Location: Coastal Plain Soil, Water and Plant Conservation Research
2025 Annual Report
Objectives
1. Conduct research to broaden the cotton genetic base, improve fiber quality, increase yield stability and adaptation to climate change, and develop cotton germplasm, along with molecular markers for effective selection.
2. Conduct innovative research that producers can use to develop cropping systems that incorporate customized cover crops to improve cotton production and fiber quality, reduce inputs, and determine soil health and/or environmental benefits.
2.A. Develop and implement novel cotton-cover cropping systems that reduce inputs and increase soil health for sustainable cotton production.
2.B. Improve the adaptation and climate resiliency of novel cover crop species that can be incorporated into southeastern US cotton production systems.
3. Develop informed predictive models for cotton breeding using high-throughput phenotyping, environmental, and genomics data.
Approach
Cotton is the world’s primary source of natural, spinnable fiber and accounts for one third of global fiber consumption. There has been slow progress in cotton improvement for yield potential; however, fiber quality, adaptation to climate change, and yield stability improvements are sorely needed. In addition, customized cropping systems are needed that decrease the environmental impacts of cotton production while maximizing ecosystem services. To meet these needs, this research aims to develop improved breeding tools, germplasm, and enhanced management practices for the US cotton. Research in Objective 1 and 3 harnesses recent genomic and phenomic advances to develop predictive breeding methods that accelerate cotton’s genetic gain and broaden the genetic base. The research identifies new, beneficial alleles from distant germplasm and deploys a strategy to increase their frequency. Research in Objective 2 develops novel cotton-cover cropping systems that conserve soil moisture, reduce inputs, and increase soil health for sustainable cotton production. The research also improves the adaptation and climate resiliency of novel cover crop species incorporated into southeastern US cotton production systems. The information gained in the research on predictive breeding will better integrate genomic and phenomic research advances into tangible outcomes that drive cotton’s future genetic gains. This research will be of use to public and private plant breeders to provide the industry with future cultivars. Cover crop research will help growers, consultants, and industry maximize cotton production while minimizing environmental impacts in cover crop integrated cotton production systems. Together, the development of new genetic resources and better crop management practices will contribute to enhanced productivity and increased sustainability of the US cotton industry.
Progress Report
ARS researchers at Florence, North Carolina used predictive breeding models for cotton improvement. The overall objective is to develop predictive breeding models to improve yield and fiber quality in elite(improved) and exotic (unimproved) cotton. To accomplish this, training populations must be assembled, genotyped with DNA markers, and evaluated in field trials. The elite set consists of 400 breeding lines developed from 2005-2020 in the USDA-ARS Pee Dee germplasm enhancement program. The exotic set consists of a collection of 300 naturally occurring day-neutral exotic landrace accessions obtained from the USDA national cotton germplasm collection. In year 2, elite and exotic sets were genotyped using the 63K single nucleotide polymorphism (SNP) array. In addition, the elite set was evaluated in the first of a two-year, replicated field trial at multiple locations in Mississippi, Georgia, North Carolina, and South Carolina. This research supports Objectives 1 and 3 of the project plan to develop robust predictive breeding models for elite and exotic cotton.
Using perennial cover crops to reduce cotton inputs. The second year of a pilot-scale (0.5 acre) field study was completed and provided a preliminary assessment of growing perennial cover crops with cotton in the southeastern U.S. cotton belt. These perennial cover crops can potentially offset chemical, labor, fuel, and time inputs necessary to manage cotton by providing a biological control for weed and insect pest pressure and reducing the number of pesticide applications. Results from the two-year trial indicated that the presence of cool-season perennial cover crops, particularly red and white clovers, substantially reduced weeds and insect pests during the growing season compared to using an annual cover crop. A single in-row herbicide and no insecticide applications were required. Additionally, cotton boll formation and position were beneficially altered when grown alongside perennial clovers compared to fallow systems or an annual grass cover crop. Data was presented at various scientific and stakeholder meetings during the year. This research supports subobjective 2A of the project plan to develop and implement novel cotton-cover cropping systems that reduce inputs and increase soil health for sustainable cotton production.
Drought tolerant perennial cover crop germplasm development. Selection and development continued for white clover and Kentucky bluegrass populations to increase drought tolerance and improve persistence in the southeastern U.S. Each of these species has potential as a perennial groundcover crop that can suppress weed pressure with minimal impacts on cotton production, but drought conditions in the southeastern U.S. cotton belt necessitate genetic improvement in each species for persistence beyond a single growing season. Cycle 1 Kentucky bluegrass and white clover seed selected for drought tolerance via germinating in 1 – 1.25% salt water were grown in isolated field nurseries from fall 2024 through harvest in May 2025. For Cycle 1 Kentucky bluegrass, half-sib family selection was conducted using plant vigor (height and crown diameter) data to select the top 33% of plants from the nursery and use seed from only those plants. For Cycle 1 white clover, seed from all plants were bulked to perform mass selection. Harvested seed were conditioned and used to conduct germination tests (early June 2025) under drought conditions in a controlled environment growth chamber. Mass screening in growth chambers was also initiated to advance Cycle 1 germplasm to Cycle 2 for both Kentucky bluegrass and white clover. A new breeding nursery of 128 plants per species will be established in September 2025 for Cycle 2 Kentucky bluegrass and white clover seedlings. This research supports subobjective 2B of the project plan to improve the adaptation and climate resiliency of novel cover crop species that can be incorporated into southeastern US cotton production systems.
Accomplishments
1. Developing an improved reference genome to enable precision cotton breeding. Recently, precision breeding methods that utilize molecular and genome-enabled tools have been applied with great success to many crops. These precision methods facilitate the development of cultivars with increased yield stability and product quality. However, their adoption has lagged in cotton, largely due to the unavailability of a critical reference genome to guide modern, biotechnology-based breeding methods. To facilitate modern molecular breeding and build a strong foundation for cotton improvement, ARS researchers in Florence, South Carolina partnered with scientists at a number of public institutions led by the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama. The partnership generated chromosome-scale reference genomes for three public modern cotton cultivars along with a substantial update to a prior reference genome. Together, the reference genomes capture more genetic diversity among cotton cultivars and also provide a more complete sequence for all four cotton genomes. This advancement brings cotton one step closer to capitalizing the potential of precision breeding methods like genomic breeding and genome editing for increased yield stability and improved cotton fiber quality.
2. Developing cotton genotypes with improved rooting. The US cotton industry set a goal to improve irrigation water use efficiency 18% by 2025. One part of the strategy to improve irrigation water use efficiency focuses on improving the cotton plant’s ability to use water more efficiently. Root system architecture has been identified as a critical trait to improve the water and nutrient capture of cotton. However, cotton root system architecture has not been explored extensively and knowledge of variation for cotton root architecture is not well known. Thus, to investigate the potential for improving cotton root architecture, ARS researchers in Florence, South Carolina partnered with scientists at Clemson University to characterize a core collection of 23 cotton genotypes that represents 74% of allelic variation in upland cotton for root traits, water use, and water use efficiency. The study found that significant variation exists among the core collection for 16 different root and shoot traits, water use, and water use efficiency. Several genotypes were identified as the best performers while several were identified as poor performers. Overall, the study found that fine root length, surface area, and total root weight were positively correlated with water use efficiency. The identified traits serve as beneficial root traits for developing new cotton varieties with enhanced water use efficiency.
Review Publications
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.
Ghimere, O.P., Spivey, W.W., Kuraparthy, V., Campbell, B.T., Jones, M., Thomas, J.W., Bridges, W.C., Narayanan, S. 2024. Phenotypic variability in the U.S. upland cotton core set for root traits and water use efficiency at the late reproductive stage. Crop Science. 64(3):1831-1845. https://doi.org/10.1002/csc2.21229.
Gowda, S.A., Fang, H., Tyagi, P., Bourland, F., Dever, J., Campbell, B.T., Zhang, J., Abdelraheem, A., Sood, S., Jones, D.C., Kuraparthy, V. 2024. Genome-wide association study of fiber quality traits in US upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 1374. Article 214. https://doi.org/10.1007/s00122-024-04717-7.
Ghimire, O.P., Kuraparthy, V., Jones, M.A., Campbell, B.T., Bridges, Jr., W.C., Alege, F.P., Delhom, C.D., Narayanan, S. 2025. Better root length distribution in the deep soil profile enhances cotton performance. Field Crops Research. 325. https://doi.org/10.1016/j.fcr.2025.109805.