Triticeae Genomics for Sustainable Agriculture

Securing food supply on a global scale requires solutions to a complex set of unprecedented problems, including rising demand due to major population increases and social mobility, global climate change, rising energy costs and land, water and nutrient limitations. Finding and implementing these solutions is a top priority for governments and scientists worldwide, and has been articulated as a key BBSRC strategic objective. Opportunities for plant science to contribute to global food security include increasing the yield and quality of crops, combatting diseases, enabling maximal crop productivity in sub-optimal growth conditions, and increasing maximal yield potential. Utilising non- food components of food crops, such as cell wall material and waste products of food production to produce energy and industrial feedstocks, has a major role in reaching sustainability and maximising overall yield of renewable resources from limited land and soils. Grass crops are essential for human existence by directly or indirectly serving as the primary source of human nutrition. Wheat, rice and coarse grains such as maize are the most important crops for human food production, therefore increasing grain production sustainably is a critically important strategic and scientific objective. Wheat is the main arable crop in the UK, planted on 60% of arable land, with an annual farm gate value of ~£2.5b and a processed product value of approximately £150bn. Yield increases in wheat are slowing compared to past gains achieved primarily through improved agronomy and also in relation to other grain crops, notably maize. Genetic and transgenic improvement of wheat is therefore a very high priority in the UK and world- wide, and large international programmes for wheat genetic improvement are underway. A high quality genomics sequence provides a complete, accurate and durable record of genes, predicted proteins and other genomic elements that today are a fundamental foundation for nearly all areas of biological research. This proposal describes a UK component of an international coordinated wheat genome sequencing project that will make decisive and innovative contributions to sequencing the wheat genome and supporting crop improvement through genomics.

Bread wheat has an exceptionally complex genome comprised of three independently- maintained genomes, each of which is approximately 6 Gb- more that the entire human genome. Wheat genes are found predominantly as small (1-4) clusters, with an average density of between 1 gene/86kb in proximal regions and 1gene/180 kb in distal regions of the chromosome. Genes and gene islands are separated by extensive tracts of nested retrotransposon repeats comprising approximately 85% of the genome. The gene content of diploid grasses is approximately 30-35,000 suggesting bread wheat has approximately three times this number of genes. The scale and complexity of this genome requires a large coordinated effort and the development and application of new technologies. Work in the International Wheat Genome Sequencing Consortium aims to generate accurate sequences of nearly all genes, annotate these and place them in a syntenic framework. Four chromosomes will be sequenced to high quality reference standards using a combination of established methods and novel sequencing technologies. Re-sequencing methods will be developed to access sequence variation in the Triticeae in concert with the pre-breeding programme. Finally, bioinformatics resources for the long- term maintenance and analysis of the sequence will be established.

The transformative effect of access to high quality genome sequence that is carefully analyzed, and directly and freely available to all users, is well known. Wheat is one of the three major crop plants of global importance, and the predicted impact of a high quality wheat genome resource on crop improvement will be profound, as genomics provides a framework for new breeding methods that are substantially faster and more effective. The wheat genome project will have two immediate impacts on a wide range of new research in wheat by researchers world-wide, and on the application of genomics to breeding and crop improvement by the breeding and agricultural biotechnology industries. Thus plant and crop scientists working in academia and industry are direct beneficiaries of the outcomes of the project. The impact of a genome sequence to these researchers will be profound. Access to and systematic study of all proteins sequence variation in the Triticeae, global gene expression, and the systems-level analysis of biological functions will transform research in crop improvement. Because many agronomic traits in wheat, such as yield and abiotic stress responses, are due to the effects of many genes, such traits will now be accessible to the full range of experimentation possible in modern biology. Consequently progress towards increasing yield stability and sustainable production will be substantially accelerated. The agricultural biotechnology and crop breeding industries, and bioinformatics and computer scientists working on genome assembly and analysis, will benefit from a similar revolutionary effect of genomics seen in rice and maize breeding. A key impact will be the direct and permanent improvements in the rate and scope of wheat breeding, leading to the production of new wheat varieties that can maintain high levels of productivity with reduced inputs. Research funding organizations are also direct beneficiaries of this project by enabling transformative research in wheat improvement, particularly through international collaborations. The impact is a major tangible contribution to meeting important societal goals in food security and sustainable production world-wide. Many indirect beneficiaries of the research can be predicted. Wheat growers will benefit from new varieties that will be more productive and with new end-uses, leading to more stable incomes and diversified production. By addressing the environmental sustainability of crop production through new genomics- lead research in nutrient- and water- use efficiency, the major environmental footprint of wheat production could be reduced, having a beneficial impact on the ecology and sustainability of the agricultural landscape. Other indirect beneficiaries are food processors, who will have access to affordable and a more secure supply of a global staple product. In turn consumers will benefit from more stable prices and access to a staple food.