CAP Workshop
A Coordinated Agricultural Project (CAP) planning meeting for cotton was held at the Texas Agricultural Experiment Station, Lubbock , TX on December 9-10, 2004 . The CAP program is one of several plant science programs administered by the USDA-CREEES-NRICGP. CAP projects are “community-based, large-scale, multimillion dollar projects that are intended to promote collaboration, open communication, and exchange of information, reduce duplication of effort, and coordinate activities among individuals, institutions, and states.” The goal is “to engage the applied plant sciences, both public and private, and involve them in the application of basic discoveries to U.S. crop or forestry improvement.” Dr. Andrew Paterson (University of Georgia) obtained funding from USDA-CSREES-NRICGP (with letters of support from many members of the cotton community) to organize this workshop with the goal of developing a plan “that reflects community consensus regarding priority areas in which new research is needed to improve the productivity and sustainability of U.S. cotton production” and that will “develop genomic tools and approaches that are needed to foster advances in these priority areas.”
Presentation Highlights
In presentations, Mr. Steve Verett of the Plains Cotton Growers Association stressed the importance of the workshop's goals to cotton producers. Dr. Ed Kaleikau of USDA-CSREES provided an overview of the CAP program goals and a discussion of the large-scale rice genomics project that was funded in FY2004, and provided detailed guidance regarding the development of a competitive cotton CAP project. Dr. David Stelly of Texas A&M University and Chair of ICGI summarized the recent ICGI biennial meeting held in Hyderabad , India in October 2004 (which was attended by many of the scientists participating in the CAP workshop). Dr. Andrew Paterson summarized the results of an on-line questionnaire that was disseminated prior to the Cotton CAP Planning workshop, regarding research priorities and coordination needs in cotton genomics.
Breakout Groups
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Traits and Breeding
David M. Stelly & Robert J. Wright
About a dozen individuals (listed at end) participated in the Traits & Breeding Workgroup. The group focused on the selection of crop trait and breeding topic(s) deemed critical to the future of the US cotton industry. The group converged on three main targets: fiber uniformity, nematode resistance and drought/salinity stress tolerance. Fiber uniformity is critical to marketing US cottons globally. Nematodes, particularly root-knot and reniform, debilitate cotton production in many areas; genetic solutions would be economically and ecologically advantageous. Drought and salinity loom as major constraints to US cotton production in several key production areas. Increased drought tolerance could help producers maintain productivity and quality, while conserving water resources. |
Markers and Mapping
Andrew H. Paterson & John Z. Yu
Thirteen of the 27 cotton CAP workshop participants attended this workgroup in full or in part and contributed to discussion of the current status and future needs of genetic markers and genome mapping in cotton, toward application to the overall priorities identified by the group as a whole (the improvement of fiber uniformity and drought tolerance, also including an albeit lesser emphasis on root knot and reniform nematode resistance). |
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Functional Genomics
Barbara A. Triplett & Paxton Payton
The overall objective of the functional genomic effort will be to determine how to achieve the full genetic potential of cotton fiber quality even under sub-optimal growing conditions. The goals of this objective will be (1) to identify genes that determine the uniformity of fiber physical properties, such as length and maturity, by comparing expression data of cotton genotypes that differ in these parameters and (2) to identify key genes whose expression is regulated by abiotic stress factors such as drought, salt, and temperature. The platform for gene expression analysis is expected to be a cotton microarray chip that is being produced jointly by two NSF Plant Genome Projects [PIs: Jonathan Wendel, Iowa State University and Z. Jeffrey Chen, Texas A&M University ] that will be available to the cotton community in the spring of 2005. The goal of this approach will be to identify which parts of the expression profile affect fiber quality and abiotic stress tolerance individually and collectively. |
Informatics
Alan Gingle & Peng Chee
The recommended informatics objectives are (1) to provide and maintain a flexible mechanism for data exchange amongst the collaborating labs, (2) to provide a Web-database resource that facilitates queries/searches and visualization of integrated datasets from the collaborating labs and (3) to provide a Web portal to collaborating lab and other cotton related Web sites as well as providing Ftp/Web hosting for education/outreach pages, a bulk data download site and Web service based data availability. Flexible data exchange will accommodate the informatics capabilities and goals of collaborating labs, and provide help, if needed, to ensure timely data submission to public repositories. Integrated data query and visualization would be based on a database architecture having the needed combination of federation and data warehousing to facilitate query criteria that cut across individual lab datasets. |
