Cereal Drought Stress Response and Resistance Networks

首席研究员：Andy Pereira（阿肯色大学） 联合首席研究员：Ruth Grene 和 Oswald Crasta（弗吉尼亚理工州立大学）、Yinong Yang（宾夕法尼亚州立大学）、Niranjan Baisakh（路易斯安那州立大学农业中心）增长会限制农作物的稳定生产。玉米、小麦、水稻和大麦等谷类作物在开花和籽粒形成期间最容易受到干旱的影响，造成严重的产量损失。该项目的目标是开发谷物干旱反应的系统生物学观点，以了解这一复杂的过程并提高抗旱性和水分利用效率。水稻和玉米干旱反应的全基因组比较转录组分析将被整合到谷物干旱基因相互作用网络中，利用直系同源信息来预测作为谷物基础的保守功能关系。将鉴定水稻和玉米之间参与干旱响应和抗性的保守直系同源调控基因，包括转录因子 (TF)、蛋白激酶和磷酸酶、激素信号传导途径中的基因、染色质结合蛋白、蛋白质降解和小 RNA 途径。作为原理证明，一组假定的水稻和玉米保守基因将通过突变体和自然等位变体的遗传分析进行测试，评估它们改变的干旱反应表型和干旱基因相互作用网络中的扰动。这些分析将验证和改进谷物基因相互作用网络预测，并为提高谷物的抗旱性/耐受性提供候选基因。就更广泛的影响而言，该项目将通过生成对全球稳定粮食生产系统发展至关重要的信息以及创建跨学科的教育环境来做出贡献。从科学角度来说，该项目将展示如何使用综合网络方法来了解复杂的植物反应，例如干旱反应和抗性。外展和培训活动被纳入跨学科植物实验室生物信息学项目中，并将通过弗吉尼亚理工大学和其他附近大学的既定项目向弗吉尼亚州和北卡罗来纳州各机构的高中生和代表性不足的本科生开放。作为 NSF 21 世纪劳动力网络基础设施培训、教育、进步和指导 (CI-TEAM) 项目一部分而开发的外展计划将为教师和学生提供使用研究数据中的社会环境案例研究进行定量数据分析的模块。博士后研究人员综合导师计划将用于促进职业发展。与“一代挑战计划”和参与干旱研究的国际农业研究磋商小组机构的国际研究合作将增强全球农业系统的能力建设。 植物基因型和项目中开发的所有数据将通过项目网站 (http://cereal-drought.vbi.vt.edu/) 提供，该网站将允许交互式访问数据和网络。使用的其他公开遗传库存将由各自的发起者通过长期公共存储库进行分发。微阵列和 EST 数据将分别存放在 GEO 和 NCBI。 生成的所有功能基因组学数据将定期存放在 Gramene 和其他公共数据库中。

PI: Andy Pereira (University of Arkansas) Co-PIs: Ruth Grene and Oswald Crasta (Virginia Polytechnic and State University), Yinong Yang (Pennsylvania State University), Niranjan Baisakh (Louisiana State University Agricultural Center)Collaborators: Guy Davenport and Jianbing Yan (CIMMYT, Mexico), Hei Leung (IRRI, Philippines)Water scarcity causing drought during essential periods of plant growth can limit stable crop production. Cereal crops such as maize, wheat, rice and barley are most affected by drought during the time of flowering and initiation of grain formation, causing drastic yield losses. The goal of this project is to develop a systems biology view of drought responses in cereals to understand this complex process and improve drought resistance and water use efficiency. Genome-wide comparative transcriptome analysis of drought responses in rice and maize will be integrated into a cereal drought gene interaction network, using ortholog information to predict conserved functional relationships as a basis for cereals. Conserved orthologous regulatory genes between rice and maize involved in drought responses and resistance will be identified comprising transcription factors (TFs), protein kinases and phosphatases, genes in hormone signaling pathways, chromatin binding proteins, protein degradation and small RNA pathways. As proof of principle, a set of these putative conserved rice and maize genes will be tested by genetic analysis of mutants and natural allelic variants, assessing them for altered drought response phenotypes and perturbation in the drought gene interaction network. These analyses will validate and improve the cereal gene interaction network predictions, and provide candidate genes for improvement of drought resistance/tolerance in cereals. With respect to broader impacts, this project will contribute through the generation of information key to the development of stable food production systems worldwide and through the creation of a transdisciplinary educational environment. Scientifically, the project will demonstrate the use of an integrated network approach to understand complex plant responses such as drought response and resistance. Outreach and training activities are integrated within the transdisciplinary plant-lab-bioinformatics project and will be made accessible to high school and underrepresented undergraduate students from institutions across Virginia and North Carolina through established programs at Virginia Tech and other nearby universities. An outreach program developed as part of a NSF-Cyberinfrastructure Training, Education, Advancement, and Mentoring for Our 21st Century Workforce (CI-TEAM) project will provide modules for quantitative data analysis for teachers and students using socio-environmental case studies from research data. An integrated mentor program for postdoctoral researchers will be used to facilitate career development. International research collaborations with the Generation Challenge Program and CGIAR institutes involved in drought research will add capacity building to agricultural systems worldwide. Plant genotypes and all data developed in the project will be made available through a project website (http://cereal-drought.vbi.vt.edu/) that will allow interactive access to data and networks. Other publicly available genetic stocks used will be distributed by the respective originators with long term public repositories. Microarray and EST data will be deposited at GEO and NCBI, respectively. All functional genomics data generated will be periodically deposited in Gramene and other public databases.