Wheat Association Genetics for Trait Advancement and Improvement of Lineages

Lead Research Organisation: National Inst of Agricultural Botany
Department Name: Centre for Research

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 proportion of 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.
 
Description A publicly available panel of 495 wheat varieties, mostly recent varieties collectively forming the elite UK winter wheat gene pool together with some important progenitor material, has been assembled, seed multiplied to kilogram quantities and high quality DNA extracted. These tandem seed and DNA resources can be requested by bona fide researchers under a simple no obligation MTA.

All members of the panel have been genotyped with the Illumina 90k wheat SNP assay from which 31,363 informative markers were scored. This gives a very high resolution and high quality sampling of variation across all three sub-genomes of hexaploid wheat, providing the first comprehensive overview of the distribution of diversity and recombination in the elite UK wheat gene pool.

As of Autumn 2013, the entire panel has been through two full season's field trials consisting of 23 successful disease nursery trials in sites dispersed around the UK, Germany, Denmark and Sweden and as well as comprehensive scoring of disease symptoms for the targeted yellow and brown rusts, Septoria and mildew (where present), many phenology traits and morphological characters have been scored at one or more sites. The great range of site-year combinations meant that diverse pathogen populations and growing environments were sampled and for the rusts and Septoria, we saw significant divergence between groups of correlated trials, suggesting different resistances were providing protection depending on the local pathogen population and environment.

We have shown, similarly to our earlier findings in barley (cf BB/D524075/1), that with this panel size and density of SNP coverage, we can map simple Mendelian traits such as a toxin susceptibility locus or the awned character to very narrow genetic intervals containing small numbers of putative candidate genes, finding in both cases SNPs completely diagnostic for the trait within our panel.

We proceeded then to scan the genome for loci with significant effects in lowering scores of specific diseases both in each separate disease trial and in a series of meta-analyses. Nintey-nine unique disease resistance loci were found, of which 21 loci passed our most stringent discovery criteria. A few could be associated with know genes (e.g.Yr7, Yr17, Lr37, Pm3) but a majority were novel discoveries. One of the yellow rust resistances was significant in 13 our of 17 analyses and most likely represents the type of broad-spectrum, population independent resistance that the GWAS strategy was designed to uncover and was validated in a multi-parent mapping population.
Finally, we developed cheap, high-throughput markers for 28 individual hits and in an extensive validation excercise by industrial partners 13 were found to have significant effects in predicting YR resistance in breeding populations.
Exploitation Route The project has given a useful perspective on the extent and limits of diversity in the resistance to fungal diseases in the elite UK winter wheat genepool which can give useful information to agronomists and growers. Due to the involvement in this LINK project of eight wheat breeding companies, and in particular their central role in the validation of high throughput molecular breeding assays which were shown to have predictive value, it is a given that the possibilities to exploit the knowledge of marker-trait associations gained in this work in marker-assisted selection breeding programmes will be explored to the full and that this will contribute to the future performance of commercial wheat breeding in securing ongoing yield progress together with genetic resistance to an ever-evolving range of disease threats.
Sectors Agriculture, Food and Drink,Environment

 
Description All commercial wheat breeding partners to a greater or lesser extent have adopted the high-throughput molecular markers developed and validated during the project as means to practise selection for durable fungal disease resistance in their breeding programmes.
First Year Of Impact 2015
Sector Agriculture, Food and Drink
 
Description BBSRC DTP Targeted Studentship, Cambridge University/NIAB
Amount £75,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2015 
End 09/2019
 
Description Newton-Mosharafa Fund PhD programme
Amount £127,600 (GBP)
Funding ID NNM18/15 
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2015 
End 09/2019
 
Description Yellowhammer: A multi-locus strategy for durable yellow rust resistance in wheat, in the face of a rapidly changing pathogen landscape
Amount £548,682 (GBP)
Funding ID BB/R019231/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2018 
End 09/2022
 
Title Database of genetic markers for disease resistance loci in wheat 
Description Database of KASP markers for wheat loci associated with resistance to 4 major diseases of wheat in northern Europe: Yellow rust, Brown rust, Septoria tritici, mildew. For yellow rust KASP markers were validated as being associated with YR resistance in current breeder material. In addition, database contains further data on each hit, including trial locations and years where loci were significant, chromosomal locations, alternative KASP markers and, for yellow rust, information on which current breeder populations had successful validation, and which did not. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact The data is now being incorporated into wheat breeding programs of UK and northern European breeding companies who were part of the Wagtail LINK project. 
 
Title High density genotype dataset for UK Association mapping panel in wheat 
Description 26000 genotype dataset (using 90K Illumina SNP array) for comprehensive UK wheat association mapping panel (560 lines). About 18000 of the markers are mapped. 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Used by academic and commercial partners in Wagtail LINK project in their research and breeding programs. 
 
Description Collaboration with CCDM, Curtin University, Australia 
Organisation Curtin University
Country Australia 
Sector Academic/University 
PI Contribution Undertake work providing supporting data for grant proposals. Arrange for Eurasmus EU visiting student placements to help undertake research Undertake joint proposals to national/international funding agencies. Undertake joint PhD proposal applications. Undertake joint scientific manuscript. Arrange NIAB 'Visiting Fellow' status for lead Australian collaborator.
Collaborator Contribution Undertake work providing supporting data for grant proposals. Undertake joint proposals to national/international funding agencies. Undertake joint PhD proposal applications. Undertake joint scientific manuscript.
Impact Joint grant proposal to french levy board 'FSOV' submitted and funded. Joint grant proposal to EU call 'ERA-CAPs' submitted. BBSRC DTP Targeted Studentship PhD studentship application (outcome pending).
Start Year 2013
 
Description Discovery of recognition factors for Blumeria effector candidates 
Organisation Imperial College London
Department Department of Life Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution We proposed that the well-characterised panel of wheat varieties developed by us in BB/J0072607/1 (WAGTAIL) would make a suitable tool to screen elite wheat germplasm for factors capable of recognising individual pathogen effector candidates, as we had success in mapping host (wheat) susceptibility factors from a simple seedling leaf infiltration assay using Stagonospora toxins (cf collaboration between NIAB and Prof. Richard Oliver of Curtin University). The University of Reading made a fresh multiplication of seed stocks of the panel in 2014 for the purposes of facilitating large-scale screening with pathogen effectors and has made seed stocks available to ICL.
Collaborator Contribution ICL has followed up its leading role in the sequencing of the Blumeria graminis genome and the characterisation of the full effector complement of this important cereal pathogen with recent production of a library of effector candidates ready to be expressed in a bacterial effector delivery system. ICL has begun the process of screening our wheat collection for factors capable of inducing a resistance response when challenged by particular Blumeria effectors.
Impact Confidential.
Start Year 2015
 
Description Use of a bacterial effector delivery vector to discover novel PAMP and effector receptors 
Organisation University of Copenhagen
Department Department of Public Health
Country Denmark 
Sector Academic/University 
PI Contribution The University of Reading provided multiplied seed of 440 lines of the WAGTAIL wheat variety panel for screening for immune responses to heterologously expressed pathogen effectors delivered using non-pathogenic bacterial strains engineered to express the Type III Secretion System. Following immune response assays at the University of Copenhagen, UoR conducted genome-wide association scans to detect genomic regions responsible for any observed immune responses.
Collaborator Contribution The University of Copenhagen cloned a variety of effector candidate genes into the bacterial effector delivery strain and conducted the immune response assays.
Impact A novel immune response factor has been located with some precision and a small number of gene candidates are being examined. The work will be published when the identity of the causative immune receptor is sufficiently proven.
Start Year 2016
 
Description Camb. Plant Sci epidemiology groups 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact A seminar to the two epidemiology groups in the University of Cambridge Plant Sciences Department. To introduce to the methods and approaches of trait mapping and genomic selection in crops, highlighting some overlaps with epidemiological methodology.
Year(s) Of Engagement Activity 2016
 
Description Conference abstract and poster submission to Monogram 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference abstract and poster submission to Monogram 2017, titled "A large-scale association mapping analysis of wheat resistance to multiple fungal pathogens in multiple years and locations in NW Europe"
Year(s) Of Engagement Activity 2017
 
Description Conference talk - ICRISAT, India, International Conference on Statistics and Big Data Bioinformatics in Agreicultural Research 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at International Agricultural Statistics Conference attended by several hundred participants. Networking and discussing of topics relating to the project with scientists with similar interests over several days.
Year(s) Of Engagement Activity 2016
URL http://isas70.icrisat.ac.in/
 
Description Conference talk, Eucarpia 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk and abstract at Eucarpia 2016 conference, Switzerland, titled "A large-scale association mapping analysis of wheat resistance to multiple fungal pathogens across three years in multiple locations in NW Europe"
Year(s) Of Engagement Activity 2016
 
Description Oral presentation at EMBRAPA-Trigo, Passo Fundo, Brazil 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact talks sparked questions and discussion afterwards

led to the formulation of a research proposal, to be submitted to the appropriate upcoming UK-Brazil call
Year(s) Of Engagement Activity 2013
 
Description Oral presentation for Cambridge University Biological Sciences undergraduate students 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact talk sparked questions and discussions afterwards

Cambridge university undergradueates schedulaed to visit again next year
Year(s) Of Engagement Activity 2014
 
Description Oral presentation to Indian crop science deligation, NIAB 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact sparked questions and discussion afterwards

helped cement ties between participants of UK-India bi-lateral funding grants.
Year(s) Of Engagement Activity 2014
 
Description Oral presentation to MAX-CROP EU PhD students 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact talk sparked questions and discussions afterwards

Students and supervisors made aware of association mapping resources available at NIAB
Year(s) Of Engagement Activity 2014
 
Description Poster at Annual UK Cereal Community Monogram Conference, Bristol, 4th April 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster on Wagtail project at annual UK academic meeting for cereals researchers ("Monogram") leading to discussions of results and potential future collaborations.
Year(s) Of Engagement Activity 2017
URL http://www.monogram.ac.uk/MgNW2017.php
 
Description Poster at Eucarpia General Congress, August 29th, 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation of a poster on the Wagtail project at International Conference. Made some contacts for future activity in this area.
Year(s) Of Engagement Activity 2016
 
Description Presentation at Monogram 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation at Monogram 2014 - the main UK cereals research conference - preliminary results of Wagtail research
Year(s) Of Engagement Activity 2014
 
Description QMPB 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact NIAB run a two week intensive course in Quantitative Methods for Plant Breeding, covering relevant aspects of statistics, quantitative genuetics and population genetics. There are 25 participants every year. To date, no-one has said they would not recommend the course to others. The course has also been put on in Australia, France, India (once at ICRISAT and once at the Punjab Agricultural University) and Malaysia. We update it every year to disseminate developments and methods resulting from out own research work in MAGIC, genomic selection, association mapping and plant breeding strategy. It has resulted in a global set of new contacts, some of which have resulted in successful collaborations.
Year(s) Of Engagement Activity 2008,2009,2010,2011,2012,2013,2014,2015,2016
URL http://www.niab.com/pages/id/360/quantitative_methods_in_plant_breeding
 
Description Talk at 2018 UKCPVS (UK Cereal Pathogen Virulence Survey) annual stakeholders meeting, March 7, 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Talk on yellow rust resistance of UK wheat varieties, including Wagtail and Yellowhammer projects, at annual cereal pathogen update meeting for UK stakeholders: cereal breeders, farmers, levy board (AHDB), scientists and chemical industry (fungicide manufacturers) . Useful discussion with several participants and presentation of benefits of our research programme to industry audience.
Year(s) Of Engagement Activity 2018
 
Description Talk at Eucarpia Biometrics Conference in Ghent Belgium, September 5th 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk on detecting genetic interactions underlying yellow rust resistance in UK wheat, using association genetics and NIAB MAGIC populaition. As a result of the talk, I exchanged ideas at the meeting with other scientists interested in investigating genetic interactions.
Year(s) Of Engagement Activity 2018
URL https://www.eucarpia-biometrics2018.be/Congres/ScientificProgramme/tabid/9954/Default.aspx
 
Description Teaching annual NIAB Quantitative Genetics Course, March 12-23, 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Teaching Quantitative Genetics to Plant breeders (academic and industry) using this project as an example of GWAS approaches
Year(s) Of Engagement Activity 2018
 
Description Turkey Wheat Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Participation in one week workshop over multiple sites in Turkey to discuss UK - Turkish collaboration over wheat research, representing the NIAB Genetics and Breeding group on behalf of Dr Alison Bentley, the Director of Genetics and Breeding. Aside from questions and discussions at the time, it resulted in an agreement to sent some of our most resistant yellow rust lines to Turkey for screening, a novel approach to participatory plant breeding incorporating genomic selection and a collaborative grant application to the GCRF.
Year(s) Of Engagement Activity 2016