Comparative Evolutionary Genomics of Cotton

Pi：Jonathan F.Windel(爱荷华州立大学)Copis：Adah Lesem-Ackerman(爱荷华州立大学)，Alan R.Gingle和Andrew H.Paterson(佐治亚大学)，Joshua A.Udall(杨百翰大学)高级人员：Barry Marler和Junkang Rong(佐治亚大学)和Nikki Hanegan(杨百翰大学)现代基因组方法与其他生物学领域的融合为深入了解植物形式的起源提供了巨大的希望。在这个项目中，将实施一个多方面的计划，以加深我们对表型背后的复杂遗传结构的理解，并阐明涉及发育、农艺和进化变化的过程。利用棉花属(Gossypium)成熟的模式系统和新的基因组资源，将揭示将原始表皮种毛转化为现代棉花品种重要的经济纤维所涉及的复杂性。实验涉及四个相互关联的部分：(1)开发和鉴定永生渐渗系，以将复杂的形态减少到更小的单位，以便进行功能基因组分析；(2)利用丰富的EST资源开发新的基因表达谱平台；(3)利用导入系研究与纤维表型自然发生变异相关的遗传网络和基因表达的扰动；以及(4)为理解选择对棉花遗传多样性的影响提供基础。由于棉花是多倍体，这项研究将探索多倍体形成为表型进化创造了独特机会的可能性。驯化了两个不同的多倍体物种，从而能够评估与驯化和形态进化相关的潜在遗传结构中的并行性。除了解决基本的生物学问题外，该项目还将为棉花研究和改良产生物质资源和智力工具，包括：(1)一个新的公共微阵列平台和一个内容丰富的、可在网上获得的棉花EST资源；(2)可公开获得的用于功能基因组和遗传分析的永生导入种群；(3)对纤维发育和农艺改良中重要的基因和生物学过程的洞察；以及(4)棉花未来多样性分析的框架。该项目产生的所有数据和种质将及时免费提供给社区。数据将通过适当渠道(例如，基因库和地球观测组织)以及我们的项目网站棉花门户网站(http://gossypium.info).)向公众开放导入系将在两个项目地点保持，并通过该项目和美国农业部国家棉花种质收藏(德克萨斯州大学站)分发。寡聚微阵列将继续在回收成本的基础上通过项目网站提供。除了为本科生、研究生和研究生提供科学培训外，该项目还特别关注初中和高中科技教育工作者。通过这一项目，将实施一项以探究为基础的实习方案，为中学教师提供在参与机构的不同实验室进行真正研究的机会。该计划将向全国教师开放。教师将从教职员工和硕士教师那里接受与植物生物学和遗传学相关的概念基础的指导。此外，将通过提供暑期讲习班，将专业发展努力扩大到包括K-4年级教师。将开发基于网络的教学单元，并与普遍使用的技术相结合，以便随时接触到课堂教师，其发展情况张贴在www.PLANGDB.org上，并在国家教育会议上传播。将制定一项硕士教师实习计划，供那些对与所在地区或地区的其他教师建立联系并向其转移技术知识的人提供。

PI: Jonathan F. Wendel (Iowa State University)CoPIs: Adah Leshem-Ackerman (Iowa State University), Alan R. Gingle and Andrew H. Paterson (University of Georgia), Joshua A. Udall (Brigham Young University)Senior Personnel: Barry Marler and Junkang Rong (University of Georgia) and Nikki Hanegan (Brigham Young University)The convergence of modern genomic approaches with other areas of biology holds great promise for providing insight into the origins of plant form. In this project a multifaceted program will be implemented to further our understanding of the complex genetic architecture that underlies phenotypes, and to elucidate the processes involved in developmental, agronomic, and evolutionary change. Using a well-developed model system from the cotton genus (Gossypium) and new genomic resources, the complexities involved in transforming primitive epidermal seed hairs to the economically important fibers of modern cotton cultivars will be revealed. Experiments involves four interrelated components: (1) developing and characterizing immortal introgression lines to reduce complex morphology into smaller units amenable to functional genomic analyses; (2) developing a novel gene expression profiling platform using a vastly enriched EST resource; (3) studying perturbations in genetic networks and gene expression associated with naturally occurring variation in fiber phenotypes, using the introgression lines; and (4) providing a foundation for understanding the effects of selection on genetic diversity in cotton. Because cotton is a polyploid, the research will explore the possibility that polyploid formation created distinct opportunities for phenotypic evolution. Two different polyploid species were domesticated, thus enabling an evaluation of parallelisms in the underlying genetic architecture associated with domestication and morphological evolution. In addition to addressing fundamental biological questions, the project will generate physical resources and intellectual tools for cotton research and improvement, including: (1) a new public microarray platform and a vastly enriched, web-accessible EST resource for cotton; (2) publicly available immortal introgression populations for functional genomic and genetic analyses; (3) insight into the genes and biological processes important in fiber development and agronomic improvement; and (4) a framework for future diversity analyses in cotton. All data and germplasm resulting from this project will be made freely available to the community in a timely manner. Data will be made accessible to the public via appropriate channels (e.g., GenBank and GEO) and also through our project website, the Cotton Portal (http://gossypium.info). Introgression lines will be maintained at two project locations and distributed through the project and through the USDA National Collection of Gossypium Germplasm (College Station, TX). Oligo microarrays will continue to be available on a cost-recovery basis through the project website. In addition to providing scientific training to undergraduate and graduate students and post-graduate scholars, this project has a special focus on middle school and high school science and technology educators. Through this project an inquiry-based internship program will be implemented that provides the opportunity for secondary teachers to conduct bona fide research in different laboratories at the participating institutions. The program will be open to teachers nationwide. Teachers will receive instruction from faculty, staff and master teachers on the conceptual foundations associated with plant biology and genetics. Additionally, professional development efforts will be expanded to include K-4th grade teachers by offering summer workshops. Web-based instructional units will be developed and interfaced with commonly accessible technology to provide ready access to classroom teachers, with developments posted at www.plantgdb.org and disseminated at national education conferences. A master teacher internship program will be developed, available to those with a strong interest in networking with and transferring technological knowledge to other teachers in their regions or districts.