A genetic dissection of traits required for sustainable water use in rice using Genome Wide Association Studies (GWAS)

水稻灌溉使用了世界上三分之一的发达淡水供应，而且往往是不可持续的。在孟加拉国，该国60%的大米生产是在冬季的婆罗季种植的，主要使用地下水。这导致了沿海地区地下水位下降和咸水流入。孟加拉国一些地区使用的地下水含有高浓度的砷(As)，这导致大米谷物中这种一级人类致癌物质的危险浓度。减少灌溉需求应该会使取水更可持续，并减少砷暴露。促成这一变化将有助于英国履行其对联合国千年发展目标的承诺，并通过大米和大米产品的消费直接造福于暴露于AS的英国人。在孟加拉国，一种名为交替干湿灌溉(AWD)的新的大力推广的灌溉方案在提高产量的同时减少了20%-50%的用水量。但目前尚不清楚AWD为什么会奏效，关键是它是否可持续。此外，还没有开展工作来确定遗传变异对AWD的适应性(适宜性)，而不是传统的淹水作物生产。该项目将结合以下几个方面来解决这些缺陷：i)对水稻适应AWD的基因进行遗传筛选(利用基因组测序技术的进步)；ii)对土壤在湿润和干燥循环期间的化学和物理分析；iii)对AWD在水稻植株中引起的变化进行详细的生理和转录学表征；以及iv)采用系统生物学方法来确定负责适应AWD的代谢途径。利用与加尔各答大学、阿萨姆邦农业大学、孟加拉国水稻研究所和国际水稻研究所建立的合作伙伴关系，我们将从孟加拉地区生产适合种植Boro的300个水稻地方品种。这将被测序到1倍的基因组覆盖范围，以提供大约。利用中国科学院的韩斌最近在上海率先提出的一种创新方法，对300万个单核苷酸多态进行了分析。这些人口将在孟加拉国的常规洪水和AWD下进行筛查，第一季在一个地点，第二季在三个地点。将收集农艺数据，以便评估对AWD的适应情况。将对同一地点(两年)的地上部和谷物进行17种宏观和微观元素的分析，以提供对重要植物和人类营养相关元素的吸收和地上部-谷物转运的详细描述。这两组数据都将受到全基因组关联图谱的影响，以确定与这些性状相关的基因组区域和候选基因，并确定是否有任何特定因素与AWD的适应性有关。将对土壤化学和强度进行详细分析，以揭示影响植物生长的物理/化学变化。同时，将测量植物激素的空间(茎和叶)和时间分析，以评估植物生长何时以及如何受到AWD的影响。一项互补的转录学研究将显示哪些基因、哪些途径受到AWD的影响。产生的数据将被合并到从RiceCyc数据库开发的基因组规模的代谢模型中。这将提供可检验的假说，说明在不同的水/土壤化学情景下，哪些代谢途径对生长是重要的，以及最有可能适合的基因类型。这些假设将在最后一年得到验证。所有数据将被整合到公众可访问的储存库中，水稻品种小组将对绘制其他特征，如干旱、耐盐、耐寒和耐热等具有极大的价值。所获得的成果将被证明对世界各地的水稻研究人员和育种者以及任何关心洪水易发地区好氧种植作物的人都是有价值的。

Rice irrigation uses 1/3rd of the world's developed freshwater supplies, and is often unsustainable. In Bangladesh, 60% of the county's rice production is grown in the winter 'boro' season using predominantly groundwater. This results in lowering of water tables and ingress of saline water in coastal areas. The groundwater used in some parts of Bangladesh contains high concentrations of arsenic (As) which leads to dangerous concentrations of this class one human carcinogen in rice grain. Reducing irrigation demand should make water extraction more sustainable and reduce As exposure. Contributing to this change would help the UK meet its commitment to the UN Millennium Development Goals, and have direct benefit to the UK population exposed to As through consumption of rice and rice products. In Bangladesh, a new, heavily promoted irrigation scheme called alternate wetting and drying (AWD) reduces water use by 20-50% while increasing yield. But it is unknown why AWD works, and crucially if it is sustainable. Also, no work has yet been conducted to determine genetic variation for adaption (suitability) to AWD over conventional flooded crop production. This project will address these shortcomings by combining; i) a genetic screen for rice genes responsible for adaptation to AWD (exploiting advances in genome sequencing technology); ii) a chemical and physical analysis of the soil during cycles of wetting and drying; iii) a detailed physiological and transcriptomic characterisation of the changes that AWD causes in the rice plant and iv) a systems biology approach to identifying the metabolic pathways that are responsible for adaptation to AWD. Using established partnerships with the University of Calcutta, Assam Agricultural University, the Bangladesh Rice Research Institute and the International Rice Research Institute we will produce a collection of 300 rice landraces from the Bengal region suitable for boro cultivation. This will be sequenced to 1 x genome coverage to provide approx. 3 million single nucleotide polymorphisms using an innovative approach recently pioneered by Bin Han at the Chinese Academy of Science in Shanghai. This population will be screened under conventional flooding and AWD in Bangladesh in one site in the first season and three sites in the second season. Agronomic data will be collected to allow adaptation to AWD to be assessed. Shoots and grain in one site (both years) will be analysed for 17 macro and micro elements to provide a detailed description of uptake and shoot-grain translocation of the important plant and human nutrition-relevant elements. Both sets of data will be subjected to genome wide association mapping to identify the genomic regions and candidate genes associated with the traits and to identify if any specific element is related to adaptability to AWD. Detailed analysis of soil chemistry and strength will be conducted to reveal the physical/chemical changes taking place that affect plant growth. At the same time, spatial (stems and leaves) and temporal analysis of plant hormones will be measured to assess when and how plant growth is affected by AWD. A complementary transcriptomic study will show which genes, from which pathways, are being affected by AWD. The data generated will be incorporated in to a genome-scale metabolic model developed from the RiceCyc database. This will provide testable hypothesis of what metabolic pathways are important for growth in different water/soil chemistry scenarios and the most likely suitable genotypes. These hypotheses will be validated in the final year. All data will be integrated into publically accessible repositories and the panel of rice cultivars will be immensely valuable for mapping other traits such as drought, salt, cold and heat tolerance. Outputs obtained will prove valuable to researchers and breeders on rice throughout the world and to anyone concerned about aerobically-grown crops in flood-prone areas.