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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

2021 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
Significant progress was made on all four project objectives during FY 2021. Under Objective 1, seed of critical accessions (including photoperiodic Gossypium barbadense) were increased via planting and harvesting at the Cotton Winter Nursery in Liberia, Costa Rica, and from the field and greenhouses in College Station, Texas. These genetic resources were distributed as requested, and new germplasm was obtained to fill gaps in the National Cotton Germplasm Collection. New germplasm was received from a collaborator in South Florida (Marie Selby Botanical Gardens). Under Objective 2, descriptors and digital images were obtained of the accessions increased from College Station field and greenhouse environments. This information was processed and uploaded to the Germplasm Resources Information Network (GRIN-Global), and CottonGen databases. A protocol was developed for germinating Gossypium thurberi seeds into seedlings for DNA extraction as the initial step in a molecular characterization effort of this species. In work with cooperators, field-based phenotypic evaluations were initiated to evaluate priority agronomic and fiber traits in 1) a nested association mapping population; 2) a national cotton variety test; 3) a regional cotton breeders' test; 4) among recombinant inbred lines selected for a fiber quality locus; and 5) among advanced breeding lines selected for cottonseed oil content. In Objective 3 work, a draft document detailing the best management practices for handling adventitious gene presence in the National Cotton Germplasm Collection was prepared after reviewing both our current protocol and the "ARS Procedures and Best Management Practices for Genetically-engineered Traits in Germplasm and Breeding Lines." This project-developed document, when finalized, will guide our efforts going forward to assure that the Collection is maintained with integrity, and that the accessions made available to the worldwide cotton community are accurate as cataloged and distributed. Work under Objective 4 progressed significantly as cotton breeding lines with increased oleic acid content in the seed were backcrossed for the second time to their agronomically improved recurrent parent. In this marker-assisted selection program, the presence of a genetic tool known as a molecular marker, linked to increased oleic acid, will be confirmed in the laboratory prior to seed harvest.

1. Salt tolerance in cotton. High salt content in the soil negatively affects plants by obstructing the ability of their roots to absorb water, causing plants to become dehydrated and, therefore, reducing plant growth and yield. Compared to most crops, cotton is more tolerant of salt stress; however, previous work indicated there was limited genetic variability that can be used to improve levels of this stress tolerance. ARS researchers at College Station, Texas, working with collaborators, showed that increasing the amount of salt compared to levels commonly used in salt studies resulted in noticeable differences in tolerance and showed the baseline level that makes cotton more tolerant to salt than are other crop plant species. Understanding the baseline tolerance is important because it becomes the foundation for interpreting this complex trait. Modern views suggest that stress tolerance involves complex pathways interacting with networks within the plant. This accomplishment is foundational in achieving the goal of defining the genetic variation that can be used for breeding stress tolerance, including salt tolerance, into improved and more environmentally adaptable cotton types for productive use by U.S. farmers.

Review Publications
Cushman, K., Pabuayon, I., Hinze, L.L., Sweeney, M., De Los Reyes, B. 2020. Networks of physiological adjustments and defenses, and their synergy with sodium (Na+) homeostasis explain the hidden variation for salinity tolerance across the cultivated Gossypium hirsutum germplasm. Frontiers in Plant Science. 11. Article 588854.
Yuan, D., Grover, C.E., Hu, G., Pan, M., Miller, E., Conover, J.L., Hunt, S., Udall, J.A., Wendel, J.F. 2021. Parallel and intertwining threads of domestication in allopolyploid cotton. Advanced Science. Article 2003634.
Campbell, B.T., Hinze, L.L., Thompson, A.L., Jones, M., Jones, D. 2021. Registration of PD 20170048, PD 20170049, PD 20170050, PD 20170053, and PD 20170054 germplasm lines of cotton. Journal of Plant Registrations.
Abdelraheem, A., Kuraparthy, V., Hinze, L.L., Stelly, D., Wedegaertner, T., Zhang, J. 2021. Genome-wide association study for tolerance to drought and salt tolerance and resistance to thrips at the seedling growth stage in US Upland cotton. Industrial Crops and Products. 169. Article 113645.
Rehman, A., Azhar, M., Hinze, L.L., Qayyum, A., Li, H., Peng, Z., Qin, G., Jia, Y., Pan, Z., He, S., Du, X. 2021. Insight into abscisic acid perception and signaling to increase plant tolerance to abiotic stress. Journal of Plant Interactions. 16(1):222-237.
Qamer, Z., Chaudhary, M., Du, X., Hinze, L.L., Azhar, M. 2021. Review of oxidative stress and antioxidative defense mechanisms in Gossypium hirsutum L. in response to extreme abiotic conditions. Journal of Cotton Research. 4. Article 9.
Elassbli, H., Abdelraheem, A., Zhu, Y., Teng, Z., Wheeler, T., Kuraparthy, V., Hinze, L.L., Stelly, D., Wedegaertner, T., Zhang, J. 2021. Evaluation and genome-wide association study of resistance to bacterial blight race 18 in US Upland cotton germplasm. Molecular Genetics and Genomics. 296:719-729.