Enhancing diversity in UK wheat through a public sector prebreeding programme

Lead Research Organisation: University of Bristol
Department Name: Biological Sciences

Abstract

Food security is becoming a critical issue both in the UK and worldwide due to rapid population expansion, dietary changes, climate change and declining fossil fuel stocks. In the next 50 years, we will need to grow as much wheat grain as has been produced since the beginning of agriculture, some 10,000 years ago. The requirement to enhance the amount of wheat grown in the UK creates a major challenge for research. We need to develop new wheat varieties which have higher yields with lower nutrient requirements, whilst retaining the quality of the grain. Historically the Plant Breeding Institute (PBI) made experimental crosses with wild wheats and related grasses, capable of transferring traits of high agronomic potential into wheat, but still requiring further breeder selection to generate varieties with elite performance. However, the PBI was privatised in 1987 and research developing new experimental crosses of this kind almost stopped. This has created a major bottleneck for wheat breeders, because they do not have the necessary new experimental lines from which to develop new varieties with increased yield. The objective of this proposal is to re-establish a pre-breeding programme in wheat developing such experimental crosses in the UK. Such a pre-breeding programme will produce wheat germplasm, characterised for the next generation of key traits, such as yield, and will identify genetic markers for selecting these traits, in breeding programmes and for the academic community. We will develop novel pre-breeding wheat germplasm, using three different but complementary strategies, to maximise the introduction of diversity and beneficial traits into a range of wheat lines. First we will develop germplasm from crosses involving wheat landraces or locally adapted varieties, derived from exiting germplasm collections. Secondly we will create synthetic hexaploid wheats by artificially crossing tetraploid or 'pasta' wheats with diploid wheat progenitors. This captures diversity in both the tetraploid and diploid wheat progenitors. The potential of these synthetics is illustrated by their success in the CIMMYT breeding programme. Thirdly we will use a technique called alien introgression, to transfer small segments of chromosomes of wild relatives containing the target genes, into wheat. Wild and cultivated relatives (alien species) provide a wealth of genetic variation for all characters of importance relative to yield, climate change and the environment. The impact of this approach has been illustrated by the transfer of rust resistance by Sears in the US saving its economy several billion dollars in the intervening years. The parental material used in the initial prebreeding crosses will be characterised to ensure the maximal levels of diversity are being exploited. New sequencing technologies will be used to generate very high density maps, providing the breeding companies with markers for 'precision' breeding, and the academic researchers with markers for fine dissection of key traits. Key target traits relating to yield, of interest to both UK breeders and academics, have been identified. We will screen for, biomass and enhanced N and P use efficiency, Take-All and insect resistance including Bulb fly and Aphids. The programme will not involve the actual cloning of the genes responsible for these particular traits, but will provide the germplasm as the starting point for such projects. The new germplasm generated in this project will be exploited by breeders for crossing with their elite lines to develop new varieties for use by farmers. All the information generated in the programme will be stored in a central database, and seed stored centrally, both being freely available within the UK to both academics and breeders alike.

Technical Summary

We propose a pre-breeding wheat programme to develop novel populations containing key agronomic traits as starting materials for the development of new varieties by plant breeders and the main resource for understanding the biological basis of these key traits. In collaboration with key stakeholders we have identified the most relevant and important yield and quality traits to study. We will focus on biomass and nutrient use efficiency, Take-all resistance and resistance to Bulb fly and Aphids. The programme will be structured around three complementary 'pillars', each of which will broaden the pool of genetic variation in wheat by a different route. The first will develop germplasm from crosses involving wheat landraces or locally adapted varieties, derived from the 'Watkins' and other collections. The second will create synthetic hexaploid wheats by artificially crossing tetraploid wheats with diploid wheat progenitors. This will capture diversity in both the tetraploid and diploid wheat progenitors. The third will use alien introgression to transfer small segments of chromosomes of wild relatives containing the target genes, into wheat. Wild and cultivated relatives (alien species) provide a wealth of genetic variation for all characters of importance relative to yield, climate change and the environment. A fourth pillar, which will involve the production of the elite performing wheat, will be undertaken independently by the breeding companies. The parental material used in the initial crosses will be genotyped, ensuring the maximal levels of diversity are being exploited. Next generation sequencing will generate very high density maps, providing the breeding companies with markers for 'precision' breeding, and academics with markers for fine dissection of key traits. Detailed phenotypic characterisation of the material will identify the best lines to be taken forward by the breeders and/or the academic partners to dissect the biology of the key traits.

Planned Impact

The development of a prebreeding programme to support the development of new varieties of wheat, a key crop for the UK, will have a major impact in addressing elements of the global challenge of food security. The beneficiaries of this work will be the UK wheat breeding community, the academic wheat community, international breeding centres and the Developing world. UK wheat breeders. The UK private wheat breeders have been consulted and engaged at every stage of the development of this proposal to ensure that this proposal and the consequent outputs are entirely relevant to their requirements. In recognition of the potential impact of this work, the British Society of Plant Breeders (BSPB), have written to BBSRC giving their strong support to the initiative. In discussion with the breeders, we have defined the populations, genotyping and phenotyping to be undertaken, with the collective objective of generating germplasm characterised for increased biomass, resource use efficiency and resistances to disease and insects. These are priority biological targets that the breeders have identified as being of most importance to them. Thus, as the germplasm is generated and characterised during the course of the programme, it will be available for trialling by the breeders within their own programmes. In addition, the breeders will be key stakeholders on the steering committee for the programme, ensuring that they remain informed and influential in determining the focus on specific populations to be generated and traits to study. This engagement will maxmise the BBSRC investment in relation to the development of economically relevant varieties. The programme will provide a direct bridge between the UK plant community funded by BBSRC and the privately funded wheat breeding programmes. Economic impact. The USDA reviewed the impact of the PBI pre-breeding programme before it closed in 1987. It concluded that the investment return of this programme for the UK economy covered the costs of all future research of an institute like the John Innes Centre well into the 21st century. There are clear examples of the exploitation of wild relatives and exotic germplasm to introduce novel resistance, yield or drought characteristics into wheat which have resulted in economic impacts globally of hundreds of million and in some cases billions of dollars. One example being the dwarfing gene for the green revolution introduced via a Japanese wheat Norin 10 from a Japanese landrace Shiro Daruma. Close on half the resistance genes for stem rust and leaf rust resistance originated in species which were not either bread or pasta wheats. More recently 25% of wheat now produced for Developing countries from CIMMYT's wheat programme is derived from wheat synthetics. If a novel source of Take-All resistance in wild species can be transferred to wheat, this would substantially alter european farming and crop rotation. International Breeding Centres. Many of the academics within this programme are also involved in interactions with CIMMYT, INRA, GATES foundation and wheat breeding programmes in the US and Australia. There is the opportunity during the course of this programme to enhance the exploitation of the germplasm generated by making it available through interactions with these international centres as many of the targets identified are also important to their own breeding programmes. Social and Training impact. Following privatisation of the PBI, wheat researchers with a whole range of skills have become dispersed across different types of institutes and universities in the UK. This programme will bring that skill base together, providing a framework within which young researchers can be trained in a wide range of skills involved in population development, genotyping and phenotyping. These key skills will be required to underpin future UK wheat programmes both in the public and private sectors.

Publications

10 25 50

 
Description The Genotyping theme part of this award is led by Prof KJ Edwards, at the University of Bristol. The objective is to genotype the new breeding material using SNPs developed in previous BBSRC programmes and next generation sequencing to develop low and very high density genotyping to characterise in detail the lines and populations generated within the project and link this to the phenotypic theme. Since the start of their project, in April 2011, the team at Bristol has achieved the following: a targeted re-sequencing next generation platform, used to sequence 48 lines has generated 99,945 varietal wheat SNPs; 5,388 wheat SNPs genotyped via KASPar-based technology on 169 lines; 81,587 wheat SNPs genotyped via iSelect-based technology on 528 lines; genetic maps in Avalon x Cadenza and Rialto x Savannah consisting of 17,626 SNP markers; a SNP based strategy capable of identifying ancestral and progenitor introgressions in hexaploid wheat; and in collaboration with JIC, a prototype web-based database aimed at integrating the genotyping and phenotyping data sets. added February 2017: 1. We have published a full description of the 35K Wheat Breeders' Axiom array and its use in high throughput genotyping. This genotyping platform is now in wide spread use by the global breeding community
2. We have used the 35K Wheat Breeders array to generate a consensus genetic map from five mapping populations consisting of ~22,000 markers
3. We have published a full description of the 820K HD wheat Axiom array and its use to analysis numerous WISP samples. The publication included a consensus genetic map of 56,000 SNPs
4. In collaboration with Nottingham, we have screened 2,688 lines using the 35K SNP Wheat Relative Axiom array, and the first of these results has been published
5. We have worked closely with the wheat breeders to analyse the data generated from both the 820K HD and the 35K wheat breeders arrays and to use this data to identify both introgressions and copy number variants
6. We have continued to update the CerealsDB and the WISP web sites and we note that the genotyping data has now been downloaded a total of 41,723 times
Exploitation Route The SNPs developed are also being used by the wheat academic community worldwide This project works closely with the wheat breeders and the genotyping company LGC, hence exploitation routes are in place and already delivering useful and used wheat SNP markers.

In addition we have worked closely with the wheat breeders and Affymetrix to develop three high throughput genotyping arrays, these provide the community (academic and industrial) with cheap reliable genotyping. We are continuing to work with our partners to develop further resources.
Sectors Agriculture, Food and Drink

URL http://www.wheatisp.org/
 
Description They are being used by the wheat community including the wheat breeders
First Year Of Impact 2012
Sector Agriculture, Food and Drink
Impact Types Economic

 
Title 10,00 wheat KASP markers 
Description 10,000 wheat KASP markers made available as a commercial product via the company LGC 
Type Of Technology New Material/Compound 
Year Produced 2015 
Impact Cheap, flexible genotyping in wheat now available to the global community; this product is now a significant product in LGC's portfolio 
URL http://www.cerealsdb.uk.net/cerealgenomics/Index_Home.html
 
Title Axiom® Wheat Breeder's Genotyping Array 
Description Axiom® Wheat Breeder's Genotyping Array: Developed in collaboration with Affymetrix for large scale high throughput genotyping of wheat; specifically designed for wheat breeders. Now a commercial product and is currently being used by Uk and European wheat breeders 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2014 
Impact 384 microarray plate design makes it suitable for ultra high throughput genotyping of large numbers of wheat samples. It is currently the only one of its kind. 
URL http://media.affymetrix.com/support/technical/datasheets/axiom_wheat_breeders_genotyping_array_datas...
 
Title Axiom® Wheat HD Genotyping Arrays 
Description Axiom® Wheat HD Genotyping Array: Developed in collaboration with Affymetrix for large scale high throughput genotyping of wheat. Now a commercial product 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2014 
Impact Now makes the large scale genotyping of wheat a possibility 
URL http://www.affymetrix.com/catalog/prod850001/AFFY/Axiom%26%23174%3B-Wheat-Genotyping-Arrays#1_1
 
Description Stakeholder Workshop: Social Responsibility and Wheat Research 13/9/18 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Stakeholders talked about their own interests (and/or those of their community) in relation to the many uses of wheat. The event also considered stakeholder responses as the basis for a report on social responsibility and wheat research targeted at policy audiences
Year(s) Of Engagement Activity 2018