Enhancing diversity in UK wheat through a public sector prebreeding programme

Lead Research Organisation: University of Nottingham
Department Name: Sch of Biosciences

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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Reynolds M (2012) Achieving yield gains in wheat. in Plant, cell & environment

 
Description Key results:
• A panel of 240 wheat lines, including 120 landraces, has provided data for the identification of suitable mapping population parents
• At low N, synthetically derived lines had the mean highest biomass and nitrogen uptake
• The highest landrace biomass yield exceeded that of the highest yielding elite line at both N levels
• Comparing synthetic-derived lines to the recurrent parents, two SHW lines had higher flag-leaf photosynthesis rate than Paragon (P< 0.05).
• Pre-anthesis light-saturated photosynthesis rate was positively linearly associated with above-ground biomass amongst a subset of 15 wheat genotypes under high N conditions.
• 8 different mapping populations, each with a Watkins landrace parent have been grown at two sites and two levels of nitrogen.

The project produced an extensive phenotyping data set on a donor panel of 240 genotypes and 8 single seed descent
(SSD) mapping populations (Paragon spring wheat x Watkins landrace crosses). The project required refinement of field
phenotyping methodologies for assessment of biomass, photosynthetic capacity traits and N-use efficiency (grain DM / N
available from soil and/or fertilizer; NUE) and NUE components. Advanced protocols were developed for scoring canopy size and senescence kinetics using spectral reflectance techniques (Normalized Difference Vegetation Index, NDVI) as well as protocols for determining stem, leaf, and ear N content (NIRS spectroscopy). These high-throughput and low cost screens allowed very large scale field phenotyping. The output of this was the identification of donor and SSD lines with
improved biomass and NUE compared to the UK elite check cultivars and the parent lines of the mapping populations for
development of genetic resources at John Innes Centre (SSD mapping populations and near-isogenic lines).
Specifically, the germplasm screened in replicated trials under low and high N conditions in the phenotyping programme in
field experiments at Nottingham in 2010/11, 2011/12 and 2012/13 comprised:
Donor Panel: (232 genotypes) in 2010/11 and 2011/12
- 119 AE Watkins landraces
- 63 Gediflux genotypes (Wide collection of European wheat cultivars)
- 40 Synthetic-derived hexaploid wheats
- 10 UK Recommended List cultivars (controls)

8 Paragon x Watkins Landrace Single Seed Descent mapping populations in 2011/12 and 2012/13

- Paragon x Watkins 034 (95 individual SSD lines)
- Paragon x Watkins 141 (96 individual SSD lines)
- Paragon x Watkins 209 (88 individual SSD lines)
- Paragon x Watkins 292 (96 individual SSD lines)
- Paragon x Watkins 352 (96 individual SSD lines)
- Paragon x Watkins 468 (96 individual SSD lines)
- Paragon x Watkins 729 (82 individual SSD lines)

In the donor trials, performance was compared at high and low N inputs, between sites (Nottingham and Rothamsted) and
across years, with in-season high-throughput growth analysis (e.g. NDVI), with final N analysis and in terms of finalbiomass and grain yields. Germplasm was idenitified for which mapping populations are now prioritized (grain yields,
biomass, NUE, high/low responsiveness) for ongoing phenotying in the BBSRC Wheat Improvement Strategic Programme (WISP).

In summary, field phenotyyping and data analysis has been completed in: i) a trial of donor germrplasm in each
of 2010-11 and 2011-12 (a total of 2,880 plots) and ii) a trial of 8 mapping populations in each of 2011-12 and 2012-13 (a
total of 9600 plots). These data have been supplied to John Innes Centre for genetic metaanlysis and database archiving.
Field methodologies have been developed for high-throughput analysis of biomass and NUE using canopy sensors. For a subset of 15 donor lines (5 Watkins landraces, 5 NIAB synthetic hexaploid wheats and 5 RL cultivars) with similar flowering date and plant height, flag-leaf photosynthetic rate (Amax) was measured using a Li-Cor LI-6400XT portable Photosynthesis System. Overall synthetic and elite RL wheats had higher pre-anthesis Amax (25.7 and 25.2 micromol CO2 m-2 s-1, respectively) compared to Watkins lines (20.1 micromol CO2 m-2 s-1). There was a positive linear relationship between flag-leaf Amax and grain yield averaged over years amongst the 15 genotypes (R2 = 0.76, P< 0.001) and Amax in turn was positively linearly related with flag-leaf relative chlorophyll content measured using a SPAD-502 meter(R2=0.74, P< 0.001).
Exploitation Route The phenotyping data generated in the field experiments at Nottingham University for the Donor panel and the Watkins x
Paragon mapping populations have been sent to collaborators at Rothamsted (for cross site-season analysis of biomass,
NUE and their physiological components) and to John Innes Centre for genetic analysis and will be placed into public
databases. All the phenotyping data will be available via data bases at John Innes Centre (based on an extension of
Germinate data base) and at University of Bristol (based on a phenotype extension to the Cereals DB). All the published
papers are freely accessible, either through the publishers or through open access sites,. We will also make our
publications available through our WISP website.

The UK Wheat breeding companies are part of the WISP consortium and will utilized the project outputs to imporve the efficiency of their breeding programmes for enhanced biomass and N-use efficiency.
Sectors Agriculture, Food and Drink,Environment

 
Description The UK private sector wheat breeding companies are represented on the management steering committee of the project. Therefore there has been exchange of phenotpying results with the private sector wheat breeders through presentations made at steering meetings and through phenotyping datasets made available on project web pages. Results from the Nottingham field experiments have shown that spectral reflectance (NDVI) correlates strongly with harvest biomass from measurements during stem elongation and shortly after anthesis (R2 ranging from 0.4 - 0.5, P
First Year Of Impact 2014
Sector Agriculture, Food and Drink,Energy,Environment
Impact Types Societal,Economic

 
Description BBSRC Industrial Case Studentship Advancing Harvest Index through Genomics Enabled Breeding
Amount £70,000 (GBP)
Funding ID 2102620 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 09/2021
 
Description BBSRC Newton Exploiting phenology and adaptation to improve nitrogen use in wheat
Amount £540,000 (GBP)
Funding ID BB/N013360/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2016 
End 12/2019
 
Description BBSRC Wheat Improvement Strategic Programme (WISP) grant
Amount £543,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2014 
End 04/2017
 
Description CONACYT PhD Studentship Genetic analysis of physiological traits to increase grain partitioning in high biomass cultivars in wheat
Amount £95,000 (GBP)
Organisation National Council on Science and Technology (CONACYT) 
Sector Public
Country Mexico
Start 10/2015 
End 09/2018
 
Description Future Food Beacon PhD studentship Manpartik Gill Novel Brassinosteroid effects in wheat
Amount £120,000 (GBP)
Organisation University of Nottingham 
Sector Academic/University
Country United Kingdom
Start 12/2018 
End 11/2022
 
Description National Council on Science and Technology (CONACYT) PhD studentship Identifying canopy architecture traits to increase radiation-use efficiency and grain yield in wheat
Amount £90,000 (GBP)
Organisation Government of Mexico 
Sector Public
Country Mexico
Start 10/2017 
End 08/2021
 
Description USDA National Institute Food Agency - International Wheat Yield Partnership Program
Amount $163,000 (USD)
Organisation U.S. Department of Agriculture USDA 
Sector Public
Country United States
Start 11/2016 
End 10/2019
 
Title Phenotyping Biomass and N Use Effciency data set 
Description 240 wheat genotypes in Diversity Panel (landraces, synthetic derivatives and elite UK cultivars) phenotyped for above-ground biomass and N-Use efficiency and component traits in 3 years in field experiments (3 replicates) under High and Low N conditions at University of Nottingham. Data collated in data template and provided to scientists at John Innes Centre. 
Type Of Material Database/Collection of data 
Year Produced 2012 
Provided To Others? Yes  
Impact Parental lines identified for crossing programme at John Innes Centre to develop Nested Association Mapping Population (Paragon X Watkins Landrace crosses). 
 
Description Partnerhsip with Dr Ali Babar at University of florida 
Organisation University of Florida
Country United States 
Sector Academic/University 
PI Contribution As a result of the research carried out in this BBSRC project, I have following discussions with Dr Ali Babar University of Florida successfully jointly applied for a NIFA-IWYP grant "Advancing harvest index through genomics enabled breeding." in which I am the PI at Nottingham University,
Collaborator Contribution Sharing of SNP mapping array data sets and wheat germplasm for genetic analysis for grain partitioning traits in wheat
Impact Multidisciplinary: genomics, physiology, breeding. Outputs include marker-trait association for grain partitioning traits for application in wheat breeding.
Start Year 2017
 
Description Partnership in International Wheat Yield Consortium 
Organisation International Centre for Maize and Wheat Improvement (CIMMYT)
Country Mexico 
Sector Charity/Non Profit 
PI Contribution As a result of the research carried out in this BBSRC project, I have following discussions with CIMMYT joined the Internatioal Wheat Yield Consortium led by CIMMYT. In this Consortium I lead sub-project 2.1 on "Enhancing ear fertility and grain number while maintaining lodging resistance". Two PhD students (Carolina Rivera and Eliseo Trujillo) are worklng in the area of optimizing DM partitioning to improve grain number with CONACYT Studentships secured from the Mexican government and registered at Nottingham on 1 October 2011. In addition a grant of $50,000 from CIMMYT has been awarded by CIMMYT to Nottingham for research activities on this sub-project.
Collaborator Contribution Prof Matthew Reynolds Head of Physiology in CIMMYT Wheat Program is co-supervisor of the PhD Studentships of Carolina Rivera and Eliseo Trujillo. The field experiments of the two PhD studentships was based at the CIMMYT Research station at Ciudad Obregon, Sonora, Mexico and co-supervised by Matthew Reynolds. CIMMYT also provide a financial contribution to the PhD living stipends of the students when they are based at at Nottingham for 6 months of each calendar year.
Impact PhD studentships and papers presented at 1st - 3rd International Wheat Yield Consortium meetings at C. Obregon Mexico 2012-2014
Start Year 2011
 
Description Partnership with KWS UK Ltd Dr Ed Byrne and Dr Jacob Lage Wheat Ear Fertility 
Organisation KWS UK
Country United Kingdom 
Sector Private 
PI Contribution Through results on project "Raising the ceiling on UK wheat yields / introgression and assessment of novel 'large-ear' CIMMYT germplasm into UK pre-breeding lines" and "Enhancing diversity in UK wheat through a public sector prebreeding programme" discussion of future genetic analysis of ear fertility traits had resulted a new iCase PhD studentship on " grain partitioning in high biomass backgrounds in wheat"
Collaborator Contribution In kind genomics analysis of wheat mapping populations and provision of wheat field plots
Impact ICASE Phd Multidisciplinary: genomics, physiology, pre-breeding.
Start Year 2015
 
Description Root Phenotyping Partnership with Prof Jonathan Lynch 
Organisation Penn State University
Department Department of Plant Science
Country United States 
Sector Academic/University 
PI Contribution Joint supervision of post doctoral and post graduate staff, and development of high-throughput methodologies for studying root anatomical traits.
Collaborator Contribution Expertise in high throughput field based root phenotyping and root anatomics.
Impact Protocols for root anatomics in wheat.
Start Year 2014