremely powerful in research on the genetics of disease and other traits in human populations. We will study a panel of 480 wheat varieties, including varieties which are commercially significant at present and their progenitors. We have chosen to study the four main diseases caused by fungi that attack the leaves of wheat plants. Together, these diseases present the main actual and potential threats to yield of wheat in UK conditions. There is currently good resistance in UK wheat varieties to powdery mildew and it is important that this desirable situation continues. Resistance to Septoria tritici has improved over the last ten years but this is still the most important wheat disease. Resistance to yellow rust is generally good by international standards but is often not durable, being quickly overcome through evolution of virulence in the fungus. There have been severe epidemics of brown rust in the UK in recent years and it is important that the average level of resistance of our wheat varieties to this disease is improved. An important goal is to generate a resource for use by the whole wheat research community. The association genetics analysis and the associated data, seed and DNA stocks will be a excellent resource for research on traits which are currently important. It will also, however, enable breeders and geneticists to respond to new threats, such as diseases which become important rapidly as a result of climate change or new agronomic practices; this has happened recently with Ramularia leaf spot of barley in northern Europe, including the UK. In summary, the association genetics approach will enhace current wheat breeding, especially for disease resistance, and enable us to be forearmed against future challenges.

Technical Summary

The central aim of this research is to create the first truly integrative map of the four foliar wheat diseases that most fungicide sprays are targeted to - Septoria tritici blotch (Mycosphaerella graminicola), yellow rust (Puccinia striiformis), brown rust (Puccinia triticina) and powdery mildew (Blumeria graminis). This will be primarily achieved by association mapping of multiple disease traits using a single panel of varieties which simultaneously varies for all the diseases. Efficient and effective genome-wide association scans have been shown to be feasible in elite wheat thanks to previous DArT-based association studies on smaller varietal panels which showed low LD decay rates coupled with the recent discovery of 1,000s of SNPs segregating in UK varieties. Specifically, we will establish and genotype a comprehensive panel of elite UK wheat varieties and make this panel and related genotype data and materials available as a community resource. Eight UK and EU breeding companies have come together with the academic partners to run the largest ever co-ordinated series of disease nursery trials ever undertaken on a single wheat panel of this size and nature. This unprecendented phenotyping effort in conjunction with the unique historic treated and untreated yield trial data series gives a unique basis on which to attempt to explore the wheat genome for factors which have quantitative effects in limiting multiple diseases without significant yield penalty. The partners will exploit their uniquely comprehensive collection of doubled haploid mapping populations from crosses between many pairs of varieties from the elite panel to validate a selection of loci discovered in association scans.

Planned Impact

Who will benefit from this research? The research proposed in WAGTAIL addresses the very important problem of how to maintain or increase yields of our major cereal crop, winter wheat, with considerably less fungicide than has become the norm in recent decades. This will benefit not only the UK wheat breeding industry, who are participants in this proposal, but arable farmers, consumers and society at large. How will they benefit? Wheat is the UK's major crop, grown on 2Mha annually, representing a farm-gate value of £1.6bn. 50% of the UK's pesticide usage is applied to wheat, accounting for 20% operating costs. Although fungicides protect crops, preventing annual yield losses worth over £300M, 6% of wheat production is currently lost to the four target diseases. EU legislation will remove many fungicides from farmers' armoury; if not mitigated, this will result in yield losses of 20-30% (figures from HGCA and CRD). The WAGTAIL consortium believes the project will enable breeders to routinely produce varieties which suffer half the current level of yield losses from disease, resulting in an annual financial benefit to farmers of £48M at current levels of fungicide usage. This figure could rise to £160-240M once EU plans to withdraw many fungicides are fully implemented at the end of this decade. The specific benefit of WAGTAIL to breeders is to increase their ability to release wheat varieties with all-round disease resistance but no yield penalty. Breeders will acquire unprecedented understanding of the trade-offs between resistance to different diseases and with yield, and their active participation in this project ensures their results will be applied in competitive private breeding programmes with a minimum of delay, for example by choosing appropriate varieties as crossing parents or by implementing strategies for marker-assisted selection. Please note that while the products of wheat breeding - i.e. wheat varieties - occupy a large proportof the UK's land area, the opportunity for the industry to profit from innovation is very small indeed. This is because wheat is a selfing plant so unless the price of seed is low, farmers can (and do) save seed from their own fields to re-sow the following year. Hence public-sector investment in the form of LINK and similar projects is vital to sustain the capacity of UK wheat breeding companies to respond to new demands, such as varieties with improved resistance. Cumulatively, many small adjustments to the disease resistance breeding process will impact in the performance of finished varieties. Since the first exploitable results will be obtained in year 2 of WAGTAIL, the first finished varieties that will be submitted to National List trials will appear approximately 7 years later and marketed to farmers 2-3 years after that. At that point farmers will begin to benefit in a concrete way from the research. Introduction of new wheat varieties which cost less to grow but have high yields will have downstream effects for consumers and for society in general. All parties will benefit from the more stable marketplace resulting from greater buffering of the production of wheat, the UK's leading crop, against the price fluctuations experienced through peaks and troughs in supply. WAGTAIL will thereby contribute to increased food security in increasingly volatile and unpredictable economic and environmental conditions. Moreover, fewer sprays applied to crops will result in lower carbon emissions, a more environmentally-benign rural environment, and less polluted water supplies.

Publications

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Description Analysis of results from this project is in progress and a detailed summary is not available at present. It will posted on Research
Fish when available.

A brief summary is that JIC conducted trials of the susceptibility of c. 500 wheat varieties in the WAGTAIL set to powdery mildew, and also coordinated and scored field trials of susceptibility to Septoria tritici blotch. These data have been integrated into the genome-wide association scans by collaborators at NIAB and Reading University and candidate loci for quantitative resistance to these two diseases have been identified.

Significant issues to be addressed by further analysis are the extent to which there is genotype-by-environment interaction in the expression of resistance which maps to the relevant quantitative trait loci (QTL), and whether responses to different diseases, whether synergistic or antagonistic, map to the same QTL.
Exploitation Route The results will be applicable to wheat breeding through the choice of parents for crossing, the design of selection schemes in breeding nurseries and the choice of elite lines to advance to official variety trials for the Classified and Recommended Lists.
Sectors Agriculture, Food and Drink

 
Description The results will be applicable to wheat breeding through the choice of parents for crossing, the design of selection schemes in breeding nurseries and the choice of elite lines to advance to official variety trials for the Classified and Recommended Lists. The exact ways in which plant breeding companies exploit information generated in this and other research projects is generally confidential.
First Year Of Impact 2014
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description WAGTAIL collaboration with NIAB & Reading 
Organisation National Institute of Agronomy and Botany (NIAB)
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Mildew and Septoria trials.
Collaborator Contribution Association genetics analysis of mildew and Septoria trials.
Impact Association genetics analysis of mildew and Septoria resistance in UK wheat varieties is in progress. Analysis is led by NIAB.
Start Year 2012
 
Description WAGTAIL collaboration with NIAB & Reading 
Organisation University of Reading
Country United Kingdom 
Sector Academic/University 
PI Contribution Mildew and Septoria trials.
Collaborator Contribution Association genetics analysis of mildew and Septoria trials.
Impact Association genetics analysis of mildew and Septoria resistance in UK wheat varieties is in progress. Analysis is led by NIAB.
Start Year 2012