Research Project: Developing Strategies and Tools to Mitigate Biotic and Abiotic Stresses in Cotton and Managing the National Cotton Variety Testing Program

Location: Crop Genetics Research

2024 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 12 month milestones set out in the project plan were just completed. The project concentrates on research designed to improve cotton grower profits and make United States (U.S.) grown fiber more competitive in the global market. Objective 1 supports research to unravel the basic physiology and molecular events involved in cotton fiber initiation and elongation. This will help us understand the mechanism behind production of short unusable fibers versus the valuable longer lint fiber used for textiles. This knowledge will be used by cotton breeders to develop cultivars that produce more and longer commercially valuable cotton fiber. Work by another research group at North Carolina State University identified two fiber shapes, tapered and hemispheric, that can be determined within two to three days after the plants flower. Tapered fibers are long and thin, and hemispheric fibers are short and thick in the middle. The tapered fiber shape seems to be associated with finer fiber at maturity, while fibers with a hemispheric 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 100% tapered fibers and ones with 80% hemispheric fibers. The seed from these crosses were planted in the greenhouse last fall, and seeds produced from those plants over the winter were to create F2 progeny segregating for the fiber shape trait. The progeny are currently in the field at Stoneville, Mississippi. Soon after flowering, bolls from the plants will be sampled and the shape of the developing fibers will be evaluated with digital imaging to determine the proportion of tapered versus hemispheric fiber shapes. Other bolls from the same plants will be harvested at maturity and the fineness of the fiber for each plant determined. Leaf tissue also will be collected and tested to identify DNA markers associated with the trait. Under Objective 2a, new breeding strategies are being developed to effectively incorporate traits that mitigate the effects of climate change into upland cotton. When transferring new beneficial traits from wild cotton into upland cotton, the progeny tend to preferentially eliminate the wild traits (genes) and keep the original trait from the adapted cultivar. Collaborative studies with another research group at New Mexico State University developed a cotton population with new traits from wild cotton. This work used a novel breeding method that reduced the elimination of the new wild genes and allowed these genes to stabilize in the agronomically adapted plants. Plants with the new genes are being evaluated under stressful environments and the best performing ones will be selected for further testing. In upland cotton, an increase in lint yield is generally associated with a decrease in the quality of the fiber. Because both yield and quality are important, one of our breeding goals is to try and create plants that do not have such a strong negative association between the traits. Plants with the new genes will be evaluated to see if any of them might be used as parents in future crosses targeting this goal. Objective 2b is using a natural genetic variant identified in cultivated cotton to develop plants with improved ginning efficiency. The variant allows the fiber to detach more easily and cleanly from the seed during the ginning process. 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 developed from this variant required less energy and gin 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. The project was on hold in 2023 due to a critical vacancy. During 2024, crosses will be made and F2 progeny generated over the winter to create cotton populations that can be used to determine the genetics underlying the faster ginning rate trait. Objective 3 is identifying novel sources of host plant resistance to insects and diseases and evaluating their effectiveness under field conditions. The lines selected for resistance will also be evaluated to determine their reaction to various climatic stresses. Cotton leaf curl virus 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 developed so the trait could be transferred without the need to screen every generation in Pakistan, where the disease is prevalent. Advanced generation lines that originated from crosses made in 2019 and were selected using these DNA markers are being increased in the field in 2024 with plans to test these in 2025 in Pakistan. As part of the previous project, cotton lines with resistance to another emerging pathogen, cotton leaf roll dwarf virus (CLRDV), were also identified. At least five sources of resistance were identified, and crosses made between the resistant lines and U.S. cultivars. The progeny were advanced to the F3 generation and screened at each generation with a DNA marker associated with resistance as well as screened in the field at two locations. In 2024, selected lines are being advanced another generation and evaluated for fiber quality. New crosses using the selected CLRDV resistant cotton and U.S. breeding lines are also being made in 2024. Objective 4 provides a venue to conduct collaborative regional and national cotton variety testing and generate supporting data that 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 2022 trials was made publicly available in 2023. In 2023, cotton breeders from 14 locations across the southern U.S. entered their best materials into the variety test for evaluation across a wide geographic range. They further supported the program by conducting yield trials at their respective locations and submitting fiber and seed samples from those trials for quality analysis. Four commercial companies and four public breeders had entries in the 2023 test. The yield data have been analyzed and shared with the program participants to assist them in choosing which breeding lines to focus on for further development during the 2024 field season. Analysis of fiber quality by ARS researchers in New Orleans, Louisiana, is in progress, and a commercial vendor is conducting seed quality analysis. The complete report for the 2023 season will be distributed after the seed and fiber analyses are completed. For the 2024 field season, 11 cotton lines from public cotton breeders and 13 commercial lines have been entered into the national cotton variety test program. Field trials at 15 locations have been successfully established.

Accomplishments
1. Genetically diverse germplasm population developed using traits from wild cotton. Introduction of novel genes from wild cotton into cultivated cotton is challenging because the cultivated cotton tends to eliminate the wild genes and keep its original genes. A new germplasm population was developed by ARS researchers in Stoneville, Mississippi. In 2008, cotton cultivars were crossed with their wild relatives. From 2008 to 2022, the hybrid progeny were advanced using a novel breeding method called random mating that reduced the elimination of the wild genes, allowing them to stabilize in the agronomically adapted plants. During this time, the germplasm population was evaluated under diverse environments. Results of field trials showed a dramatic increase in genetic variation in the germplasm population for yield and fiber quality, including a few lines with both high lint yield and high fiber quality. In 2023, the manuscript describing the germplasm population named it MDRM (which originated from Mississippi Delta Random Mating). The population can be used for molecular analysis to identify desirable novel genes and is ideal for cotton breeders to develop new cultivars for both high yield and improved fiber quality.

Review Publications
Zeng, L., Hinze, L.L., Fang, D.D., Delhom, C.D., Zhang, J. 2023. Analysis of a cotton introgression population derived through multiple generations of random mating in multiple-parents crosses. Euphytica. 219. Article 101. https://doi.org/10.1007/s10681-023-03213-1.
Abdelraheem, A., Zhu, Y., Zeng, L., Stetina, S.R., Feng, C., Wheeler, T., Zhang, J. 2024. Identification of new genetic sources of resistance to bacterial blight race 18 in diploid Asiatic cotton and resistance transfer to tetraploid cotton (Gossypium hirsutum). Euphytica. 220:85. https://doi.org/10.1007/s10681-024-03342-1.
Kim, H.J., Liu, Y., Zeng, L. 2024. Fourier transform infrared (FT-IR) spectroscopy and simple algorithm analysis for rapid and non-destructive assessment of cotton fiber maturity and crystallinity for plant mapping. Sensors. 24(9):2888. https://doi.org/10.3390/s24092888.
Thyssen, G.N., Condon, B.D., Hinchliffe, D.J., Zeng, L., Naoumkina, M., Jenkins, J.N., Mccarty,J.C., Sui, R., Madison, C., Li, P., Fang, D.D. Flame resistant cotton lines generated by synergistic epistasis in a MAGIC population. PLOS ONE. 18:e0278696.2023. https://doi.org/10.1371/journal.pone.0278696.
Sreedasyam, A., Lovell, J., Mamidi, S., Khanal, S., Jenkins, J., Plott, C., Kempton, B., Li, Z., Shu, S., Carlson, J., Goodstein, D., Santiago, L., Kirkbride, R., Calleja, S., Campbell, B.T., Koebernick, J., Dever, J., Scheffler, J.A., Pauli, D., Jenkins, J.N., Mccarty Jr, J.C., Williams, M., Boston, L., Webber, J., Udall, J.A., Chen, Z., Bourland, F., Stiller, W., Saaki, C., Grimwold, J., Chee, P., Jones, D., Schmutz, J. 2024. Genome resources for three modern cotton lines guide future breeding efforts. Nature Plants. https://doi.org/10.1038/s41477-024-01713-z.
Aboughanem-Sabanadzo, N., Allen, T.W., Frelichowski, J.E., Scheffler, J.A., Sabanadzovic, S. 2023. Discovery and analyses of caulimovirid-like sequences in upland cotton (Gossypium hirsutum). Viruses. 15(8). Article 1643. https://doi.org/10.3390/v15081643.
Hussain, A., Farooq, M., Naqvi, R.Z., Aslam, M.Q., Siddiqui, H.A., Amin, I., Liu, C., Liu, X., Scheffler, J., Asif, M., Mansoor, S. 2022. Whole genome resequencing deciphers new insight into genetic diversity and signatures of resistance in cultivated cotton Gossypium hirsutum. Molecular Biotechnology. 65:34-51. https://doi.org/10.1007/s12033-022-00527-8.
Abdelraheem, A., Zhu, Y., Zeng, L., Stetina, S.R., Zhang, J. 2024. A genome-wide association study for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in diploid cotton (Gossypium arboreum) and resistance transfer to tetraploid Gossypium hirsutum. Molecular Genetics and Genomics. 299:30. https://doi.org/10.1007/s00438-024-02130-9.