Project Outline
Overview
Purpose and Research activities
Core Project objectives
Scientific Protocols
Staff
Overview
The UK government is committed to the sustainable development of agriculture. Wheat is grown on a larger area and is more valuable than any other arable crop in the UK. The genetic improvement of wheat has the potential to make a very significant contribution to the sustainable development of the arable sector. The overall aim of this project is to provide the core management and research facility of the Defra Wheat Genetic Improvement Network and to generate pre-breeding material carrying novel traits to breeders of wheat grown in the UK. This project will also provide access to advanced breeding technologies thereby ensuring the means are available to produce new, improved varieties.
The Wheat Genetic Improvement Network (WGIN) of which this project will be the core will unite the UK public-sector research activity on genetic improvement of wheat. The WGIN will aim to promote a close working relationship between researchers and "end users". The WGIN will ensure that UK researchers have a shared objective to promote the sustainable development of the sector.
The core project will be managed by the research partners in conjunction with Defra. They will form a management team which will also include ex-officio representatives of UK-based plant breeding companies, University of Bristol, University of Nottingham, ADAS, NIAB, HGCA and BBSRC. The project management team will ensure the project and its outputs are communicated to the wider scientific and end user communities, via a web site, an electronic newsletter, a stakeholders' forum, focused meetings, peer reviewed publications and the provision of germplasm and breeding facilities. The WGIN will ensure collaborations with equivalent operations overseas to ensure the Network as a whole is internationally competitive.
The WGIN will comprise scientists from eight different organisations who between them represent the substantial majority of the UK's expertise in wheat genetics and breeding. The Network's activities will be managed through a small Management Team comprising representatives from the partners (Rothamsted Research (RRes), the John Innes Centre (JIC)), Defra and with ex-officio representation from the University of Nottingham (UoN), ADAS, University of Bristol (UoB) , NIAB, HGCA , BBSRC and the UK-based plant breeding companies. The management team will be chaired by Professor Peter Shewry (RRes). The WGIN will establish a close interaction with research centres in the UK engaged on genetic improvement of other cereal crops (barley and oats). In this context, WGIN will organise and host an annual workshop on cereal genetics, genomics and breeding to ensure opportunities to achieve added value from shared knowledge and technology are not missed. The WGIN management team will also establish and maintain close interactions with leading research groups in Europe, Australia, USA, China and Mexico (CIMMYT) to facilitate exchange of materials and information as well as create synergy and an opportunity for benchmarking. Where appropriate, the WGIN will exploit global activities in rice genomics that are in the public domain to hasten achievement of some specific objectives such as gene isolation and marker development. The WGIN Management Team will pay particular attention to ensuring easy and unfettered access to materials and technologies that will most efficiently allow commercial production of wheat genotypes carrying traits that can be expected to impact significantly on agricultural sustainability. The WGIN will assemble a "Stakeholders' Forum" comprising breeders, other research customers, (eg. HGCA), scientists with shared interests and "end-users" to provide a critique of past activities and future plans. The "Stakeholders' forum" will meet annually, possible in association the workshop for cereal genetics referred to above.
Purpose and Research Activities
Hexaploid wheat is grown on a larger area and is more valuable than any other arable crop in the UK. In 2002, wheat was grown on 1.99 millions hectares of UK land and produced 16.1 million tonnes of grain (average yield 8 tonnes/hectare). In 2000/01 full specification bread wheat prices returned an average farm gate value of £76.46 tonne, feed wheat prices returned an average of £64.91 per tonne (http://www.hgca.com/c-stats/c-stats.htm"). The total value of the UK wheat produced in 2001 (calendar year) was £1,534M according to Defra. The crop has a significant "environmental footprint" as well as being a major primary economic commodity of UK agriculture. Changes in crop production practice, particularly through the genetic improvement of crops, have the potential to make significant, beneficial economic and environmental impact through increasing resource use efficiency and reducing inputs. Prior to the 1970s inputs to wheat crops were low but, over the last 30 years, inputs of fertilisers and plant protection products (herbicides, insecticides and fungicides) have increased substantially. In response to these circumstances, plant breeders have concentrated on the production of varieties that will deliver the highest possible yield when grown under high-input conditions. There are strong economic and environmental reasons to reduce costly inputs to the crop that are dependent on depletion of non-renewable natural resources (particularly fossil carbon), result diffuse pollution and have adverse impacts on biodiversity.
Genetic improvement for sustainable agriculture
Maintaining or elevating crop yield continues to be a major objective of genetic improvement programmes. In the context of creating sustainable systems, per acre yield increases allows economic levels of production from less crop land and thereby releases land (often less productive areas) for alternative uses including those which achieve environmental gains. There are many opportunities to exploit natural genetic variation within the germplasm of wheat types and near-relatives to breed varieties to achieve these objectives. Some examples of the way in which targets for genetic improvement will impact on sustainability follow below.
Reduced nitrogen fertiliser inputs and nitrate losses from agricultural systems:
Nitrogen fertilisers represent a significant input of fossil fuels into the production system and economic cost for the grower. Nitrates may also leach from soil or run-off to pollute water courses. Large quantities of nitrogen are applied to wheat crops in order to achieve grain with the protein content required for bread-making. This may lead to direct loss of nitrogen if not correctly applied to the crop. Similarly, when grain is used for animal feed, nitrogen is excreted and pollution occurs. Varieties that displayed greater nitrogen-use efficiency or those that could be managed specifically to produce feed-wheat with low protein content could have a beneficial influence on sustainability by reducing both inputs of nitrogen and losses.
Reduced herbicide use:
Herbicides are used routinely to achieve high levels of weed control in wheat crops. However, some of these chemicals (typically isoproturon) can leach from soil to pollute ground water and there is a significant cost associated with both detection in and removal from drinking water. It has been demonstrated experimentally that modern varieties of wheat are less competitive with weeds than those that were commonly grown before the advent of herbicides. Varieties with the appropriate architecture and physiology to allow them to compete better with weeds are likely to allow a reduction in the herbicide usage currently required to achieve consistent and adequate yields. There are also prospects for exploiting the natural allelopathic chemistry of plants to create genotypes that are weed-suppressive.
Reduced fungicide and other pesticide use:
Routine fungicide use will usually result in an increase in yield, even in the absence of obvious disease. If this input could be eliminated or reduced, there would be cost savings through reductions in pesticide use. There are a range of different options for the production of wheat varieties that could be grown without the need for heavy and regular fungicide applications.
Effective virus resistance, in particular, could have a significant influence on insecticide use because the aphid vectors can usually be maintained below damaging levels by the use of biological control. However at present biocontrol approaches are insufficiently complete to reduce damaging levels of virus transmission.
Reduced / minimal tillage:
Ploughing is both time-consuming and demanding on fossil-fuel use as well as having an adverse effect on soil structure and fauna such as earthworms. However, while reduced tillage methods may have advantages, they depend on effective herbicide use and can also increase the incidence of diseases originating from crop debris. Varieties that combine the attributes of resistance to certain diseases and may also require less herbicide could enable a more extensive uptake of environmentally beneficial soil management practices.
Reduced insecticide use:
Insecticides are used on wheat at least once in most years to control aphids that spread virus diseases as well as several other pests that can result in significant direct damage. Varieties with a greater level of resistance to or tolerance of insect pests are likely to allow more predictable reliance on natural biological control systems such as predators, parasitoids and insect-pathogenic fungi. In this context, breeding could provide a synergistic supplement to advances in biological control technologies under development for cereal crops.
Overall, there are a number of targets, achievable through genetic improvement, that have the potential simultaneously to increase profitability of farms, reduce environmental pollution, save renewable resources and provide time savings to farmers (allowing them a prospect of leisure and greater integration with local society). These targets address the three components of sustainability (economic, environmental and social) enunciated in government policy.
The efficiency of selecting varieties with improved traits to achieve sustainable wheat production in the UK would be significantly enhanced by improved knowledge on the genetic basis of many of the traits under consideration.
Core project objectives will be pursued in seven main research activities
Activity 1. The provision and evaluation of key wheat genetic stocks will underpin most of the WGIN projects. These stocks will be held within the National Wheat Collection at the John Innes Centre (JIC).
Activity 2. Two key mapping populations will be established and populated to high resolution with PCR-based molecular markers. The chosen mapping populations and marker types will reflect both the short and longer term needs of many projects. The availability of molecular markers will improve the efficiency of plant selection by wheat breeders and provide researchers with the tools for gene discovery and isolation.
Activity 3. A hexaploid genotypic diversity screen will be performed to determine the total diversity available in elite North European winter wheat germplasm. This will assist the breeders in the selection of parents with potential novel traits or variant alleles.
Activity 4. The identification and characterisation of traits especially important for sustainable agriculture and knowledge on their inter-dependence, will be pursued within a joint annual field experiment, involving JIC, RRes and an appointed sub-contractor. A central, searchable database using a controlled vocabulary will be established, to combine existing prior knowledge on specific traits of interest with the new data generated within WGIN.
Activity 5. A related diploid wheat species will be exploited to identify novel sources of resistance to all the major UK fungal and viral pathogens. The novel traits and genes identified can be exploited through the molecular identification of the comparable allele in hexaploid wheat.
Activity 6. Two large mutagenised hexaploid wheat populations will be generated, to provide an immediate source of trait diversity to wheat breeders. The non-selected population will be saved and this will permit researchers to identify novel variant alleles of key genes of interest for functional evaluation.
Activity 7. The PCR TILLING technique will be used in both diploid and hexaploid wheat to identify variant alleles of specific genes either arising naturally or via induced mutation. The Rht dwarfing genes, the gibberellin (GA) biosynthetic genes and three global regulators of disease resistance will initially be examined for variant allele -novel trait associations. Once other genes of high value to sustainable agriculture are identified, the same approach will be pursued to provide breeders with a wide repertoire of novel trait variants.
Three activities of short duration will also occur within the WGIN. Firstly, there will be an annual donation of F1 wheat seed and the two parental stocks by breeders to the National Wheat Collection. This will reduce substantially the lead-in time for new genetic analysis projects. Secondly, grain will be achieved for 1 year from the traits field trial. This would provide researchers working on non-core projects, adequate materials for analyses. Thirdly, and only when appropriate, bioinformatics analyses will be undertaken to exploit micro-synteny between rice, barley, maize and wheat and thereby identify tightly linked markers and candidate genes sequences for important traits.
SCIENTIFIC PROTOCOLS
The use of molecular markers has the potential to enhance several aspects of wheat breeding. Firstly, to identify the gene diversity pools that exist within past and present elite cultivars. This will assist the breeder to track the inheritance of traits through lineages, to identify likely sources of novel traits and to construct with this new knowledge novel pedigrees and hence trait combinations. Secondly, molecular markers will be used to identify major genes and quantitative trait loci (QTLs) that can enhance the efficiency of selection of complex traits. Very closely linked markers or within gene markers can then be used by the breeders for marker-assisted selection (MAS). This approach which is especially effective for complex traits, will remove the need for time and resource consuming trait identification in the field, glasshouse or laboratory. Thirdly, marker assisted introgression of traits means that fewer cycles of breeding are required to move a specific trait from a donor line to an elite line, whilst segregating away the rest of the donor parent DNA.
For QTL mapping using molecular markers, both a suitable mapping population and a genetic map with a dense coverage of markers need to be available. Currently in the public domain, no mapping population exists of sufficient size and type involving elite UK germplasm, for the fine mapping of traits and QTLs. In Table 1 a description is given of the ten mapping populations currently available. Therefore a long term strategic effort is required to provide within the public domain two desirable mapping populations of sufficient size (200-250 lines), of the correct type (double haploids) and with the diversity of traits, to underpin the UK's wheat research and wheat improvement efforts. There is also the need to select a suitable marker type for uptake by the widest number of users, ie., researchers and breeders alike. SSRs are currently the most prevalent wheat marker available in the public domain ("http://www.scri.sari.ac.uk/ITMI/Default.htm"). It is anticipated, due to international efforts, that the opportunity to use single nucleotide polymorphism (SNP) markers will increase. However, the adoption of SNP markers to the core research platform will depend upon their overall utility to the UK wheat breeding community. The publicly available ITMI spring wheat population and associated SSR map, based on a wide cross (Opata x a CIMMYT line) ("http://www.scri.sari.ac.uk/ITMI/Default.htm") will also be used for gene mapping but not trait identification.
Trait characterisation of diverse germplasm and mapping populations is a key component of the WGIN activities. This will permit the identification of traits which are determined jointly (pleiotropic) or are linked, will define those traits which are physiologically incompatible, complementary or synergistic, and provide new information on the possible inter-dependencies and trade-offs between traits. During year 1 the management team will decide collectively upon the exact traits to be assessed for sustainability. An appointed sub-contractor will perform a 30 accession field trial to determine an appropriate nitrogen regime within which to examine sustainability traits and to examine methodologies for robustness to be used in trait characterisation. It is also imperative that prior existing knowledge on specific traits of interest to sustainable wheat production is placed in a central and searchable database using a controlled vocabulary. A database of this type for UK cultivars does not yet exist in the public domain. Sources of the non-collated knowledge on the specific traits selected include desk-studies, breeders' notebooks, refereed papers and others authenticated sources. In subsequent years, the natural variation for specific traits will be explored by using the diverse germplasm collection, heritability studies completed using the available mapping populations and molecular marker established for key traits. The management team will encourage appropriate consortia to develop bids for LINK-funded research into specific traits of value to sustainable agriculture.
The mutagenesis of a hexaploid wheat genotype and the development of a large mutagenesis population of M8 fixed lines, by the method of single seed descent, will provide an immediate and potentially rich source of trait diversity. Earlier generations of this mutagenised population will be used by researchers to identify novel variant alleles of key genes of interest for subsequent functional evaluation. Seed from the entire non-selected mutagenised population will be preserved and will become a valuable resource from which many additional projects can be initiated.
Diploid Triticum monococcum is closely related to the progenitor of the AA genome of hexaploid wheat and is considered a rich source of novel genes and variant alleles. For example, the vernalisation gene Vrn-A2 residing on chromosome 5AL was initially discovered in diploid wheat accessions, and this lead to the subsequent mapping of Vrn-A1 gene in hexaploid wheat. However, the range of diversity within this genome is much wider than is present in the A genome of bread wheat. This is because the polyploidisation event that combined the AA and BB genomes occurred some 0.5 Mya, and thereafter the A genome in the polyploidy species has remained genetically isolated from its diploid relatives. Also, the diploid genome never experienced the polyploidisation process which can result in gene silencing (1). Trait expression in diploids is therefore less likely to be hindered by suppressor loci that reside on homoeologous chromosomes in the hexaploid genome.
T. monococcum is attractive as a model for detection of traits, genes and alleles, defining phenotype:genotype relationships and assigning the function of variant alleles. This is because it is considerably faster and less resource demanding to map and identify genes in a diploid than in a hexaploid genome. Furthermore, T. monococcum represents a bridge between the model crop rice (and maybe even Arabidopsis thaliana) and hexaploid wheat, so that the function of wheat homologues of genes isolated in these models can be tested without the complications of polyploidy. Homologues of functionally important genes in diploid wheat can be straightforwardly identified in hexaploid wheat EST collections, via synteny or via specific PCR primer searches. For novel genes and alleles conferring the most desirable traits, appropriate 'within the gene' (genic) markers will be developed for subsequent use by the wheat breeders via marker assisted selection. Although trait introgression from diploid to hexaploid wheat via established sexual crossing procedures is feasible, this activity will not be undertaken within the core WGIN project. Mutagenesis of diploid wheat will probably reveal greater trait variation than in comparable hexaploid based experiments, since recessive mutations will not be masked by the presence of unaltered homoeologue(s). The A genome diploid was selected for this exercise because it is threshable and processable. Seed from the entire non-selected mutagenised diploid population(s) will be preserved and will become a valuable resource from which additional projects can be initiated.
The T. monoccocum programme will focus on identifying and characterising novel sources of resistance to some of the UK's major fungal and viral pathogens. A collection of diploid accessions will be screened for disease resistance / susceptibility. Key accessions will then be used to generate mutagenised populations and F2 mapping populations segregating for different disease resistance traits. These genetic resources will be assayed for variant alleles of genes known to be functionally important to plant defence in model systems, ie. Arabidopsis and rice. In the first instance, the global regulators of plant defence signalling, NPR1, RAR1 and SGT1 will be explored for functionality. The chromosome locations of each gene in diploid will be defined. Diploid lines revealed to posses distinct variant alleles of each gene will be tested for disease resistance / susceptibility with the appropriate pathogens. Genetic segregation of variant alleles within F2 populations will be used to confirm specific allele - trait associations. Hexaploid accessions will then be assessed for the presence / absence of each gene and gene variant. Based on these results selected hexaploid lines can be assayed to reveal maintenance of the trait and therefore commercial exploitation by the wheat breeders though marker-assisted selection. Non-expression of a trait in hexaploid wheat, even though the correct sequence variant is present, is also a possible outcome. This could be due to the presence of additional suppressor loci or the lack of a second locus. Therefore a few hexaploid lines with the correct gene variant will be crossed to lines belonging to distinct gene diversity pools and the progeny evaluated. Positive trait expression in progeny could occur because of the presence of the correct combination of the additional loci required. Alternatively, and only when considered appropriate, either the Hobbit sib wheat individual chromosome deletion series or the Chinese Spring based series will be crossed to the selected hexaploid lines to identify the location of possible suppressor loci causing trait non-expression. As additional genes of functional important to defence against multiple pathogens are identified in model species, the same resources and approach will be used to explore allelic variants for function in diploid wheat.
A major obstacle in any plant breeding programme is the effort and resources required to identify variation in a trait that has commercial potential. With ever increasing amounts of sequence information available in searchable databases, locus-to-phenotype reverse genetics strategies have become increasingly popular alternatives to phenotypic screens for functional analysis. Wheat transcriptome EST expression experiments when undertaken in conjunction with mapping studies and syntenic cereal genome comparisons will identify within a genetic interval a pool of candidate genes of interest to specific traits. Likewise from the literature gene sequences coding for important traits are already known to function in both cereal and non-cereal species. Therefore a high throughput method is required to identify additional variant alleles of these genes and test their functionality. This technique should not involve the production of GM plants.
TILLING (Targeting Induced Local Lesions in Genomes) is a high throughput PCR based technique that can identify mutations in specific genes within a large population (2, "http://tilling.fhcrc.org:9366/"). Two types of TILLING are envisaged within the core project. Mutations will be identified in selected genomic region from pooled individuals of a mutagenised population and from pools of diverse germplasm (EcoTILLING). Data on sequence variation will be obtained for both diploid and hexaploid wheat. The technique will be applied initially to candidate genes of known biological and agronomic importance in two demonstration projects. The traits selected, affecting plant height/pre-harvest sprouting and broad spectrum disease resistance, are visually easy to quantify. This will permit functional associations to be made between sequence variants and specific trait types. By comparing the same genomic region in diploid and hexaploid wheat, it will also be possible to determine which genome type is the richer source of novel trait variants. From year 3 onwards, additional genes of known importance to sustainable wheat production will be selected by the management team for exploration by TILLING. These experiments will identify a pool of germplasm containing novel gene variants for follow up trait characterisation and subsequent exploitation by the wheat breeders.
Where appropriate, the WGIN will exploit global activities in rice genomics that are in the public domain to hasten achievement of some specific objectives such as gene isolation and marker development. For example, analysis of rice-barley-maize-wheat synteny in specific genome regions where the wheat mapping data indicates important traits reside, will permit a pool of candidate genes to be selected for functional evaluation or potential sequences surveyed for the development of closer linked markers for wheat.
Annually, each UK wheat breeder makes a large number of crosses. It has been suggested that the wheat breeders donate each year to the WGIN germplasm collection some of this FI seed and samples of the exact parental material used. Although each F1 seed sample would be a finite resource, its availability would reduce the lead in time for many new projects.
The annual trait characterisation field trials are a key component of the research core activities. To increase its utility still further, 10 Kg grain samples will be collected from each plot and stored for 1 year and a further 1 Kg sample at -15C indefinitely. This activity would permit other research projects, funded outside the WGIN, to examine grain quality and relate these results to the field trait datasets. Obtaining data on final grain quality may be especially useful when exploring complex traits.
Staff
