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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

2015 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
In work during FY 2015, 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 were met (Objective 1). Seed increases for the Collection were challenged because of termination of the National Cotton Council-managed Counter Season Nursery activities in Tecoman, Colima, Mexico. In greenhouses at College Station, Texas, more than 300 critical accessions representing at least 40 cotton species were increased. Maximum use was made of the College Station field plantings, with 605 accessions being grown for seed increase, characterized with standardized morphological and agronomic descriptors, and photographed for a digital image library. Images were formatted for uploading into the database at More than 7,000 images were gathered in mid-to-late FY 2014 and another 4,800 are expected from the FY 2015 growing season (Objective 3). Seed requests for more than 2,000 lines made by 145 requesting groups were filled. Tissue samples and cuttings for propagation (138 accessions by 8 requesting groups) were sent in place of seed for critical accessions. Progress continued on project objectives to systematically apply molecular technology to characterize the Collection and increase the effectiveness and efficiency of its management (Objective 2). Progress was made in identifying molecular markers for characterizing the Collection and its component parts. A core set of genetic tools known as SSR markers were identified that are informative in characterizing the diversity within the "A" diploid species, and a set of lines representing one quarter of the available diploid "D" accessions in the Collection were identified for marker characterization. Preliminary analysis of genetic diversity was achieved in the "A" diploid species of the Gossypium Diversity Reference Set. In efforts to meet the objective of developing genetic resources and research tools (Objective 4), progress was made in documenting the priority traits of cottonseed oil and protein content. Seed protein and oil content data are being formatted for submission to the CottonGen database together with SSR molecular data collected on the same 2,250 accessions. Quantitative genetic analysis of sixteen populations with a range of values for cottonseed oil content was published.

1. Molecular diversity of the U.S. National Cotton Germplasm Collection. To be effective sources of variability for genetic improvement, germplasm collections must be genetically well-characterized. Knowledge of the structure of diversity within a collection is also necessary for its efficient and effective conservation and maintenance. ARS researchers at College Station, Texas; New Orleans, Louisiana; Stoneville, Mississippi; and Maricopa, Arizona, systematically characterized genetic resources within the National Cotton Germplasm Collection and were able to identify genetic variation that facilitated differentiation between the commercial cotton species. Molecular diversity that could partially differentiate among wild and improved lines within cultivated species was also identified, and molecular markers were used to identify varying levels of introgression among lines within these species. The use of molecular markers to characterize the Collection will allow the curator to efficiently and effectively increase and preserve the diversity of the Collection while maintaining the purity of its individual lines. Characterization of the Collection with molecular markers also allows breeders and geneticists to make more informed choices in their improvement efforts which will facilitate development of superior cotton varieties and products for the consumer.

2. Standardized descriptors, visual descriptor keys, and digital images for cotton germplasm. The usefulness of a germplasm collection to plant breeders and others interested in improving cotton is determined to a large degree by how well the contents of a given collection are described. Otherwise, the contents of a collection would essentially be just a random assemblage of seed. ARS researchers at College Station, Texas, in cooperation with database managers of CottonGen ( at Washington State University, standardized morphological descriptors for the National Cotton Germplasm Collection, created a visual descriptor key, and downloaded all descriptor data obtained since 2006. Descriptor data obtained prior to 2006 were transformed to the new standardized descriptor categories. This greatly expanded, highly detailed description of the Collection will enable users to more accurately identify materials of interest to their research, will reduce the amount of poorly targeted germplasm requests, and will enhance the efficiency of breeding efforts to develop new and improved cotton varieties for productive use by farmers in the U.S. and worldwide.

Review Publications
Hinze, L.L., Fang, D.D., Gore, M.A., Scheffler, B.E., Yu, J., Frelichowski, J.E., Percy, R.G. 2015. Molecular characterization of the Gossypium diversity reference set of the US National Cotton Germplasm Collection. Theoretical and Applied Genetics. 128(2):313-327.
Hinze, L.L., Horn, P.J., Kothari, N., Dever, J.K., Frelichowski, J.E., Chapman, K.D., Percy, R.G. 2015. Non-destructive measurements of cottonseed nutritional trait diversity in the US National Cotton Germplasm Collection. Crop Science. 55:770-782.
Puckhaber, L.S., Frelichowski, J.E., Bell, A.A., Stipanovic, R.D. 2014. New HPLC methods to quantitate terpenoid aldehydes in foliage of cotton (Gossypium). Journal of Natural Products. 4(3):188-195.
Hulse-Kemp, A.M., Lemm, J., Plieske, J., Ashrafi, H., Buyyarapu, R., Fang, D.D., Frelichowski, J.E., Giband, M., Hague, S., Hinze, L.L., Kochan, K., Riggs, R., Scheffler, J.A., Udall, J.A., Ulloa, M., Wang, S., Zhu, Q., Bag, S.K., Bhardwaj, A., Burke, J.J., Byers, R.L., Claverie, M., Gore, M.A., Harker, D.B., Islam, M.S., Jenkins, J.N., Jones, D.C., Lacape, J., Llewellyn, D.J., Percy, R.G., Pepper, A.E., Poland, J.A., Rai, K., Sawant, S.V., Singh, S., Spriggs, A., Taylor, J.M., Wang, F., Yourstone, S.M., Zheng, X., Lawley, C.T., Ganal, M.W., Van Deynze, A., Wilson, L.W., Stelly, D.M. 2015. Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L.). Genes, Genomes, Genetics. 5:1187-1209. doi:10.1534/g3.115.018416.