Enhancing diversity in UK wheat through a public sector prebreeding programme

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

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

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Jones H (2013) Strategy for exploiting exotic germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss. example. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

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Moore G (2015) Strategic pre-breeding for wheat improvement. in Nature plants

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Shih PM (2016) Biochemical characterization of predicted Precambrian RuBisCO. in Nature communications

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Wingen LU (2014) Establishing the A. E. Watkins landrace cultivar collection as a resource for systematic gene discovery in bread wheat. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

 
Description Together with phenotyping at RRES and Nottingham, and private sector wheat breeders, we have developed a seamless pipeline to increase grain yield per unit of available nitrogen fertiliser (Nitrogen Use Efficiency, NUE), biomass (BM) potential, BM partitioning, and selected pest/disease resistances to wheat breeding and fundamental research. These traits are agreed targets of the WISP steering committee, representing UK strategic interests in the context of global grand challenges to wheat production.

The major output of this part of the WISP programme funded at John Innes was the development of pre-breeding germplasm derived from landraces. Over 800 landrace accessions remain in the A E Watkin landrace collection. Genotyping has enabled these accessions to be reduced to a core set of 120 landraces, capturing most of the inherent diversity. Each of the lines was crossed to an elite line Paragon, and segregating populations developed. These new populations of some 9000 unique individuals were genotyped to produce over three million data points. The populations were phenotyped for the traits described above, and within the WISP ISP (the follow-on ISP) the combination of genotyping, pehnotyping and population development results in more than 130 QTLs for yield, NUE, biomass being identified.

The combined activities of WISP lola, and the follow-on WISP iSP generated 26,000 prebreeding lines of which 20,000 were derived from landraces (JIC), 5000 from synthetics (NIAB) and 1000 from wild relatives (Nottingham). From this pre-breeding gemrplasm, lines are now being identified for further development along with the private sector breeding.
Exploitation Route 1) Six monthly reports reviewing progress and available germplasm for the breeders.
2) Showcasing the toolkit lines at a "Breeders day" at JIC, June 2013, 2014, attended by representatives of all major European breeding companies, BBSRC, DEFRA, HGCA, KTNs, and at the Cereals Show in a joint WISP display with RRES to the UK Cereal Farming community.
Sectors Agriculture, Food and Drink,Environment

URL http://wisplandracepillar.jic.ac.uk/
 
Description Three pre-breeding lines derived from initial landrace crosses in this programme, and further developed during the follow-on WISP ISP programme to reduce the size of introgressed segment, exhibited increased yields over just the elite line to 10 private sector breeding plots.
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description Conference organiser of PAG San Diego attracting 3800 plant and animal researchers 
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 I am on the organising committee of the largest plant and animal ag genomics conference attracting some 3800 researchers, policy makers, industry etc
Year(s) Of Engagement Activity Pre-2006,2006,2007,2008,
 
Description DFW Presentation to DEFRA chief science advisor 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact A discussion of the outcomes and impact of WISP and DFW programmes
Year(s) Of Engagement Activity 2019
 
Description Member of the board of the G20 wheat initative 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I am a board member of the G20 wheat initiative set up by the G20 agricultural ministers to facilitate coordination of wheat research in the G20 countries. We organise working group to facilitate such coordination, and to identify priorities for funding by funding agencies within the G20 countries
Year(s) Of Engagement Activity 2011,2012,2013,2014,2015
 
Description Member of the management board of CGIAR wheat programme (CIMMYT and ICARD) to breed wheat for the resource-poor in the developing World 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A management board member of CGIAR wheat programme (CIMMYT and ICARD) to breed wheat for the resource-poor in the developing World
Year(s) Of Engagement Activity 2011,2012,2013,2014,2015
 
Description Organisation a day workshop at Eucarpia meeting , Clermont_Ferrand Paris, with INRA (French) and Proweizen (German ) and CIMMYT researchers 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The worship was to discuss possible collaborations which could lead to bids into the EU for funding
Year(s) Of Engagement Activity 2018
 
Description Presentation on DFW at the DEFRA stakeholders WGIN meeting at RRES 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Request for more information on the programme
Year(s) Of Engagement Activity 2017