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

利用全基因组关联研究 (GWAS) 对水稻可持续用水所需的性状进行遗传剖析

• 批准号: BB/J002062/1
• 负责人: Hao Zhang
• 金额: $ 17.32万
• 依托单位: Lancaster University
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FJ002062%2F1
• 关键词: genetic; dissection; traits; required; sustainable

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.

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，该县60%的水稻产量是在冬季主要使用地下水种植的。这导致沿海地区地下水位下降和盐水进入。孟加拉国部分地区使用的地下水含有高浓度的砷（As），导致米粒中这种一类人类致癌物的浓度达到危险水平。减少灌溉需求应使水提取更可持续，并减少砷暴露。促进这一变化将有助于联合王国实现其对联合国千年发展目标的承诺，并直接造福于通过食用大米和大米产品而暴露于砷的联合王国人口。在孟加拉国，一种新的、大力推广的灌溉计划，称为交替湿润和干燥（AWD），减少了20-50%的用水量，同时提高了产量。但目前还不清楚AWD为什么有效，关键是它是否可持续。此外，还没有进行工作，以确定遗传变异的适应性（适用性），以AWD超过传统的淹没作物生产。该项目将通过以下方式解决这些缺点：i）对负责适应AWD的水稻基因进行遗传筛选（利用基因组测序技术的进展）; ii）在湿润和干燥周期期间对土壤进行化学和物理分析; iii）AWD在水稻植物中引起的变化的详细生理和转录组学特征以及iv）一个系统生物学的方法来确定负责适应AWD的代谢途径。利用与加尔各答大学，阿萨姆农业大学，孟加拉国水稻研究所和国际水稻研究所建立的伙伴关系，我们将从孟加拉地区收集300个适合博罗种植的水稻地方品种。这将被测序至1 x基因组覆盖率，以提供大约。300万个单核苷酸多态性，使用最近由上海中国科学院的韩斌开创的创新方法。第一季将在孟加拉国的一个地点和第二季的三个地点对这一种群进行常规洪水和AWD筛查。将收集农艺学数据，以评估对AWD的适应性。在一个网站（两年）的芽和粮食将分析17个宏量和微量元素，以提供一个详细的描述吸收和芽粒转运的重要植物和人类营养相关的元素。两组数据将进行全基因组关联作图，以鉴定与性状相关的基因组区域和候选基因，并鉴定是否有任何特定元素与AWD适应性相关。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。一项补充的转录组学研究将显示哪些基因、哪些途径受到AWD的影响。生成的数据将被纳入从RiceCyc数据库开发的基因组规模代谢模型中。这将提供可检验的假设，什么代谢途径是重要的生长在不同的水/土壤化学情景和最可能的合适的基因型。这些假设将在最后一年得到验证。所有数据都将被整合到可访问的数据库中，水稻品种小组将对绘制其他性状（如耐旱性、耐盐性、耐寒性和耐热性）具有巨大价值。所获得的产出将证明对全世界水稻研究人员和育种者以及任何关心洪水易发地区需氧作物的人都是有价值的。

项目成果

Localized flux maxima of arsenic, lead, and iron around root apices in flooded lowland rice.

• DOI: 10.1021/es501127k
• 发表时间: 2014
• 期刊: ENVIRONMENTAL SCIENCE & TECHNOLOGY
• 影响因子: 11.4
• 作者: Williams, Paul N.;Santner, Jakob;Larsen, Morten;Lehto, Niklas J.;Oburger, Eva;Wenzel, Walter;Glud, Ronnie N.;Davison, William;Zhang, Hao
• 通讯作者: Zhang, Hao

Effects of soil drying and wetting-drying cycles on the availability of heavy metals and their relationship to dissolved organic matter

土壤干燥和干湿循环对重金属有效性的影响及其与溶解有机物的关系

• DOI: 10.1007/s11368-015-1090-x
• 发表时间: 2015-07-01
• 期刊: JOURNAL OF SOILS AND SEDIMENTS
• 影响因子: 3.6
• 作者: Li, Zhu;Wu, Longhua;Christie, Peter
• 通讯作者: Christie, Peter

Measurement of labile arsenic speciation in water and soil using diffusive gradients in thin films (DGT) and X-ray absorption near edge spectroscopy (XANES)

• DOI: 10.1071/en14047
• 发表时间: 2015-02
• 期刊: Environmental Chemistry
• 影响因子: 4.3
• 作者: Trang T. X. Huynh;H. Harris;Hao Zhang;B. Noller

Uncertainty evaluation of the diffusive gradients in thin films technique.

• DOI: 10.1021/es504533e
• 发表时间: 2015-02-03
• 期刊: ENVIRONMENTAL SCIENCE & TECHNOLOGY
• 影响因子: 11.4
• 作者: Kreuzeder, Andreas;Santner, Jakob;Zhang, Hao;Prohaska, Thomas;Wenzel, Walter W.
• 通讯作者: Wenzel, Walter W.