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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

2016 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 2016, objectives to efficiently and effectively acquire, maintain, distribute, and regenerate genetic resources of cotton and related wild species, and to expand morphological characterizations and digital imaging of the National Cotton Germplasm Collection (NCGC) were met. A new Counter Season Nursery (CSN) was established in Liberia, Costa Rica under the direction of Cotton Incorporated and in collaboration with Bayer Crop Sciences, Inc. Only 192 accessions were sent because of the establishment of new procedures specific to Costa Rica, and the training of a new labor force. In greenhouses at College Station, Texas, over 300 critical accessions representing at least 40 cotton species were increased. Maximum use was made of the College Station field planting, with 649 accessions grown for seed increase, characterized with standardized morphological and agronomic descriptors, and photographed for a digital image library. Project scientists coordinated with the cooperators at Washington State University to incorporate trait scores (over 384,000) evaluated on cotton germplasm (9K) into CottonGen, ( Images were formatted for uploading into the database. Over 4100 images were gathered in the summer of FY 2015 from College Station and another 900 from the CSN in the spring of FY 2016. Seed requests for over 2490 accessions made by 182 requesting groups were filled. Tissue samples and cuttings for propagation (200 accessions by 11 requesting groups) were sent in place of seed for critical accessions. Progress continued on project 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 tetraploid species were expanded with the characterization of a subset of G. hirsutum with SNP markers and the initiation of a resequencing project. In addition, efforts to develop genetic resources and research tools were enhanced through identifying and establishing individual core collections for wild and cultivated samples of both commercial tetraploid species. A field study jointly analyzing accumulation of oil in seeds and development of fiber at various growth stages was completed.

1. Determination of the molecular diversity of the two commercial species of cotton in 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 also is necessary for its efficient and effective conservation and maintenance. ARS researchers at College Station, Texas, New Orleans, Louisiana, and Stoneville, Mississippi, along with collaborators from Cornell University, systematically characterized the two commercial tetraploid species within the National Cotton Germplasm Collection and identified sources of genetic variation between and within the two species. Some samples were characterized as being intermediate between the two species, indicating interbreeding. More wild than cultivated samples had indicators of introgression. The use of molecular markers to characterize the Cotton Germplasm 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, resulting in superior cotton varieties and products for the consumer.

2. National Cotton Germplasm Collection (NCGC) descriptor data and digital images posted online to the CottonGen database. The online depiction of a germplasm collection is critical to maximize the utility to plant breeders and researchers of cotton. Otherwise it is just a random collection of seed. ARS researchers at College Station, Texas, in cooperation with database managers of CottonGen ( at Washington State University, standardized morphological descriptors for the Germplasm Collection, created a visual descriptor key, and downloaded all descriptor data obtained since FY 2006. Descriptors data obtained prior to FY 2006 were transformed to the new standardized descriptor categories. The dataset covers more than half of the NCGC and has evolved to the extent that users have more accurately created subsets of the NCGC for their research or breeding purposes and greatly reduced the size of seed orders. Gaps in this dataset more clearly prioritize future seed increases and characterizations of the NCGC.

3. Collecting and GPS tracking of a wild cotton in Arizona. Genetic diversity for desirable traits such as disease or insect resistance often resides in wild relatives of cultivated species. With genetic advances, this diversity has become increasingly accessible for use in the improvement of cultivated species. Therefore, it is important to collect and preserve the diversity of these wild relatives. A collection trip to Arizona in FY 2016 resulted in thirty seven populations of Gossypium thurberi, a wild relative of cotton, being identified, their locations being recorded with GPS coordinates, and seed harvested from 27 of them. The representation of the genetic diversity of this species in the National Cotton Germplasm Collection is now greatly improved, and the GPS locations will enable monitoring of native populations for in situ conservation. This information will also update the Crop Wild Relative Database collaborative research by USDA-ARS scientists in the National Plant Germplasm System.


Review Publications
Hinze, L.L., Gazave, E., Gore, M.A., Fang, D.D., Scheffler, B.E., Yu, J., Jones, D.C., Frelichowski, J.E., Percy, R.G. 2016. Genetic diversity of the two commercial tetraploid cotton species in the Gossypium Diversity Reference Set. Journal of Heredity. 107(3):274-286.
Stipanovic, R.D., Puckhaber, L.S., Frelichowski, J.E., Esquivel, J.F., Westbrook, J.K., O Neil, T.M., Bell, A.A., Dowd, M.K., Hake, K., Duke, S.E. 2015. Gossypolhemiquinone, a dimeric sesquiterpenoid identified in cotton (Gossypium). Phytochemistry. 122:165-171.
Kothari, N., Campbell, B.T., Dever, J.K., Hinze, L.L. 2015. Combining ability and performance of cotton germplasm with diverse seed oil content. Crop Science. 56:19-29.