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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

2020 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 fiscal year 2020. Under Objective 1, critical accessions (including photoperiodic Gossypium barbadense) were planted and harvested at the Cotton Winter Nursery (CWN) in Liberia, Costa Rica, and at greenhouses at College Station, Texas (CS). Also under Objective 1, genetic resources were regenerated and distributed as requested, and new germplasm was obtained to fill gaps in the National Cotton Germplasm Collection. New germplasm was received from collaborators in Australia (Commonwealth Scientific and Industrial Research Organization, CSIRO), Seeds of Success (Bureau of Land Management), and from the Borderlands Restoration Network. Under Objective 2, descriptors and digital images were obtained of the accessions in Objective 1 from both the CWN and CS locations. This information was processed and uploaded to the Germplasm Resources Information Network (GRIN-Global) and CottonGen databases. Under Objective 2, accessions from a previous collection trip to Puerto Rico were grown in the greenhouse. DNA has been extracted and accessions will be genotyped. Under Objective 3, information regarding the status of the National Cotton Germplasm Collection was reported to the Cotton Crop Germplasm Committee for the preparation of a one-page crop vulnerability statement. Under Objective 4, cotton breeding lines with increased oleic acid were developed using a molecular marker closely linked to the genetic region responsible for this trait. Several segregating populations are growing in the field. Flowering plants are being crossed back to their recurrent parent, and the presence of the molecular marker will be confirmed in the laboratory.

1. Genetic variation and gene discovery for Fusarium tolerance in cotton. Fusarium wilt Race 4 is a soil-borne fungal disease that is an emerging threat to cotton production in the U.S. Currently, all commercially available cotton cultivars are vulnerable to this disease. ARS researchers at College Station, Texas, provided diverse samples from the U.S. National Cotton Germplasm Collection to collaborators at New Mexico State University to evaluate cotton for tolerance to Fusarium wilt Race 4. The samples were evaluated under controlled conditions of high and low temperature, and fungal spores were applied to create a disease reaction. Researchers learned that many of the samples had variation within them for tolerance and susceptibility to the disease, and lower temperatures caused more severe disease symptoms as compared to higher temperatures. Genetic regions linked to tolerance to Fusarium wilt were identified, and some regions were recognized that also provided tolerance to another soil-borne fungal disease, Verticillium wilt. With this knowledge, breeding methods can be modified to increase the frequency of identifying plants with tolerance to Fusarium wilt Race 4. It will also facilitate the identification of markers that will be a valuable tool for researchers to identify tolerance to diseases in the presence of varying levels of spores in the field environment.

Review Publications
Grover, C.E., Yoo, M., Lin, M., Murphy, M.D., Harker, D.B., Byers, R.L., Lipka, A.E., Hu, G., Yuan, D., Conover, J., Udall, J.A., Paterson, A.H., Gore, M.A., Wendel, J. 2020. Genetic analysis of the transition from wild to domesticated cotton (G. hirsutum L.). G3, Genes/Genomes/Genetics. 10(2):731-754.
Zhang, J., Abdelraheem, A., Zhu, Y., Wheeler, T.A., Dever, J., Frelichowski, J.E., Love, J., Ulloa, M., Jenkins, J.N., McCarty Jr, J.C., Nichols, R., Wedegaertner, T. 2020. Assessing genetic variation for Fusarium wilt race 4 resistance in tetraploid cotton by screening over three thousand germplasm lines under greenhouse or controlled conditions. Euphytica. 216:108.
Abdelraheem, A., Elassbli, H., Zhu, Y., Kuraparthy, V., Hinze, L.L., Stelly, D., Wedegaertner, T., Zhang, J. 2019. A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cotton. Theoretical and Applied Genetics. 133:563-577.
Rehman, A., Atif, R., Qayyum, A., Du, X., Hinze, L.L., Azhar, M. 2020. Genome-wide identification and characterization of HSP70 gene family in four species of cotton. Genomics. 112(6):4442-4453.