Comparative Evolutionary Genomics of Cotton

PI: Jonathan F. Wendel（爱荷华州立大学）CoPIs: Adah lesham - 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）现代基因组学方法与生物学其他领域的融合为深入了解植物形态的起源提供了巨大的希望。在这个项目中，一个多方面的计划将被实施，以进一步我们对复杂的遗传结构的理解，这是表型的基础，并阐明涉及发育，农艺和进化变化的过程。利用来自棉花属（Gossypium）的成熟模型系统和新的基因组资源，揭示了将原始表皮种子毛转化为现代棉花品种经济上重要的纤维所涉及的复杂性。实验包括四个相互关联的组成部分：(1)开发和表征不朽的渗入系，将复杂的形态简化为更小的单元，以适应功能基因组分析；(2)利用丰富的EST资源开发新的基因表达分析平台；(3)利用基因渗入系研究与自然发生的纤维表型变异相关的遗传网络和基因表达扰动；(4)为理解选择对棉花遗传多样性的影响奠定基础。由于棉花是多倍体，本研究将探索多倍体形成为表型进化创造独特机会的可能性。两个不同的多倍体物种被驯化，从而能够评估与驯化和形态进化相关的潜在遗传结构的并行性。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提供物理资源和智力工具，包括：(1)一个新的公共微阵列平台和一个丰富的棉花EST资源；(2)用于功能基因组和遗传分析的可公开获取的不朽渐渗群体；(3)深入了解纤维发育和农艺改良中重要的基因和生物过程；(4)未来棉花多样性分析的框架。该项目产生的所有数据和种质资源将及时免费提供给社区。数据将通过适当的渠道（例如GenBank和GEO）以及我们的项目网站——棉花门户网站（http://gossypium.info）向公众开放。渗入线将在两个项目地点进行维护，并通过项目和美国农业部国家棉种质收集（德克萨斯州大学城）进行分发。Oligo微阵列将继续在成本回收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高中科技教育工作者。通过该项目，将实施一项基于探究的实习计划，为中学教师提供机会，在参与机构的不同实验室进行真正的研究。该项目将向全国教师开放。教师将接受教师、职员和硕士教师的指导，了解与植物生物学和遗传学相关的概念基础。此外，专业发展工作将通过提供暑期讲习班扩大到包括k -4年级教师。将开发基于网络的教学单位，并将其与一般可获得的技术相结合，以便向课堂教师提供随时可用的机会，并在www.plantgdb.org上公布发展情况，并在国家教育会议上传播。将制定一项高级教师实习计划，为那些对与所在地区或地区的其他教师建立联系并将技术知识传授给他们有浓厚兴趣的教师提供服务。

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.