Low Temperature Transcriptional Networks

该项目的长期目标是系统地了解植物对非生物胁迫的反应，并利用获得的第一原理来开发新的策略，以提高重要农业作物的抗逆性。这些目标很重要，因为非生物胁迫限制了可种植作物的地理位置，并占了每年产量损失的大部分。总体目标是确定植物进化而来的抵御寒冷的低温转录网络。由于冰冻和脱水伤害之间存在直接联系，这些结果还应该为人们进一步了解赋予干旱和其他脱水压力耐受性的基因模块的性质提供了进一步的见解。该项目的具体目标有两个。首先是详细了解拟南芥的低温转录网络，并确定哪些成分与耐寒性有关。这将通过确定在配置低温转录组中起关键作用的转录因子和其他调控蛋白；鉴定这些调控蛋白发挥作用的顺式作用DNA调控元件；以及鉴定有助于抗冻性(以及潜在的抗旱性和其他非生物胁迫)的调控程序和基因模块来实现这一点。该项目的第二个目的是确定赋予拟南芥耐冷性的低温转录网络和基因模块在冷适应植物中是否保守(即，对低非冰冻温度的响应提高了抗冻性)，以及这些网络和基因模块中的“缺陷”是否有助于那些不冷适应植物的冷冻敏感性。这一目标将通过对耐冷性不同的三个密切相关的茄子物种进行比较基因组分析来实现：商业茄子、马铃薯和番茄。总之，拟议的研究包括在基因组水平上确定基因表达，对模式和作物物种进行比较基因组分析，以及结合计算分析和经验测试来重建和模拟转录调控网络，这些网络对植物生命至关重要，在农业中具有重要意义。更广泛的影响提高农作物的非生物胁迫耐受性对于满足未来对粮食和纤维的需求至关重要。此外，在美国每年生产足够的生物质，以用可再生资源生产的生物燃料取代相当大比例的石油运输燃料，这是新兴国家愿景的关键组成部分。这些研究直接涉及到这些重要的领域，因为它们将提供更深入的了解植物为应对非生物胁迫而进化的基因组机制，并有可能为提高植物的非生物逆境耐受性提供遗传工具。在这些研究过程中产生的微阵列数据将通过项目网站(http://aztec.stanford.edu/cold/index.html))以及地球观测组织和ArrayExpress获得。该项目还将有助于培训下一代科学家，他们在将基因组、生物信息学和计算方法应用于生物学基本问题方面经验丰富。最后，该项目包括一个暑期本科生教育和研究培训计划，旨在纳入我们社会中代表性不足的群体。目的是为学生提供更多了解基因组研究不同领域的机会，并广泛和非正式地讨论与追求科学事业有关的问题。

PI: M. Thomashow (Michigan State University)CoPIs: C. Chan (Michigan State University) and T. Chen (Oregon State University; subawardee)Collaborator: S.-H. Shiu (Michigan State University)The long range goals of the project are to gain a systems level understanding of plant responses to abiotic stress and to use the first principles gained to develop novel strategies to improve the stress tolerance of agriculturally important crops. These goals are important as abiotic stresses limit the geographical locations where crops can be grown and account for the majority of losses in yield on an annual basis. The overall objective is to identify the low temperature transcriptional networks that plants have evolved to survive freezing. As there is a direct link between freezing and dehydration injury, the results should also provide further insights into the nature of gene modules that impart tolerance to drought and other dehydration stresses. The specific aims of the project are two-fold. The first is to develop a detailed understanding of the low temperature transcriptional network of Arabidopsis and determine which components contribute to freezing tolerance. This will be accomplished by identifying transcription factors and other regulatory proteins that have key roles in configuring the low temperature transcriptome; identifying the cis-acting DNA regulatory elements through which these regulatory proteins function; and identifying the regulatory programs and gene modules that contribute to freezing tolerance (and potentially tolerance to drought and other abiotic stresses). The second aim of this project is to determine whether the low temperature transcriptional networks and gene modules that impart freezing tolerance in Arabidopsis are conserved in plants that cold acclimate (i.e., increase in freezing tolerance in response to low non-freezing temperatures) and whether "deficiencies" in these networks and modules contribute to the freezing sensitivity of those plants that do not cold acclimate. This aim will be accomplished through comparative genomic analysis of three closely related Solanum species which differ in cold tolerance: S. commersonii, potato and tomato. Together, the proposed studies incorporate the determination of gene expression at a genome level, a comparative genomic analysis of model and crop species, and the integration of computational analysis and empirical testing to reconstruct and model transcriptional regulatory networks that are fundamental to plant life and have importance in agriculture. Broader ImpactsImproving the abiotic stress tolerance of crops is crucial to meeting future demands for food and fiber. In addition, it is a key component of an emerging national vision to produce sufficient biomass per year in the U.S. to replace significant percentages of petroleum-based transportation fuels with biofuels produced from renewable resources. The studies proposed here directly relate to these important areas as they will provide a deeper understanding of the genomic mechanisms that plants have evolved to cope with abiotic stress and have the potential to provide genetic tools to improve the abiotic stress tolerance of plants. Microarray data generated in the course of these studies will be available through a project website (http://aztec.stanford.edu/cold/index.html) and through GEO and ArrayExpress. The project will also contribute to the training of a next generation of scientists who are experienced in bringing genomic, bioinformatic and computational approaches to bear on fundamental questions in biology. Finally, the project includes a summer undergraduate education and research training program which will target inclusion of underrepresented groups of our society. The goal is to provide the students with opportunities to learn more about different areas of genomic research and to discuss broadly and informally issues that relate to pursuing careers in science.