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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Research Project #434259

Research Project: Cotton Genetic Resource Management and Genetic Improvement

Location: Crop Germplasm Research

2019 Annual Report

Objective 1: Efficiently and effectively acquire genetic resources of cotton and its wild relatives; maintain their safety, genetic integrity, health, and viability; and distribute them and associated information worldwide. Sub-objective 1A: Regenerate about 5% of the NCGC (approx. 500 accessions) annually at the Counter Season Nursery, Liberia, Costa Rica, and at 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. Sub-objective 1B: Distribute viable seed and associated information for all available accessions to users of the NCGC. Sub-objective 1C: Strategically broaden the genetic diversity of the NCGC through the acquisition of additional cotton germplasm by means of germplasm exchanges and plant explorations. Objective 2: Develop more effective genetic resource maintenance, evaluation, and genetic marker characterization methods and apply them to priority genetic resources of cotton and its wild relatives. Record and disseminate evaluation and characterization data and digital images via GRIN-Global, CottonGen, and other data sources. Sub-objective 2A: Characterize about 5% of the NCGC annually using a comprehensive and standard descriptor set developed for community use and upload into GRIN-Global and CottonGen. Sub-objective 2B: Create standardized digital image libraries of the NCGC 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. Sub-objective 2C: Systematically analyze genetic diversity using new/revised core sets of molecular markers specific to primary and secondary gene pools of cotton to increase the efficiency and effectiveness of cotton genetic resource management and genetic improvement. Sub-objective 2D: Coordinate the cooperative evaluation of cotton genetic resources for priority agronomic traits. Objective 3: With other NPGS genebanks and Crop Germplasm Committees, develop, update, document, and implement best management practices and Crop Vulnerability Statements for cotton genetic resource and information management. Objective 4: Devise more efficient and effective cotton genetic enhancement approaches, and apply them to generate breeding stocks incorporating genes from cotton land races and wild relatives for improved yield, fiber quality, seed quality, and/or resistance/tolerance to biotic and abiotic stresses.

The Gossypium genus is composed of at least 50 recognized species of differing ploidy levels and contains a wealth of genetic variability ranging from highly improved allotetraploid species to wild diploid species. The National Cotton Germplasm Collection contains much of the diversity of the genus, and its long-term objectives are to acquire, conserve, characterize, evaluate, and distribute accessions, with the goal of making these resources available for genetic improvement efforts within and outside the USDA. Under the current project, we will make efforts to acquire new germplasm through plant explorations and exchanges that target current gaps in the Collection. To make the inherent variability of the Collection useful, it must be described and evaluated. For this reason, this project will generate phenotypic descriptions of genetic resources, and evaluate these materials for drought stress tolerance, agronomic traits, and fiber quality. Recent advances in cotton molecular genetics have provided the molecular markers needed to measure genetic diversity, characterize new acquisitions, ascertain areas of deficiency, and maintain the integrity of accessions while regenerating the Collection. Recognizing that parts of the Collection are not readily usable due to species incompatibilities, day-length flowering responses, and the perennial nature of accessions, pre-breeding efforts are needed to improve access to and utility of these portions of the Collection. Information generated by this project will be made publicly available in the GRIN-Global and/or CottonGen databases.

Progress Report
Progress was made on all four project objectives during FY 2019. Genetic resources were regenerated and distributed as requested and an exploration trip was made to the Florida Keys (Objective 1). The exploration trip to the Florida Keys covered 8 days and 1600 miles and included site work to private lands, and state and federal parks that have reported wild cotton plants. Nine locations of wild or feral cotton plants were found and collection trips back to these locations and additional sites known by park rangers are planned at later dates once collection permits are approved by the State of Florida and federal parks offices. The fourth season of plantings was made at the Cotton Winter Nursery in Liberia, Costa Rica. Almost 400 accessions were sent to this tropical nursery for regeneration. More than 100 accessions are currently being increased in the field at College Station. At both sites, descriptors and digital images are also being obtained to characterize the accessions (Objective 2). This information is being processed and uploaded to the GRIN-Global and CottonGen databases. Accessions from a previous collection trip to Puerto Rico are growing in the greenhouse. Descriptors and images will be recorded for these new accessions. DNA is being extracted and accessions will be genetically characterized by the end of CY 2019 (Objective 2). Project scientists are working with the Cotton Crop Germplasm Committee and providing data necessary to prepare a vulnerability statement for the National Cotton Germplasm Collection (Objective 3). We are continuing a research project to develop cotton breeding lines with increased oleic acid using a molecular marker closely linked to the genetic region responsible for this trait (Objective 4). This work is being initially performed in the greenhouse as the donor line is photoperiodic and only flowers during short days of the winter season. The plants with the correct genetic composition will then be grown in the field and selected to flower during the summer season.

1. Increased understanding of salt stress tolerance in cotton. Build-up of high salt concentrations in the soil dehydrates cotton plants and reduces plant growth and yield. Relative to most crops, cotton is more tolerant of salt stress; however, there are knowledge gaps in quantifying the high levels and types of exposures to salt that cotton can tolerate, as well as the genetic variability of cotton's coping mechanisms to high salt levels. ARS scientists at College Station, Texas, in collaboration with scientists at Texas Tech University and the BASF Corporation, showed that increasing the amount of salt compared to the levels commonly used in salt studies revealed noticeable differences in tolerance among plants, as well as in the distribution of increased sodium within the plant. Understanding the foundations for the baseline tolerance is essential for interpreting the complex pathways and interacting networks within the plant. These results are the initial step in addressing the long-term goal of identifying the genetic variation that can be used for stress tolerance breeding in cotton.

Review Publications
Adams, R.P., Tebeest, A.K., Ulloa, M., Scow, B., Frelichowski, J.E., Hinze, L.L. 2018. Comparison of hydrocarbon yields in SA-2269 cotton grown in four test plots in Texas and Utah. Phytologia. 100(4):199-204.
Jenderek, M.M., Frelichowski, J.E. 2019. Fiber crops: cotton and hesperaloe. In: Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F., editors. North American Crop Wild Relatives. Volume 2: Important Species. New York, NY: Springer, Cham. p. 543-578.
Majeed, S., Rana, I., Atif, R., Ali, Z., Hinze, L.L., Azhar, M. 2019. Role of SNPs in determining QTLs for major traits in cotton. Journal of Cotton Research. 2:5.
Grover, C.E., Arick, M.A., Thrash, A., Conover, J.L., Sanders, W.S., Peterson, D.G., Frelichowski, J.E., Scheffler, J.A., Scheffler, B.E., Wendel, J.F. 2018. Insights into the evolution of the New World diploid cottons (Gossypium, subgenus Houzingenia) based on genome sequencing. Genome Biology and Evolution. 11(1):53-71.