Location: Crop Germplasm Research
2025 Annual Report
Objectives
Objective 1: Conduct research to develop genetic resource maintenance, evaluation, or characterization methods and, in alignment with the overall NPGS Plan, apply them to priority cotton genetic resources to avoid backlogs in genetic resource and information management.
Sub-objective 1.A: Apply core sets of molecular markers to systematically characterize underutilized cotton genetic resources. Sub-objective 1.B: Apply sequence-based methods to develop characterization profiles of cotton accessions to assist in priority genetic resource management activities.
Objective 2: Acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority cotton genetic resources and associated descriptive information.
Sub-objective 2.A: Strategically broaden the genetic diversity conserved by the NCGC through acquisition of cotton and wild relative germplasm from exchanges and explorations. Sub-objective 2.B: Distribute viable seed and associated information for all available accessions to users of the NCGC. Sub-objective 2.C: Maintain safety, genetic integrity, and viability of priority cotton genetic resources and associated descriptive information.
Objective 3: Conduct research to develop genetically-enhanced germplasm that broadens the diversity available for improving cotton by incorporating superior traits from cultivars, landraces, and wild relatives into adapted genetic backgrounds and genepools.
Sub-objective 3.A: Evaluate cotton accessions and develop germplasm with improved seed traits. Sub-objective 3.B: Conduct research to broaden the diversity available for improving cotton by incorporating diverse alleles from landraces and wild relatives.
Objective 4: Conduct research to develop, augment, and/or improve genomic tools for elucidating genetic variability of the primary and secondary cotton gene pools, as well as natural and synthetic cotton populations, and demonstrate effectiveness of these new tools.
Sub-objective 4.A: Develop priority genome and pan-genome sequences and assemblies for cotton species and accessions that contain genes controlling traits important to the cotton industry. Sub-objective 4.B: Construct a practical haplotype graph for cotton genomic diversity.
Objective 5: Conduct research to identify and manipulate economically valuable genes and/or genetic systems in cotton genomes and apply the information to improve priority traits, such as yield and quality of fiber and seed, and tolerance to biotic and abiotic stress.
Sub-objective 5.A: Identify and map genes or QTLs that improve fiber quality. Sub-objective 5.B: Engineer or modify genes/genetic systems for enhanced cotton productivity under abiotic stress conditions.
Objective 6: Expand and manage the current cotton database and bioinformatics systems to provide genomics and bioinformatic tools for efficiently exploiting cotton genetic variation for crop improvement.
Goal: Coordinate genomic, genetic, and breeding data availability in CottonGen to enrich the delivered content and streamline users' centralized searches for specific information.
Approach
The U.S. National Cotton Germplasm Collection (NCGC) contains much of the diversity of the Gossypium genus – with genetic variability ranging from highly improved allotetraploid species to wild diploid species. The long-term goals of this project are to conserve, describe, and distribute accessions of the NCGC, as well as conduct genetic and genomic research to make these resources available to researchers. Cotton growers need cultivars with genetic variability to provide resilience to biotic and abiotic stresses and improved fiber quality to obtain premiums at harvest. Cotton seed industries have been negatively impacted by decreasing seed size which has not been addressed due to increased relative value of fiber. Recent advances in molecular genetics and genome sequencing have provided the molecular markers needed to measure genetic diversity and the basis for tools such as pan-genomes, haplotype graphs, plant transformation, and gene editing to better explore and understand the cotton genomes to address producer and industry needs. Much of this information is available to the cotton community through the CottonGen database. The proposed research will advance cotton germplasm, genomics, and breeding research by characterizing both underutilized and potentially redundant accessions to allow for better use and management of the NCGC (Objective 1); acquiring accessions through plant explorations in the U.S. and Australia as well as continuing to maintain and deliver high quality cotton genetic resources to customers (Objective 2); developing germplasm with improved seed and fiber traits (Objective 3); obtaining cotton genome/pan-genome sequences and developing a practical haplotype graph to fully capture cotton genetic variation (Objective 4); identifying fiber quality genes and developing heat tolerance and male sterility systems through genetic engineering and genome editing (Objective 5); and enhancing the CottonGen database with new content as well as bioinformatic tools to effectively utilize the information for cotton improvement (Objective 6).
Progress Report
Work under this project during FY 2025 resulted in significant progress in the management and genetic improvement of cotton genetic resources including DNA extractions of targeted germplasm accessions, distribution and increases of germplasm material, construction of genome sequences and pangenomes, development of transformed seed using a molecular technique known as CRISPR-cas9, and updates to the cotton community database, CottonGen. Specific progress under Objective 1 included DNA extraction from leaf tissue of 100 cotton accessions that were determined to be underutilized genetic resources; the samples will be genetically characterized using a genetic technique known as a Single Nucleotide Polymorphism (SNP) array. DNA was also extracted from 89 accessions with duplicate names. Work under Objective 2 included assisting GRIN-Global database users, including first-time foreign users, in searches for selections of accessions of cotton from the USDA owned/managed U.S. National Cotton Germplasm Collection. Project assistance to users included scientific and educational focus, distributing seed to users as requested, and adding accession descriptor data to GRIN-Global. Routine seed increases were conducted for the National Collection. Approximately 540 accessions were increased through cultivation in greenhouses, summer field plots, and a Costa Rican cotton winter nursery. Project work under Objective 3 included planting and growing a set of 100 accessions, selected on the basis of their varying seed size in a single field environment in Florence, South Carolina. When the crop matures in late FY 2025, we will collect a seed and fiber trait data set. Additional field trials are planned for FY 2026 to obtain a multi-environment data set. Under Objective 4, high-quality DNA was isolated from several priority cotton accessions for construction of genomic libraries. Some high-quality genome sequences were developed and analyzed for cottons that vary genetically in such traits as fiber properties and nematode resistance. These new genome sequences, along with more than 50 other recently published sequences were identified, downloaded, and aligned using the relational database framework via a technology known as Practical Haplotype Graph 2.0. Progress under Objective 5 included isolation of genomic DNA from leaf tissues of individual plants of what are known as F2 mapping populations; the work included measurement of individual fiber samples of the same segregating F2 progeny populations. Work also included the construction of 7-gene multiplex CRISPR-cas9 editing cassettes in a molecular "carrier" known as a plasmid vector. Samples were evaluated by a well-known genetic tool, Polymerase Chain Reaction or PCR, and by other appropriate assays. Using appropriate techniques as applied to a cotton type known as Coker-312, transformed cotton seed were obtained and will be analyzed for desirable genetic and productivity traits. Objective 6 work focused on the CottonGen database which serves the worldwide cotton community. It currently includes a total of 59 cotton genome assemblies, 117,300 molecular markers, 414,255 phenotypic datapoints, and 553 molecular tools known as Quantitative Trait Loci (QTL). Results from many genome-wide association studies were added to CottonGen along with gene expression datasets. The database user manual was updated, and monthly short training videos/quarterly newsletters were released to help users in efficient utilization of database tools. Between July 1, 2024, and June 30, 2025, CottonGen served 1,349,514 pages to the user communities and was accessed 62,129 times by cotton researchers from 179 countries.
Accomplishments
1. Nematode-resistance genes for cotton improvement. Cotton is the most valuable fiber crop, and the second most valuable oilseed crop grown in the United States. The reniform and root-knot nematodes are two of the most destructive pests to American "Upland" cotton and continue to be a major threat to U.S. cotton production and profitability. Effective cotton breeding for host-plant resistance to these nematodes is crucial for protecting crop yields and farmer profits. ARS researchers at College Station, Texas, analyzed high-quality genome sequences from cotton cultivars with nematode-resistance conveyed by incorporating genomic regions from both American "Pima" cotton and American "Upland" cotton. The work provided valuable insights to, and a foundation for ongoing work to exploit natural genetic sources of nematode resistance in cotton. New cotton strains are expected to be developed that will resist or be immune to the damaging effects of nematodes in U.S. cotton production, and that will help assure ongoing viability of this critical fiber and oilseed crop in U.S. agriculture.
Review Publications
Arslanova, S., Ernazarova, Z., Ernazarova, D., Turaev, O., Sugiulina, A., Toshpulatov, A., Kholova, M., Azimova, L., Rafieva, F., Gapparov, B., Khalikov, K., Khidirov, M., Iskandarov, A., Kodirov, D., Turaev, O., Maulyanov, S., Udall, J.A., Yu, J., Kushanov, F. 2025. Development and characterization of synthetic allotetraploids between diploid species Gossypium herbaceum and Gossypium nelsonii for cotton genetic improvement. Plants. 14(11). Article 1620. https://doi.org/10.3390/plants14111620.
Wan, S., Kahanal, S., Brown, N., Kumar, P., West, D., Lubbers, E., Kothari, N., Jones, D., Hinze, L.L., Udall, J.A., Bridges, W., Delhom, C.D., Patterson, A., Chee, P. 2025. Phenotypic validation of the cotton fiber length QTL, qFL-Chr.25, and its impact on AFIS fiber quality. Plants. 14(13). Article 1937. https://doi.org/10.3390/plants14131937.
Cohen, Zachary P., Perkin, Lindsey C., Wagner, Tanya A., Liu, Jinggao, Bell, Alois A., Arick II, Mark A., Grover, Corrine E., Yu, John Z., Udall, Joshua A., Suh, Charles P-C. 2024. Nematode-resistance loci in upland cotton genomes are associated with structural differences. G3, Genes/Genomes/Genetics. Article jkae140. https://doi.org/10.1093/g3journal/jkae140.
Yu, L., Nelson Dittrich, A.C., Melandri, G., Skirycz, A., Thorp, K.R., Hinze, L.L., Nelson, A.D., Pauli, D. 2024. Regulation of a single inositol 1-phosphate synthase homeologue by HSFA6B contributes to fibre yield maintenance under drought conditions in upland cotton. Plant Biotechnology Journal. 22(10):2756-2772. https://doi.org/10.1111/pbi.14402.
Hinze, L.L., Campbell, B.T., Percy, R.G. 2025. Registration of 13AFX6 and 13AFX13 cotton germplasm lines with fiber strength and length. Journal of Plant Registrations. 19(1). Article e20414. https://doi.org/10.1002/plr2.20414.
Ming, Q., Xie, P., Xu, Z., Tang, J., Hui, L., Gu, J., Gu, X., Jiang, S., Rong, Y., Zhang, J., Udall, J.A., Grover, C.E., Wendell, J., Zheng, K., Chen, Q., Kong, J., Wang, M., Lin, Z., Jin, S., Zhang, X., Yuan, D. 2025. Pangenome analysis reveals yield- and fiber-related diversity and interspecific gene flow in Gossypium barbadense L. Nature Communications. 16. Article 4995. https://doi.org/10.1038/s41467-025-60254-x.