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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Research Project #424619

Research Project: Conservation, Genetic Analyses, and Utilization of Cotton Genetic Resources

Location: Crop Germplasm Research

2014 Annual Report

The long-term goal of this project is to conserve, describe, evaluate, and distribute accessions of the National Cotton Germplasm Collection. An integral part of distributing accessions of the Collection is providing descriptive and evaluation information to the research community through public databases. To accomplish this mission, the project works closely with its sister project that will develop genetic, genomic, and bioinformatics tools to support the evaluation and characterization of germplasm. During the next five years this project will focus on the following objectives. Objective 1: Efficiently and effectively acquire, maintain, back-up, and regenerate genetic resources of cotton and related wild species, and distribute samples and associated information worldwide. Subobjective 1A: Regenerate up to 10% of the Collection (c.a. 1000 accessions) annually at the Cotton Winter Nursery, Tecoman, Mexico, and field and greenhouse resources at College Station, TX. Produce quantities of seed sufficient to meet the needs of the research community and to maintain accessions in long-term backup storage. Subobjective 1B: Distribute viable seed and associated information for all available accessions to users of the Collection. Subobjective 1C: Strategically broaden the genetic diversity of the Collection through the acquisition of additional cotton germplasm through germplasm exchanges and plant explorations. Objective 2: Systematically apply new core sets of Simple Sequence Repeat (SSR) markers to increase the efficiency and effectiveness of cotton genetic resource management and genetic improvement. Subobjective 2A: Create diversity reference sets of accessions that represent cotton genomes, species, or traits of interest. Subobjective 2B: Identify genome- or species-specific core SSR markers and apply these markers to genotype prospective diversity reference sets. Subobjective 2C: Analyze genetic variability and diversity structure within diversity reference sets, and use this information to identify sources of uniqueness, redundancy, and introgression, and to assess the genetic integrity of accessions. Objective 3: Expand morphological characterizations, digital imaging, and evaluations of priority agronomic traits for cotton genetic resources, and promote coordinated, cooperative evaluation efforts nationally and internationally. Subobjective 3A: Characterize up to 10% of the Collection annually using a comprehensive and standard descriptor set developed for community use, and upload into GRIN-Global. Subobjective 3B: Create standardized digital image libraries of the Collection to document the morphological diversity of its contents, and make these libraries available to users through placement in the public databases GRIN-Global and CottonGen. Subobjective 3C: Coordinate the cooperative evaluation of cotton genetic resources for priority agronomic traits. Objective 4: Develop genetic resources and research tools for more efficient and effective genetic enhancement of cotton for priority traits such as yield, fiber quality, and resistance/tolerance to biotic and abiotic stresses.

To regenerate the collection (subobjective 1A), 10% of all accessions will be grown and harvested for seed increase annually at the Cotton Winter Nursery in Tecoman, Mexico, and in greenhouses and the field at College Station, TX. The genetic diversity of the collection will be strategically increased, filling gaps identified using taxonomic, pedigree, or geographic records, as well as molecular genetics data (Subobjective 1C). The primary means for filling gaps in the collection will be through explorations and germplasm exchanges with other nations' collections. To better characterize and more efficiently maintain the collection, diversity reference subsets will be developed that represent genomes, species, or other taxonomic groups. In creating reference sets, criteria for selecting accessions for inclusion will be geographic diversity, ecological diversity, morphological diversity, and differing degrees of human manipulation within the set. Once assembled, the genetic diversity within reference subsets will be determined using SSR molecular markers. To maximize the genotypic information acquired from SSR genotyping, genome- or species-specific SSR markers will be identified (subobjective 2B). Criteria for marker inclusion in core subsets are: SSRs with known map positions, high polymorphism information, high PCR quality, and easily scored and analyzed. DNA marker profiles for accessions within diversity reference subsets, will be evaluated for genetic diversity (subobjective 2C). Phylogenetic relationships will be evaluated using combinations of population genetic software, including JMP Genomics, GENALEX, NTSYSpc, STRUCTURE, and/or MEGA. Routine phenotypic characterizations of germplasm will be made and/or verified for approximately 1,000 accessions annually in the CWN, or in our greenhouses at College Station, using passport and descriptor data for cotton that follow the guidelines set by Bioversity International (subobjective 3A). Approximately 10% of collection will be digitally recorded annually and image libraries created for public use in CottonGen and GRIN databases (subobjective 3B). A standardized set of images of leaves, flowers, and bolls will be recorded using high resolution cameras. Evaluations of the collection for priority agronomic traits will be conducted as cooperative efforts with public research groups. The project will aid collaborators and independent evaluation projects by developing relevant sets of accessions for testing, providing seed for testing, and developing and making available uniform descriptors and techniques for characterizing accessions (subobjective 3C). A series of meetings will be held with cooperators to jointly develop uniform measurements for evaluating water use efficiency, drought tolerance, heat tolerance, etc. Several pre-breeding projects will be conducted to develop genetic resources for cotton improvement efforts. These projects vary in goals from day-length conversion in G. barbadense, to fiber quality improvement in G. hirsutum, to oil content improvement, and vary in methods from recurrent selection, to pedigree breeding, back-cross breeding, and single-seed descent.

Progress Report
Project work in FY 2014 met objectives to efficiently and effectively acquire, maintain, and regenerate genetic resources of cotton and related wild species, and to expand morphological characterizations and digital imaging of the National Cotton Germplasm Collection. Seed increases for the Collection were successful, with 800 lines grown and harvested at the Cotton Winter Nursery and over 200 critical lines representing at least 40 cotton species increased in greenhouses at College Station, Texas. Characterization of the Collection continued, with descriptors taken and images made in the Cotton Winter Nursery and in another planting of nearly 1,000 lines in College Station. Images (presently over 23,000) were formatted with Photoshop(R) and annotated for easy sorting by descriptors, and uploaded into the database at Seed requests for over 3,015 lines made by 105 requesting groups were filled. Tissue samples and cuttings for propagation were sent in place of seed for certain accessions. New lines were added to the Collection: 19 from the National Collection in Fort Collins, Colorado; 15 (disease resistant) lines were donated from cooperators at EMBRAPA, Brazil; 3 from cooperators in Australia; and 71 were collected from sites in Puerto Rico. A protocol for testing all incoming lines for the presence of adventitious transgenes was implemented, and all new lines proposed for addition to the Collection are in the process of being tested. Progress was made on project objectives to systematically apply molecular technology to characterize the Collection and increase the effectiveness and efficiency of its management. Molecular markers were identified for characterizing the Collection and its component parts. Markers were screened to identify those that are informative in characterizing the diversity within the "A" diploid species, and a set of lines representing the geographic distribution of the diploid "A" species was identified for marker characterization. In efforts to meet the objective of developing genetic resources and research tools, progress was made in enhancing the priority traits of cottonseed oil and protein content. Sixteen populations with a range of values for cottonseed oil content were developed and evaluated in replicated tests.

1. Collecting in Puerto Rico adds new lines to the National Cotton Germplasm Collection. The National Cotton Germplasm Collection has preserved much of the diversity within cotton, but gaps exist. Better characterization and documentation during collection trips facilitate identification and filling of gaps ranging from morphological, to molecular, to geographical. ARS researchers at College Station, Texas, collected 71 Puerto Rican cotton plants/populations which were photographed and tagged with GPS coordinates. The application of morphological descriptors, digital images, geographical descriptors, and location coordinates to the collected wild and feral Puerto Rican cottons addresses gaps in the National Collection and provides new sources of genetic variability for cotton improvement efforts.

2. National Cotton Germplasm Collection evaluated for seed protein and oil content. A well described and characterized National Cotton Germplasm Collection is essential to maximize its usefulness for cotton improvement efforts. ARS researchers at College Station, Texas, in collaboration with scientists from the University of North Texas, evaluated a representative sample of over 2,000 lines of the Collection for cottonseed oil and protein content. A large amount of variation for the two traits was detected in the Collection, exceeding that found in current commercial cultivars. The work established that much of the variation needed to improve oil and protein content can be found within cultivated cotton species and, therefore, these characteristics can be readily transferred into improved breeding material. The phenotypic (observable physical traits) evaluation of cottonseed quality provided by this work will enable geneticists and breeders to more efficiently identify and utilize germplasm for improvement in both cotton quality and productivity.

Review Publications
Beyer, B.M., Smith, C.W., Percy, R.G., Hague, S.J., Hequet, E.F. 2014. Test cross evaluation of Upland cotton accessions for selected fiber properties. Crop Science. 54:60-67.
Percy, R.G., Frelichowski, J.E., Arnold, M., Campbell, B.T., Dever, J., Fang, D.D., Hinze, L.L., Main, D., Scheffler, J.A., Sheehan, M., Ulloa, M., Yu, J., Yu, J. 2014. The U.S. National Cotton Germplasm Collection – its Contents, Preservation, Characterization, and Evaluation. In: Abdurakhmonov, I. Editor. World Cotton Germplasm Resources. Rijeka, Croatia: InTech. 167-201. Available:
Zhang, J., Percy, R.G., McCarty Jr, J.C. 2014. Introgression genetics and breeding between Upland and Pima cotton: A review. Euphytica. 198:1-12.
Fang, H., Zhou, H., Sanogo, S., Flynn, R., Percy, R.G., Hughs, S.E., Ulloa, M., Jones, D.C., Zhang, J. 2013. Quantitative trait locus mapping for Verticillium wilt resistance in a backcross inbred line population of cotton (Gossypium hirsutum x Gossypium barbadense) based on RGA-AFLP analysis. Euphytica. 194:79-91.