Combining field phenotyping and next generation genetics to uncover markers, genes and biology underlying drought tolerance in wheat.

Food security is internationally recognised as one of the major global challenges of the 21st century. By 2050, it is predicted that world food production will have to increase by 50% to meet demand. This is against the pressures of global climate change and resource limitations. Meeting this challenge is going to require the development of innovative strategies to make use of our unprecedented knowledge of modern bioscience in the post genomic era. Developing new varieties of wheat will be fundamental to meeting the 2050 goal.
For wheat growers Internationally and specifically in India one of the key issues is drought. Drought means farms cannot always guarantee a good harvest with major implications for the livelihoods and household food security of small-holder farmers. Low rainfall also reduces the land area that can be farmed. Throughout the last century improvements in drought tolerance have come through breeding crops that grow in such a way that drought and drought sensitive stages of growth do not coincide. There is however, huge potential to breed new varieties capable of maintaining stable yields in drought conditions.

In collaboration with the University of Bristol and the John Innes Centre (Norwich), work at the University of Liverpool has generated sequence data for the wheat genome. Using this information we have developed new methods to rapidly uncover the genetic variation in wheat. By combining an understanding of genetic variation with a careful study of performance under drought conditions it becomes possible to associate genetic variation with improved drought tolerance. Using this genetic information "molecular marker" tools cab be built, that can be used to rapidly select for lines that are drought tolerant. It is also possible to stack up multiple markers for different traits. As a consortium of interdisciplinary research scientists from the UK and India we plan to use this approach to identify molecular markers associated with drought tolerance in wheat and lay the foundations of an accelerated breeding program to incorporate drought tolerance into Indian wheat varieties.

The approaches we will be using will provide a blueprint for how state-of-art technologies can be applied to important food security issues. Much of the output we generate can be used to identify markers for other traits. It will also result in highly trained researchers in India and the UK capable of applying these new approaches. Through outreach work we aim to engage with other researchers and stakeholders and apply this methodology to other traits in wheat and different crops.

The overall aim of this project is to combine physiological and modern molecular breeding approaches to provide tools to accelerate wheat breeding associated with abiotic stress tolerance. This project will use an enrichment platform developed in Liverpool, to genotype by sequencing a diversity panel of wheat. This will generate tens of thousands of varietal SNPs for genotyping and provide the raw materials for a SNP-based molecular breeding program in India and an international resource. Information to users will be made publicly available through a web browser interface for immediate impact. The panel of lines will be phenotypically scored for yield, and physiological traits associated with water use efficiency over two seasons under drought regimes at four sites across India. Statistical analysis will be used to associate genomic regions in specific lines, with drought tolerant phenotypes and a series of markers for yield stability identified and tested. Further methods of genotypic selection and bulk segregation will be utilised to further narrow down genomic regions with the aim of potentially identifing candidate genes conferring enhanced drought tolerance. Upon completion, this project will have generated a series of drought tolerant markers matched to drought conditions in India, thus providing important raw materials for breeding programmes aimed at achieving sustainable yield under drought conditions. Drought is also a problem in the UK, with 30 % of wheat grown on drought-prone soils and drought related losses accounting for £224-448M each year. Therefore, this proposal is also likely to have impact on UK breeding as well as in India. Finally, the aim of this project is to generate trained individuals in both India and the UK in the area of computational biology and phenotyping, specifically, how next generation genomic approaches can be applied to crop breeding.

The secure supply of affordable sustainably produced wheat is of fundamental importance to global food security and to poverty alleviation. Wheat is the UK's largest cereal crop with an estimated annual production of 14 million tonnes, and total value (seed and processed products) of circa £15 billion. In India, wheat is a widely grown crop and is integral to the rice-wheat rotation of the Indo-Gangetic plains (IGP) which constitutes 10 million hectares in India and as a rotation is one of the world's largest agricultural production systems, occupying 24 million hectares of cultivated land on the IGP and in China. Wheat is a key staple essential to the household food security of 800 million people in India, many living on an income of less than $5 a day.

The key beneficiaries of this research programmes will be the wheat breeding community in India and the UK and the seed producing sector (both public and private) in both countries, and ultimately farmer co-operatives and farmers and through to consumers at large, though increased yield and through resilience in wheat production. Additional beneficiaries will be the plant and crop science community involved in crop improvement through the use of 'omic technologies.

The research will provide immediate value to wheat breeders through the provision of sets of SNPs, which can be used as molecular markers in wheat breeding. Additionally by the conclusion of the project, further impact will be achieved through the identification of molecular markers for gene pathways that confer enhanced drought tolerance in wheat. Whilst being of value to breeders in the UK and worldwide, this information will have national relevance to Indian wheat breeding programmes, being conducted on cultivars pre-adapted to agro-ecological zones in regions of the IGP where both drought stress and water logging can substantially reduce attainable yield. The impact of this research will be to provide new tools for wheat breeders to accelerate wheat breeding and enable deployment of new cultivars for small holder agriculture in a timely way to address cropping sustainability in relation to changing patterns of water resource availability. The provision of improved breeding lines for cultivar development is fundamentally important as a plank in addressing poverty alleviation.

Strategically the proposed research will contribute to elevating the wheat yield potential in the face of global climate change, which in the UK in high input systems is targeted at 20 ha-1, through improvements in plant breeding and crop management. The potential economic impact of a 50% increase in UK wheat production (current attainable yield on average 8 t ha-1) is in excess of £7 billion pa to the UK economy. Whilst Indian agriculture is characterised by dominance of small holder agriculture, wheat yields vary from ~4 t ha-1 on productive larger farms in the north-eastern plains zones to 0.7 t ha-1 in the southern hills zone. Irrigated regions are under threat of reduced water availability and the emphasis of governmental agricultural policy is to improve productivity in rainfed systems. Matching the increasing demographic demand for wheat in India by 2020 will require a 2.2% annual increase in production which in rainfed systems will require abiotic stress tolerant germplasm. This research will directly contribute to attaining that goal.

The research project will provide capacity building at the cutting-edge of molecular plant breeding and phenotypic trait analysis for drought tolerance, through training of Indian research fellows and through knowledge exchange amongst partners at annual workshops. By implementation of a clearly defined impact pathway, knowledge will be disseminated widely across plant breeding groups in India and the UK and through networked collaborations with other international wheat improvement programmes coordinated through CIMMYT and ICARDA.