Location: Crop Genetics Research
2025 Annual Report
Objectives
1. Conduct research to unravel the basic physiology and/or molecular events involved in cotton fiber initiation and density to understand the mechanism behind production of fiber versus lint, and work with breeders to develop germplasm with high fiber production.
2. Conduct research to identify sources of tolerance to abiotic stresses in cotton and develop Upland cotton cultivars with tolerance to multiple abiotic stresses via proven or novel introgression methods combined with innovative molecular techniques to improve tolerance to abiotic stresses and climate change resilience.
2a. Identify germplasm lines, populations, breeding lines and better strategies to reduce negative associations between lint yield and fiber traits or effectively introgress traits that mitigate the effects of climate change.
2b. Use genetic variation identified in cultivated cotton as well as measurement techniques available to develop cotton lines that gin more cost effectively and are resilient to environmental changes.
3. Identify novel sources of host plant resistance to insects and diseases, including natural variants, conduct research to determine their reaction to various climate change stresses, and use them to develop new cotton germplasm via proven or novel introgression methods.
4. Conduct collaborative regional and national cotton variety testing to generate supporting data for breeding and use the information to develop genetic and/or production strategies to improve the cotton crop.
Approach
This project will combine the expertise and plant materials of four scientists to provide a coordinated approach for improving grower profits by decreasing input costs and providing high yielding cotton lines that will meet the fiber quality needs of the modern textile industry. There is a need to improve cotton grower profits and make U.S. grown fiber more competitive in the global market. U.S. breeders must now search more widely for unique germplasm and find novel ways to generate new cotton lines to improve cultivar fiber quality. However, yield is always the top priority for growers, and a major challenge remains to reduce the existing negative association between yield and fiber quality. As the climate changes and growing conditions become more unstable, additional challenges become relevant as it is essential to develop plants with the ability to tolerate and thrive under warmer temperatures as well as changing weather patterns. These changing patterns can also allow diseases and insects to become more of a threat. This plan will study the mechanisms that allow cotton to tolerate the changing environment and pest threats and use this knowledge to develop new cotton lines with improved traits. Grower profits can also be increased through reducing input, harvesting or ginning costs and developing cotton that detaches more easily and cleanly from the seed is one way to reduce these costs. A venue is then needed to test elite lines and new varieties. The National Cotton Variety Test program will provide coordinated multi-location testing for breeders and provide a database of performance data across locations and years.
Progress Report
This project began in March 2023, and the 24-month milestones set out in the project plan were just completed. The project concentrates on research designed to improve cotton grower profits and make U.S. grown fiber more competitive in the global market. Changing weather patterns allow diseases and insects to become more of a threat to cotton production. This project studies the mechanisms that allow cotton to tolerate the changing environment and pest threats and uses this knowledge to develop new cotton lines with improved more resilient traits. Grower profits can also be increased through reducing input or ginning costs. Developing cotton fiber that detaches more easily from the seed is one way to reduce these costs. A venue is also needed to test elite lines and new cultivars. The National Cotton Variety Test program provides coordinated multi-location testing for breeders and provides a database of performance data across locations and years.
Objective 1 supports research to unravel the basic physiology and molecular events involved in cotton fiber initiation and elongation in order to understand the mechanism behind production of short unusable fibers versus the valuable longer lint fiber used for textiles. This knowledge will be used by breeders to develop cultivars that produce more and longer commercially valuable cotton fiber. Work by another research group identified two fiber shapes [tapered (T) or barrel-shaped (B)] present at 2-3 days post flower opening (anthesis, DPF). The tapered fiber shape seems to be associated with finer longer fiber at maturity, while fibers with a barrel-shape were associated with broader coarser fibers. We are working with this group to confirm this relationship and determine the underlying genetic and physiological basis of the trait. In 2023, crosses were made between cotton lines with 90:10 % T:B fibers and ones with 30:70% T:B fibers, then advanced the F1 seed to the F2 generation to create F2 progeny segregating for the fiber shape trait.
In 2024, progeny were grown in the field at Stoneville, Mississippi. Immature bolls were collected and ovules (immature seed) from the bolls were removed and stored in a fixative solution to preserve them until the ovules could be evaluated with digital fluorescent imaging to determine the proportion of T versus B fiber types. At maturity, open bolls were harvested and the fiber quality traits determined for each plant. Leaf tissue was also collected and is being tested on a 30K SNP Array to identify DNA markers known as SNPS (single nucleotide polymorphisms) associated with the trait. Based on 2023 preliminary results, additional crosses were made in 2024 between parents with 100% T fibers and ones with only 20% T fibers to enhance the chances of identifying DNA markers associated with the T fiber trait. These were advanced to the F2 generation and the F2 seed was planted in the field in 2025.
In addition, another method to visualize the immature fibers on the ovules was developed by a scientist on this project in cooperation with a scientist in Beltsville, Maryland. The method called variable-pressure scanning electron microscopy (VP-SEM) allowed us to visualize intact fibers without any extensive preparation and fixation. This method allowed us to see more natural fiber images with less damage. The minimal preparation time increased the number of samples that could be analyzed and because the method did not require expensive fixation (especially with gold coatings) it dramatically decreased the cost per sample. This innovative, low-damage imaging method has been optimized for immature cotton ovules with intact fibers. The method is flexible and can be used for other crops and tissues, creating opportunities for broader adoption beyond cotton fiber research.
A study from Objective 2 is using a natural genetic variant identified in cultivated cotton that allows the fiber to detach more easily and cleanly from the seed. This allows the harvested cotton to be ginned using less energy and decreases some forms of gin trash. New measurement techniques developed at Stoneville, Mississippi were used to evaluate which cotton lines required less energy to gin as well as more quickly and cost effectively. This project is evaluating the genetics behind the trait and developing DNA markers to improve the efficiency of selecting for the trait. During 2024, crosses were made and F2 progeny generated over the winter to create mapping populations to evaluate the genetics underlying the easier detachment and faster ginning rate. These were planted in the field for 2025 and the F2 progeny will be evaluated for ginning efficiency and fiber properties. Leaf samples will also be collected and analyzed for DNA markers associated with easy detachment of fiber from the seed.
New breeding strategies were developed to identify germplasm lines and populations that exhibit reduced negative associations between lint yield and fiber traits and effectively introgress traits that mitigate the effects of changing weather patterns. When transferring new beneficial traits from wild cotton into adapted cotton cultivars, the progeny tend to preferentially eliminate the wild traits (genes) and keep the original trait from the adapted cultivar. As part of this research, a collaboration with a group in New Mexico developed a population with new stably inherited traits from wild cotton by using a novel breeding method that reduced the elimination of the new wild genes (traits) and allowed these genes to stabilize in the adapted plants. The population is being further evaluated under stressful environments including irrigated and non-irrigated field experiments. The first field test was in 2024 with a second year of testing in 2025. The best performing plants will be selected for further testing.
Other studies planned for Objective 2, have been put on hold due to the long term vacancies of two scientists and vacancies of three technicians responsible for this part of the project plan.
Objective 3 is identifying novel sources of host plant resistance to insects and diseases and evaluating their effectiveness under field conditions. Cotton leaf curl virus (CLCuV) causes cotton leaf curl disease (CLCuD), a devastating disease that would threaten U.S. cotton production if it came to the U.S. In a cooperative proactive breeding program with Pakistan, the previous project identified cotton lines with resistance to CLCuD and used them in a crossing program to transfer the resistance to adapted U.S. cultivars. DNA markers were also developed so the trait could be transferred without screening every generation in Pakistani diseased screening fields. From 2019 through 2023 crosses made between improved sources of resistance and U.S. breeding lines and each generation the progeny were selected using the DNA markers. Seed increases of advanced generation selected lines were grown in the field in 2024 with the plan to evaluate them at multiple locations in Pakistan during the 2025 field season to confirm their resistance and performance under disease infected field conditions. The field evaluation in Pakistan is now delayed until 2026 because of delays in obtaining permission to send the seed and receive the required permits.
As part of the previous project, cotton lines with resistance to another emerging disease, cotton leaf roll dwarf virus (CLRDV), were also identified. At least five sources of resistance have been identified from accessions in the USDA Cotton Germplasm Collection. Crosses were made between the resistant lines and U.S cotton lines. Progeny were then advanced to the F4 generation and screened each generation with a DNA marker associated with resistance as well as screened in the field at two locations where the disease was present. In 2025, selected lines are being advanced another generation and evaluated for fiber quality. The lines will be evaluated for field resistance at Stoneville, Mississippi if the disease is present.
Because the disease is not always prevalent at Stoneville, the ARS scientist had organized a collaboration to evaluate the advanced lines in southern Alabama where the disease is endemic. The collaboration would require the scientist to make regular trips to southern Alabama to plant, maintain and evaluate the plants and collect samples. Because of the limitations on travel, the field testing will be delayed to 2026.
Objective 4 provides a venue to conduct collaborative regional and national cotton variety testing. The yield and fiber quality data from advanced elite lines and new cultivars tested can be used by breeders to develop new cotton cultivars or by plant scientists to determine new production strategies to improve the cotton crop. The final report from the 2023 trials was made publicly available in 2024. In 2024, researchers and breeders from 13 locations across the southern U.S. conducted trials at their respective locations and submitted fiber and seed samples from those trials for quality analyses. Five commercial companies and four public breeders had entries in the 2024 test.
The yield data from the 2024 trials have been shared with the program participants to allow them to make selections for the 2025 field season. ARS researchers in New Orleans, Louisiana, have completed the fiber analyses. The seed will also be analyzed for protein and oil by a commercial vendor as soon as the FY2025 funds are released. The report for the 2024 season will be distributed as soon as the seed trait measurements are completed. For the 2025 field season, nine cotton lines from public cotton breeders and 13 commercial cultivars were entered into the national cotton variety test program. Field trials at 14 locations have been successfully established.
Accomplishments
1. New method to visualize cotton fiber development. Cotton produces both short unusable fibers and the valuable longer lint fiber used for textiles. Whether the fiber initial becomes a short fiber or a long fiber is determined within the first few days after the flower opens. Previous research by collaborators have identified two fiber types present at fiber initiation. The first type is associated with finer longer fibers (T type) while the other is coarser and often shorter (B fibers). In order to study the two types, a fast, easy, low- cost preparation protocol was needed. Using variable- pressure scanning electron microscopy (VP- SEM) a method was developed to visualize intact fibers which provides more natural fiber images with less damage. The minimal preparation time increased the number of samples that could be analyzed and because the method did not require expensive fixation (especially with gold coatings) it dramatically decreased the cost per sample. This innovative, low-damage imaging method was optimized for immature cotton ovules with intact fibers. However, the method is flexible and can be used for other crops and tissues, creating opportunities for broader adoption beyond cotton fiber research. Being able to select directly for more economically valuable long cotton fibers per seed should increase fiber yields and improve farmer profit.
2. Developed cotton lines with extremely high fiber strength. Fiber strength in cotton is critical to produce high quality yarn that is able to withstand the speeds of the new textile production methods. Cotton lines with extremely high fiber strength were developed by crosses between high yield cotton cultivars and wild cotton with strong fiber traits. The newly developed high fiber strength lines can be used by cotton breeders to develop new cultivars with fiber that won’t break as easily during the yarn spinning process at the textile mill. They can also be used by scientists to identify genes controlling fiber strength and determine genetic mechanisms underlying the high fiber strength trait. The lines were released in 2025 and available.
Review Publications
Zeng, L., Sacks, E.J., Fang, D.D., Zhang, J. 2025. Registration of three cotton germplasm lines with extremely high fiber strength derived from crosses between Upland cotton and diploid Gossypium species. Journal of Plant Registrations. 19(1). https://doi.org/10.1002/plr2.20422.
Bai, F., Jansen, M.A. 2025. Advancing cotton fiber research with variable-pressure scanning electron microscopy. Frontiers in Plant Science. 16:2025. 1562682. https://doi.org/10.3389/fpls.2025.1562682.
Bai, F., Scheffler, J.A. 2024. Genetic and molecular regulation of cotton fiber initiation and elongation. Agronomy. 14:1208. https://doi.10.3390/agronomy14061208.
Naoumkina, M.A., Thyssen, G.N., Zeng, L., Shockey, J.M., Neumann, N., Florane, C.B., Jenkins, J.N., McCarty, J.C., Fang, D.D. 2024. Interaction of the cyclin-dependent kinase inhibitor GhKRP6 with RING-Type E3 ligase influences the fiber length in upland cotton. Industrial Crops and Products. 222(3) Article 119789. https://doi.org/10.1016/j.indcrop.2024.119789.
Mohammed, J., Thyssen, G.N., Hinze, L.L., Zhang, J., Zeng, L., Fang, D.D. 2025. A GWAS identified loci and candidate genes associated with fiber quality traits in a new cotton MAGIC population. Theoretical and Applied Genetics. 138. Article 10. https://doi.org/10.1007/s00122-024-04800-z.