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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

2017 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
Progress was made on all four project objectives during FY 2017. Genetic resources of cotton and related wild species were efficiently and effectively acquired, maintained, distributed, and regenerated. Hundreds of morphological characterizations and digital images of the National Cotton Germplasm Collection (NCGC) were obtained. A second season of plantings was made at the Counter Season Nursery (CSN) in Liberia, Costa Rica, under the direction of Cotton Incorporated (Objective 1). A conservative number of 208 accessions were sent because of heavy local rains that forced a late planting and thus accessions with faster growth were sent for the short growing season. In greenhouses at College Station, Texas, more than 150 critical accessions representing nearly 40 Gossypium species were increased. Maximum use was made of the College Station field plantings with 716 accessions grown for seed increase. The accessions were characterized with standardized morphological and agronomic descriptors, and photographed for a digital image library (Objective 3). Descriptors and companion digital images were formatted for cooperators at Washington State University to facilitate uploading into the CottonGen database ( More than 4,200 images were gathered from College Station and another 268 from the CSN. The low number of images from the CSN are due to the late planting which still left most plants in the vegetative stage. Seed requests for 1,336 accessions made via 125 orders were filled (Objective 1). Progress continued on objectives to systematically apply molecular technology to characterize the germplasm collection and increase the effectiveness and efficiency of its management. Previous accomplishments in characterizing the cotton species known as tetraploids were expanded with a resequencing project (Objective 2). The resequencing work is being conducted in coordination with the development of individual core collections for wild and cultivated samples of both commercial tetraploid species (Objective 2). A germplasm development project continued with identification of superior selections for fiber quality; eleven selections and five check cultivars were advanced to a replicated evaluation in two locations (Objective 4).

1. Molecular characterization of cotton germplasm. Cotton grown throughout the world contains beneficial genetic variations that breeding methods can exploit to develop cultivars adapted to emerging environmental and climate conditions. For the National Cotton Germplasm Collection, continual characterization and evaluation using the latest technologies are vital to accurately describe the resources and allow potential users to request the most relevant accessions for cotton research and improvement. Recently, the cotton community established a high-throughput molecular biology-based system, known as the CottonSNP63K array, which enables any researcher to simultaneously analyze large numbers of genetic "markers" in cotton and obtain highly repeatable results. ARS researchers at College Station, Texas, used this Single Nucleotide Polymorphism (SNP) array to evaluate accessions from the Collection as well as cotton cultivars submitted by researchers. The work assessed the diversity and potential of these genetic types (genotypes) for improving the cotton crop. The markers distinctly separated the most common species from other species and distinguished the wild from cultivated types. The markers also efficiently discerned differences among cultivars to provide other cotton researchers with a large genome-wide variation data set for cultivated cotton. Thousands of markers in representative genotypes provide an opportunity to finely discriminate among cultivated cottons to select those best suited for research programs and to avoid costly duplications within germplasm collections.

Review Publications
Kaleem, M.N., Rana, I.A., Shakeel, A., Hinze, L.L., Atif, R.M., Azhar, M.T. 2016. Genetic analysis of some agronomic and fiber traits in Gossypium hirsutum L. grown in field conditions. Turkish Journal of Field Crops. 21(2):240-245.
Hinze, L.L., Hulse-Kemp, A., Wilson, I., Zhu, Q., Llewellyn, D., Taylor, J., Spriggs, A., Fang, D.D., Ulloa, M., Burke, J.J., Giband, M., Lacape, J., Van Deynze, A., Udall, J., Scheffler, J.A., Hague, S., Pepper, A., Frelichowski, J.E., Lawley, C., Jones, D., Percy, R.G., Stelly, D. 2017. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. Biomed Central (BMC) Plant Biology. 17:37.
Adams, R., Tebeest, A., Frelichowski, J.E., Hinze, L.L., Percy, R.G., Ulloa, M., Burke, J.J. 2017. Survey of cotton (Gossypium sp.) for non-polar, extractable hydrocarbons for use as petrochemicals and liquid fuels. Phytologia. 99(1):54-61.
Shockey, J., Dowd, M., Mack, B., Gilbert, M., Scheffler, B., Ballard, L., Frelichowski, J., Mason, C. 2017. Naturally occurring high oleic acid cottonseed oil: identification and functional analysis of a mutant allele of Gossypium barbadense fatty acid desaturase-2. Planta. 245:611-622.
Sturtevant, D., Horn, P., Kennedy, C., Hinze, L.L., Percy, R.G., Chapman, K. 2017. Lipid metabolites in seeds of diverse Gossypium accessions: Molecular identification of a high oleic mutant allele. Planta. 245:595-610.
Raza, H., Rana, I.A., Shakeel, A., Hinze, L.L., Frelichowski, J.E., Azhar, M.T. 2017. Genetic diversity in Gossypium hirsutum L. for cotton leaf curl disease in association with agronomic and fiber traits. Pakistan Journal of Phytopathology. 29(1):47-56.