Genome-wide association mapping and landscape scale modelling of heritable ionomic diversity in Arabidopsis thaliana populations

The proposed research utilizes genetic approaches to identify the genes that control the way plants take up mineral nutrient found in fertilizers such as potassium and phosphorus and potential toxic substances such as sodium (for the plant), and arsenic and cadmium (for humans that eat the plants). By understanding how different forms of the genes we discover are used by plants to allow them to grow in soils containing different levels of mineral nutrients or potentially toxic elements we can understand the role these genes play in allowing plants to adapt to the varied soil conditions they are exposed to in their natural habitats. A better understanding of these adaptations in natural populations of plants would have significant practical benefits for agriculture by providing the information needed for the development of new varieties of crops better able to provide the increased yields needed to meet the future demand for more cereals for biofuels, more grain for meat, and more food for the additional 2 billion people expected by 2050. The increased crop yields needed to meet these coming challenges will require a significant increase in irrigated agricultural production which will bring with it increased salinity (elevated sodium) in soils and associated yield losses. Crops adapted to maintain yields in the face of increasing salinity will therefore be essential. More efficient use of mineral nutrient fertilizers by crops would also improve yields for farmers, enhance productivity of crops on poor soils, and limit the environmental and ecological damage the production and excess use of fertilizers causes. For most of the world's population, plants are also the major source of essential dietary mineral nutrients such as calcium, potassium, manganese, iron and zinc, and therefore efforts to improve the mineral nutrient content of staple foods such as rice, maize and cassava would have significant human health impacts. Plants are also the primary entry point for a variety of toxic minerals into the food chain such as arsenic and cadmium. A better understanding of how natural plant populations have evolved over thousands of years to grow in mineral nutrient poor soils or soils with elevated salinity, cadmium or arsenic would help guide how we develop crop varieties for the future that could deliver the needed increases in yield and quality while insuring these gains against a changing climate to ensure food security for all.

The proposed research utilizes association, linkage and molecular genetic approaches to identify genes that underlie heritable natural diversity in mineral nutrition and trace element accumulation in natural Arabidopsis thaliana populations. Landscape scale modelling of this diversity will allow exploration of associations between this genetic diversity and the environment, providing a pathway to understanding the ecological function of these alleles in adaptation to soils. Incorporation of predicted climate scenarios within these landscape models will generate projected allele distributions across future landscapes, providing an approach to understanding and tracking climate change . This project builds on the PIs recent success in using genome-wide association (GWA) mapping to identify the causal genes underlying natural variation in foliar accumulation of sodium and cadmium in A. thaliana, and establishes a new collaboration with Prof. Pete Smith and Dr Alex Douglas. This partnership will allow the linking of plant genetic diversity to ecological function using the agriculturally and ecologically relevant trait of mineral nutrient and trace element homeostasis. The approach will combine genome-wide association mapping (validated by linkage mapping and molecular genetics) with landscape scale modelling. It utilizes the large pool of genetic diversity in natural populations of A. thaliana to identify genes, alleles and mechanisms of value in adaptation to the varied edaphic conditions A. thaliana populations encounter across the landscape. Once characterized this natural diversity offers potentially new approaches to manipulate such agriculturally important traits as salinity tolerance and mineral nutrient efficiency to develop crop varieties that are more resilient to the predicted impacts of climate change on soil fertility, and to improve yields in a more sustainable manner to deliver the yield gains required to meet future population growth.

Results from the research could have a significant long term positive impact on agricultural and horticultural crop yields through improved mineral nutrient use efficiencies and enhanced stress tolerance (e.g. salinity, nutrient deficiencies, trace element toxicities). Such improvements could provide direct commercial benefits to seed companies by facilitating the development of cultivars better adapted to current and future changing environmental conditions. Commercial farmers would benefit from these improved varieties through improved and sustainable yields with less inputs (fertilizers and water) and through the ability to utilize new cultivars to adapt their agricultural practices to changing climatic conditions. Further, such improvements in agricultural and horticultural crops will also benefit subsistence farmers with limited access to inorganic fertilizers (primarily nitrogen, phosphate and potassium, secondarily sulphur and magnesium), helping to reduce the cost burden such fertilizers impose by improving the value/cost ratio for fertilizer usage. In addition, reduced utilization of fertilizers, achieved through improved mineral nutrient use efficiencies, will limit the environmental and ecological damage their production and excess use causes, benefiting the general public through enhanced quality of life.

Results from the research could also impact food quality in the long term by helping to increase the content of essential mineral nutrients and reduce toxic trace elements in food crops. For most of the world's population plants are the major source of essential minerals such as calcium, potassium, manganese, iron and zinc, and therefore efforts to improve the mineral nutrient content of staple foods such as rice, maize and cassava will have a positive impact on public health both in the UK and internationally. Plants are also the primary entry point for a variety of toxic minerals into the food chain such as arsenic and cadmium, and being able to limit there accumulation in food would also have a positive impact on public health both in the UK and internationally.

By providing improved agricultural and horticultural crops for food production the proposed research will help in efforts to move the UK and international agricultural systems towards more sustainable food production, providing improved food security against the backdrop of a changing earth's climate and surface chemistry.