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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

2018 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
During FY 2018, significant progress was made on all four project objectives. Genetic resources of cotton and related wild species were efficiently and effectively acquired, maintained, distributed, and regenerated (Objective 1). A collection trip was made in Arizona and several new populations of Gossypium thurberi were found. A third season of plantings was made at the Counter Season Nursery (CSN) in Liberia, Costa Rica. The number of accessions sent was 276 and an additional 15 were carried over from the previous season. In greenhouses at College Station, Texas, over 150 critical accessions representing nearly 40 Gossypium species were increased. Maximum use was made of the College Station field planting, with 555 accessions self-pollinated for seed increases, characterized with standardized morphological and agronomic descriptors, and photographed for the digital image database (Objective 3). Descriptors and companion digital images were formatted for cooperators at Washington State University and uploaded into the CottonGen database ( Seed requests for 1988 accessions were filled from 82 orders. Progress continued on project objectives to systematically apply molecular technology to characterize the germplasm collection and increase the effectiveness and efficiency of its management (Objective 2). Previous accomplishments in characterizing the tetraploid species were expanded by genotyping a new set of accessions from Africa donated to the Collection. A germplasm development project continued with evaluations of superior selections for fiber quality (Objective 4). Over the life of this project, genetic resources within the U.S. National Cotton Germplasm Collection were successfully regenerated and distributed. Major advances were made in characterization and evaluation of accessions. Standardized descriptors, visual descriptor keys, and digital images were generated and made available to the cotton community through the CottonGen database. A core set of molecular markers was used to genotype >10% of the Collection. The genotyped accessions were also evaluated for seed oil and protein content with all data submitted to CottonGen. Germplasm acquisition trips were made to Puerto Rico and Arizona with approximately 100 new accessions added to the Collection. Two cotton germplasm lines possessing superior fiber quality were publicly released for use by cotton researchers to improve fiber quality in commercial cotton. This project expired in FY 2018 and was replaced by 3091-21000-041-00D which is continuing and expanding upon the work.

1. Improved sampling procedure for estimation of fiber quality of hand-harvested cotton. Cotton is a natural fiber; therefore, variation in fiber quality is expected. However, cotton fibers compete with man-made fibers which can be precisely engineered to exactly meet consumer textile demands. Improved accuracy in measurement of cotton fiber quality traits is needed to optimize the efficiency of the textile manufacturing process. ARS scientists at College Station, Texas, in collaboration with Texas A&M AgriLife Research scientists, identified the best method for cotton breeders to use in selecting bolls to be picked by hand that will most accurately represent fiber quality of a genotype as picked by mechanical harvesters. This accomplishment will directly benefit cotton researchers who use hand-harvested cotton boll samples to measure fiber quality. Cotton bolls harvested from the top half of the plant generally have lower fiber quality than bolls harvested from the bottom half of the plants. A sample that combines bolls from all areas within the plant provides the best estimates of fiber quality.

Review Publications
Kothari, N., Hague, S., Hinze, L.L., Dever, J. 2017. Boll sampling protocols and their impact on measurements of cotton fiber quality. Industrial Crops and Products. 109:248-254.
Adams, R.P., TeBeest, A.K., Ulloa, M., Witt, T.W., Burke, J.J., Frelichowski, J.E., Hinze, L.L. 2017. Comparison of hydrocarbon yields in cotton from field grown vs. greenhouse grown plants. Phytologia. 99(3):200-207.
Adams, R., Frelichowski, J.E., Hinze, L.L., Ulloa, M. 2018. Survey of cotton (Gossypium sp.) for non-polar, extractable hydrocarbons for use as petrochemicals and liquid fuels. Phytologia. 100(1):37-44.