In recent years analysis of genetic variation has focused on the study of changes in DNA coding for proteins. It is now becoming increasingly clear that this only accounts for one aspect of heritable variation and for many traits, notably complex, quantitative traits, the level of gene expression is also likely to be of great importance. If changes in gene expression underlie many evolutionary changes in phenotype, then identifying the genetic variants that regulate gene expression is a significant and important endeavour. A key problem in genetics is how to identify this type of variation. We propose a robust, quantitative approach to efficiently identify plant genes that harbour such regulatory variants. The approach is novel and particularly amenable to plants since it is based on monitoring gene expression in experimentally created hybrids. A successful outcome will provide a new mechanism to connect genotype to phenotype based on changes in gene expression rather than changes in the structure of an encoded protein. This approach will be used to characterize a series of genes with the objective of identifying potential candidates for tolerance to drought and blast resistance in rice. Through this knowledge, we will develop new breeding tools for application in rice breeding for Asia and Africa. The approach is generic and widely applicable with the potential to reveal new sources of genetic variability for deployment in plant breeding and biotechnology programmes.

The PhotoBoost project addresses the widening gap between agricultural productivity and the global market demand for food/feed and bioenergy crops in an environmentally friendly manner by increasing the efficiency of photosynthetic CO2 fixation. This will be achieved by developing enhanced C3 crops that combine two or more of the following approaches: a) the optimisation of light reactions; b) the integration of an algal CCM; c) the introduction of an engineered photorespiratory bypass mechanism, improved by the knockout of the native plastid glycolate-glycerate transporter; and d) the optimisation of source-sink capacity, improved by the knockout of phloem-mobile tuberisation signal SP6A, thus enhancing the resilience of heat-sensitive cultivars to climate change. The consortium members have increased photosynthetic efficiency by up to 15% using individual approaches, but the stacking of multiple approaches in the same plant has never been attempted before. We will also explore e) the adaptation of stomatal conductance to improve the water-use efficiency, and f) the integration of an O2 scavenging mechanism as a novel strategy to boost photosynthesis. Experience from past and/or ongoing EU and B&MGF projects clearly indicates that although the individual approaches can be effective, they are insufficient to achieve the ambitious objectives of the current call. Therefore, the PhotoBoost project will generate optimised lines representing two major food crops (potato and rice) by simultaneously targeting multiple constraints limiting photosynthetic efficiency. We aim to increase photosynthetic efficiency under diverse environmental conditions by at least 20–25% in terms of photosynthesis rates and by at least 25–30% in terms of biomass yield. Our published results demonstrate that such approaches are viable and there is no a priori reason to doubt that combining multiple approaches in the same plant will achieve even higher levels of biomass yield and productivity.

Rice is a staple food for more than half of the world's population. However, rice is largely consumed as polished grain (white rice) and its consumption, as part of the adoption of a Western diet and increasingly sedentary life style, is associated with increased risk of a range of chronic diseases including type 2 diabetes, obesity, cardio-vascular disease and forms of cancer. Hence it is important to consider the impact of rice on nutrition and health as well as traditional quality attributes. Consequently, the two most important targets for quality improvement of polished white rice are to reduce the rate of digestion in the human gastrointestinal tract (through starch structure manipulation and increasing the percentage of resistant starch) and increase the content of dietary fibre while retaining high yield and good cooking and sensory properties. The research project will carry out detailed analyses of grain composition of a wide range of rice lines to identify lines with increased health benefits combined with good consumer acceptability. Cutting-edge genetics and bioinformatics will then be used to identify molecular markers that can be used to select for quality traits by breeders. The improved lines and markers will then be delivered to national and international rice breeding programmes to allow them to develop new commercial varieties.

The world's major river deltas - hotspots of agricultural production that support rural livelihoods and feed much of the global population - are facing a major sustainability crisis. This is because they are under threat from being 'drowned' by rising sea levels, with potentially severe consequences for the 500 million people who live and work there. In particular, the process of 'drowning' means that deltas are rapidly losing land (up to 20% of land is projected to be lost to sea-level rise by 2100 in the major deltas of south and southeast Asia alone), while simultaneously exacerbating problems of flooding and soil salinization. These problems are creating a 'perfect storm' that makes agriculture increasingly challenging, at precisely the time when the pressure is increasing for these rich, fertile, landscapes to produce more food to support rapidly growing global populations. The world's third largest delta, the Mekong, is SE Asia's rice basket and home to almost 20 million people, but it is being exposed to severe environmental risks as a result of climate change and rapid economic development, most notably from the development of hydropower dams in the Mekong's catchment upstream which are cutting off the supply of sediment to the delta. The Mekong is therefore not only representative of many of the issues facing the world's deltas, but reliable data are urgently needed to help inform the sustainable management plans required to provide a safe operating space for the delta's inhabitants. In our prior work we have demonstrated that flows of water, sediment and associated nutrients within and through deltas are critical to the resilience of rice cultivation strategies. The sediments that are deposited in the delta help to offset sea level rise and they are very fertile because of the abundant nutrients (nitrogen and phosphorous) they contain. The key issue that is the focus of this proposal is that many of the Mekong delta's poor farmers (over 3.5 million farmers live below the poverty line) rely on the free fertilisation provided by river sediment deposition to reduce their 'input' costs (the portion of their income that is spent on purchasing and applying artificial fertiliser to maintain rice production). There is therefore a trade-off between the positive effects (delta building and free fertilisation) of natural sediment deposition versus the negative effects of the flooding process that causes it. As sediment and nutrient fluxes decline in the future (as a result of sediment trapping by dams upstream), new approaches are needed to inform adaptation strategies (such as managed flooding) to ensure that vulnerable communities can continue to farm sustainably in the future. In this proposal we will collaborate with Vietnamese partners to bring UK expertise in (i) the modelling of floods, sediment transport and nutrient fluxes; (ii) agricultural livelihoods; (iii) participatory stakeholder engagement processes and (iv) social-ecological systems dynamics to bear on this challenge. By bringing together this blend of expertise and working closely with our Vietnamese colleagues and stakeholders we will be able to define policy relevant scenarios of future change, quantify the links between flooding, sediment and nutrient deposition and agricultural livelihoods, and develop new modelling tools that will be able to evaluate the trade-offs between flooding and nutrient supply as the future environment changes. We will be able to concept-proof a new approach that can deliver an integrated assessment of the factors driving changes to livelihoods and explore the effects of adaptations that could enable more sustainable intensification of rice agriculture. This will be done within a globally significant, iconic, delta, providing a template for similar analyses in other vulnerable deltas in the Global South.