Cereal Drought Stress Response and Resistance Networks

Pi：Andy Pereira(阿肯色大学)共同PIs：Ruth Gree和Oswald Crasta(弗吉尼亚理工大学和州立大学)，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)合作者：Guy Davenport和Jian建兵(CIMMYT，墨西哥)，Hei Leung(IRRI，菲律宾)在植物生长的关键时期干旱会限制作物稳定产量。玉米、小麦、水稻和大麦等粮食作物在开花期和籽粒形成初期受干旱影响最大，造成严重的产量损失。该项目的目标是发展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。对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，使用直系同源信息来预测保守的功能关系，作为谷物的基础。水稻和玉米之间与干旱反应和抗性相关的保守的同源调控基因将被确定，包括转录因子(TF)、蛋白激酶和磷酸酶、激素信号途径基因、染色质结合蛋白、蛋白质降解和小RNA途径。作为原理的证明，一组假定保守的水稻和玉米基因将通过突变和自然等位基因变异的遗传分析进行测试，评估它们的干旱反应表型变化和干旱基因相互作用网络中的扰动。这些分析将验证和完善谷物基因互作网络预测，并为提高谷物抗旱性/耐性提供候选基因。关于更广泛的影响，该项目将通过产生对全世界稳定的粮食生产系统的发展至关重要的信息以及通过创造跨学科的教育环境来作出贡献。科学上，该项目将展示使用综合网络方法来了解复杂的植物反应，如干旱反应和抗逆性。推广和培训活动被整合到跨学科的植物-实验室-生物信息学项目中，并将通过弗吉尼亚理工大学和附近其他大学的现有项目，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-面向21世纪劳动力的网络基础设施培训、教育、促进和指导项目(CI-Team)的一部分，一项外展计划将利用研究数据中的社会环境案例研究，为教师和学生提供定量数据分析模块。针对博士后研究人员的综合导师计划将用于促进职业发展。与世代挑战计划和参与干旱研究的CGIAR研究所的国际研究合作将增加世界各地农业系统的能力建设。项目中开发的植物基因类型和所有数据将通过项目网站(http://cereal-drought.vbi.vt.edu/))提供，该网站将允许交互访问数据和网络。所使用的其他公开可获得的基因库将由各自拥有长期公共储存库的发起者分发。微阵列和EST数据将分别存放在GEO和NCBI。所有产生的功能基因组数据将定期存储在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.