Wheat research in the UK

Why is wheat important?

Wheat, barley, maize and rice are the main source of nutrition for humans and domesticated animals. Wheat is of fundamental importance to world agriculture with an estimated 2007 harvest of ~ 550 m tonnes. In the UK, DEFRA reported that, in 2007, 17% of UK arable land (2,870,600 hectares) was planted with cereals, of which 63% (1,815,900 hectares) was wheat, 31% (897,900 hectares) was barley, 5% (129,400 hectares) was oat and 1% (27,400 hectares) other cereals such as rye, maize and Triticale. The average UK wheat yield in 2007 was ~7.2 tonnes per hectare, with the total UK yield being ~13,074,480 tonnes (7.2 x 1,815,900). The current spot price of wheat is £199 per tonne, valuing the unprocessed 2007 UK wheat crop at approximately £2.6 billion. Drought in Australia, low stocks and biofuel production has combined to drive up world wheat and coarse grain prices and further feed market volatility (World Agriculture supply and Demand Estimates. WASDE-460 ISSN: 1554-9089). This has led to food riots, political instability, and a renewed political focus on food security.

UK breeders and farmers have been highly successful in developing and growing wheat varieties with higher yield potential: over the period 1948 to 2006, average yields in the UK increased from ~3 tonnes per hectare to ~8.0 tonnes. Unfortunately, wheat production increases have not kept pace with increased demand. Furthermore, wheat productivity is threatened by disease, competition for high quality agricultural land, resource limitations, and adverse environmental conditions that dramatically reduce optimal yields. It has been estimated that in Europe productivity needs to double to keep pace with demand and to maintain stable prices. Therefore, by narrowing the gap between theoretical maximal and actual yields, and increasing maximal potential yields, sustainable/adequate production of one of the world’s most important crops could be secured.

Wheat genetics is complex; the genome (2n=6x=42, AABBDD) is allohexaploid (see our article on wheat evolution for further information) derived by the recent (less than 10,000 years ago) hybridisation of the D genome of Aegilops tauschii with the Triticum turgidum (durum wheat) AABB tetraploid genome. The total genome size is approximately 16,000 Mb or 35 times the size of the rice genome and 5 times the human genome. Fortunately, the grass family share a remarkably high conservation of gene order and gene sequence due to their relatively recent origin approximately 50-75 mya. This conservation enables gene identification in wheat and barley using comparative genomics with the smaller genomes found in close relatives. This approach has been successfully employed to identify wheat genes using the genome sequence of the related wild grass Brachypodium distachyon, which has a genome of less than 300 Mb.

The large wheat yield increases achieved in the past have been primarily due to genetic improvements by plant breeders (NIAB-BSPB Report 2008) and there is major potential for further increases in yield and quality within existing germplasm. The main challenges are to facilitate molecular breeding programmes, identify QTL and genes for enhanced yield, quality, and disease and stress tolerance, and enable a far wider range of experimentation in wheat. The strategy in our laboratory for meeting these challenges is to use next generation sequencing technology, gene enrichment methods and a novel sequence alignment and assembly approach to identify and validate sequence polymorphisms in key UK germplasm. Wheat research in the UK has recently taken on new levels of urgency. This is partly in response to the 2009 Royal Society Report, Reaping the Benefits, and partly to a change in UK funding emphasis towards high quality research which has impact.

Wheat research in the UK is carried out in a variety of organisations including BBSRC associated institutes such as Rothamsted Research, and John Innes Institute . In addition organisations such as the National Institute of Botany (NIAB) and ADAS) carry out a significant amount of basic and applied wheat research. In addition to the above organisations, UK universities also carry out a significant amount of wheat research, for instance Nottingham University’s Sutton Bonington campus and the University of Reading both have significant laboratory and field based facilities for wheat research. Below is a link to the home page of various well known wheat researchers across the UK.

In addition to the above centres, Bristol University also carries out a significant amount of research into the growth and development of wheat. Currently the Wheat Functional Genomics group, headed by Prof. K. Edwards, has several projects including the BBR project (Biological and Bioinformatics Resources) which part funds this and the associated web sites. Below is a full list of projects along with a brief description for each.

A community resource for wheat functional genomics (2008-2013)

The aim of this project is to develop a web based resources for wheat functional genomics. This five-year project began in February 2007 with funding supplied by BBSRC under the Bioinformatics and Biological Resources (BBR) program. The aim is to provide a one-stop shop for wheat functional genomics providing UK researchers with authenticated data and biological resources, which are freely available without restriction. The first step in this program was to upgrade the monogram network website to provide an up-to-date hub from which to disseminate information. The second phase of the program is to update the resources held at Bristol including images, sequence and microarray data and make these available under the Monogram network umbrella. We hope that in future, other research groups will add their own datasets to the Monogram network site and search facilities. We report on progress made with Bristol based resources and comment on the future activities including plans to incorporate forthcoming 454 sequence data for wheat. We will also show how we have been streamlining the search for resources at the Monogram network Website so that users can get at the data they need without needing to check, or indeed be aware of, multiple databases based in different institutes. Finally we invite interested parties to email us at the above address to suggest tools and/or resources that they can contribute to the Monogram network or are an unmet need by the UK wheat and cereals research community.

Mining the allohexaploid wheat genome for useful sequence polymorphisms (2009-2011)

In this project, which is now completed, we used two complementary next generation sequencing procedures in which we and our partners (Liverpool, and the JIC) have considerable expertise to generate significant amounts of wheat genome sequences. In August 2010 as required by our terms and conditions, we released the 5x fold coverage of the Chinese Spring (line 42) genome sequence via the CerealsDB web site. In addition in June 2011 we released the first batch of SNP-based molecular markers - this work has been published and may be downloaded here, or a summary can be viewed on this site. While this project is now completed Bristol is continuing to develop further SNPs all validated via the KASP genotyping technology developed by LGC Genomics (formerly KBioscience).

Via the International Wheat Genome Sequencing Consortium (IWGSC) it is hoped that a full joined up genome sequence for wheat will soon be released.

Large scale mapping of wheat transcripts and simultaneously defining the A, B and D genome contribution to the hexaploid transcriptome (2008-2012)

This project aims to investigate the use of next generation sequencing to catalog and map homoeologous SNPs (i.e. sequence variations which exist between the different genomes (A, B and D) which make up the hexaploid wheat genome.

Increasing genetic diversity in wheat by interfering with mismatch repair (2008-2012)

The long term goal of this project is to generate wheat plants with elevated levels of genetic diversity and/or recombination. To produce such plants we have generated various transgenic lines designed to interfere with the expression of key genes (PMS2, Msh2 and Msh6/7) known to be involved in mismatch repair. We hypothesized that such plants will have two interesting characteristics; firstly, they will be unable to repair damage to their DNA and therefore they will carry an increased genetic load, and secondly, as mismatch repair is thought to be involved in homologous and homoeologous recombination, they will show elevated levels of recombination between related, but divergent sequences, for instance on homoeologous chromosomes.

Our initial results suggest that while lines designed to interfere with Msh2 expression do have reduced mismatch repair activity, lines designed to interfere with PMS2 and Msh6/7 expression do not.

To provide the project with a focus, initially we intend to use the Msh2 RNAi lines to generate novel combinations of HMW-glutenin alleles; however, we envisage that such lines could be a valuable source of novel alleles for any number of interesting genes

Enhancing diversity in UK wheat through a public sector pre-breeding programme (2011-2014)

Food security is becoming a critical issue both in the UK and worldwide due to rapid population expansion, dietary changes and declining stocks of fossil fuels. Total wheat grain production over the next 50 years must exceed that previously produced over the last 10,000 years, since agriculture began. The UK's current food and farming ecological footprint is up to six times the food growing area of the UK. It is no longer feasible for the UK to rely on wealth created from its service sector to buy a decreasing supply of grain on the open market. The US are planning to double maize yields by 2030 using 30% less land, water and energy through the deployment of biotechnology. The UK needs a similar vision for food production covering its major crops, such as wheat, to address the potential market failure.

Addressing this market failure will require a unified approach by academic institutions to develop a wheat pre-breeding programme. This need is endorsed in the second key recommendation by the Royal Society 2009 report, ""Reaping The Benefits", on addressing Food security which recommended funding for the UK public sector to undertake pre-breeding in wheat. The objective of the proposed programme is the development of pre-breeding germplasm, characterised for key traits, and the identification of genic markers for selecting these traits, for use both in commercial breeding programmes and for in academic research.

Development and validation of a flexible genotyping platform for wheat

This project is being carried out in collaboration the John Innes Centre and LGC Genomics (KBioscience); it will develop both a wheat SNP database and a flexible genotyping platform for wheat. The utility of both will be validated by applying the tools and technologies to several exemplar projects. The project highlights the close link between UK academics and the wheat breeders in that within the project all parties are working together to increase the efficiency of breeding for: nutrient use efficiency, resistance to pests and disease, yield potential, and seed structure/composition, The outcome of the work proposed here will impact on all of these areas. It is an issue of the highest priority, only possible now due to great strides in DNA sequencing technology, that UK breeders can gain access to diagnostic molecular markers for the genes controlling these traits. This work will provide those markers at an unprecedented scale and low cost and build a common low cost platform for academic and commercial use. This commonality will greatly aid the translation of UK scientific excellence into better UK wheat.

The background to this project can be found in the 2009 Royal Society report, Reaping The Benefits. The report pointed out that "The challenge of a growing population is compounded by new threats, such as pests, diseases and climate change, and this further indicates the need for constant research into new varieties and practices, and goes on to say "The biggest gains from technology, come from combinations of improved crops and improved practices".

Developing new strategies to manipulate yield and pest and disease resistance by marker-assisted selection (MAS) underpins the UK's strategy to generate improved wheat varieties. Academic laboratories, genotyping service providers and breeding companies use MAS to track the inheritance of a host of loci controlling desirable traits such as disease resistance, drought tolerance and yield. Until recently most laboratories used microsatellite markers in their MAS projects, while these markers continue to be used, for many species Single Nucleotide Polymorphisms (SNPs) have become the marker of choice due to their ease of use and scoring and their ability to be automated with relative ease. However, in allohexaploid wheat the task of identifying similar useful sequence polymorphisms is problematical due to the occurrence of homoeologs from the A, B and D genomes.

Other wheat research being carried out by UK academics:

If you are interested in identifying all the funded wheat projects currently active in the UK we suggest that you start by looking at the BBSRC website; one is able to search for individual researchers or by keywords for all BBSRC funded projects including wheat-based projects. The extent of wheat-based funding just might surprise you!