Comparative Evolutionary Genomics of Cotton

01 Mar 2009 28 Feb 2017

Jonathan Wendel (PI) , Andrew H Paterson (CoPI), Alan Gingle (CoPI), Adah Leshem (CoPI), Joshua A Udall (CoPI)


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.