Location: Soil Dynamics Research
2025 Annual Report
Objectives
1. Determine biological, ecological, and molecular characteristics of cotton leaf roll dwarf virus (CLRDV) and other pathogens to prevent and mitigate diseases that may negatively impact agronomic crop production.
1.A. Develop molecular and serological methods to improve CLRDV detection in the vector, the cotton host, and alternate hosts.
1.B. Perform high throughput sequencing to characterize the virome of cotton and cotton infesting aphids to generate knowledge about potential mixed infections with other viruses.
1.C. Monitor variants of CLRDV and other introduced diseases that have potential to reduce yield.
2. Mitigate negative impacts of CLRDV through improved understanding of pathogen epidemiology, including insect vectors, alternative plant hosts, and climate conditions.
2.A. Quantify CLRDV incidence, symptomology, and vector dynamics to identify soil and environmental factors correlated with at-risk production areas.
2.B. Characterize progression and titers of CLRDV over time.
2.C. Measure cotton plant physiological response (i.e., photosynthetic activity, stomatal conductance) to CLRDV infection under ambient and elevated CO2 levels over time.
3. Develop agronomic practices for diverse cotton germplasm in large- and small-scale production systems to minimize yield loss from CLRDV and other diseases.
3.A. Develop agronomic and weed management practices to reduce CLRDV incidence.
3.B. Define CLRDV symptoms and differentiate them from nutrient deficiency symptoms in cotton.
Approach
Recent increases in temperature, drought, and extreme weather events create additional stresses on key commodity crops. These stresses have a number of impacts, but one is that they can lower the plant’s immune response which can increase disease incidence and severity and insect infestations, ultimately reducing yields. One pathogen, present in other parts of the world for many years but first discovered in the United States (U.S.), (Alabama) in 2017, is the cotton aphid-transmitted cotton leafroll dwarf virus (CLRDV). Since that time, the virus has been found across 10 states of the U.S. Cotton Belt, but the U.S. CLRDV strain is genetically different from previously identified ‘typical’ and ‘atypical’ strains that cause cotton blue disease in Asia and South America. This research will investigate how to mitigate infection, spread, and yield loss caused by CLRDV using molecular, genetic, and management techniques to understand host-virus-vector dynamics and symptomology that will complement and enhance agronomic practices. In objective 1, we will improve detection techniques to confirm presence of CLRDV, characterize the virome of both host and aphid vectors, and monitor for variants of the virus. These aspects are important because cotton plants may appear asymptomatic, although growth is inhibited, which can result in yield losses. In objective 2, we will focus on how the vector transmits and spreads CLRDV, characterize the symptomology of the disease, and monitor how cotton plant physiology is affected over time following infection. Management practices may be one factor that could influence observed variability in CLRDV yield losses, but these effects are currently unknown. In objective 3, we will examine interactions between CLRDV and management practices that include stalk destruction methods, conservation tillage and non-host high residue cover crops, as well as soil nutrient levels to better define yield loss variability. This interdisciplinary project will benefit the U.S. cotton industry by providing better assessment tools for the disease as well as applied solutions to minimize negative impacts of CLRDV in the U.S.
Progress Report
In 2025, ARS scientists in Auburn, Alabama concluded several long-term research efforts associated with the project that included the sentinel plot study initiated in 2020, investigations into short-term management practices designed to mitigate Cotton Leafroll Dwarf Virus (CLRDV), and development of an infectious clone which will catalyze future breeding and genetic advancements.
The sentinel plot study underscored the regional nature of CLRDV by identifying consistently higher CLRDV incidence in the Southern Coastal Plain compared to minimal impact in northern locations. These findings offer a roadmap for exploring regional factors that may contribute to virus prevalence, including climate conditions, weed reservoir species, cultivation practices, and aphid population dynamics.
Short-term management strategies, such as cotton stalk pulling and the use of cover crops, did not significantly reduce the inoculum load across the landscape. Inoculum sources besides cotton stalks could be so abundant across the landscape that destroying cotton stalks has minimal effect on CLRDV infections from the other inoculum sources. This finding further reinforces the need for continued research on alternative host plants and the role herbicides could play on controlling potential hosts.
Ongoing aphid resistance studies are evaluating variability in leaf sugar and gossypol concentrations in upland cotton to determine whether aphid populations can survive at extreme levels of these compounds. These insights will help uncover host factors involved in virus infection and support the development of resistant cultivars.
The current scope of our project has a major focus on CLRDV, but research efforts have expanded to include additional cotton pests, such as nematodes and foliar pathogens. Funds provided to our university collaborators are supporting eight graduate students conducting research across these areas. In addition, the university is finalizing the hiring of a Research Cotton Geneticist in 2025 that will foster collaborative efforts to accelerate genetic and genomic research addressing CLRDV and other emerging threats. Unfortunately, an ARS supported post-doc working in CLRDV virology took another job, which leaves the project with no ARS pathology/virology expertise.
Accomplishments
1. Survey confirms CLRDV-AL strain is endemic in Southern United States cotton. Cotton leafroll dwarf virus (CLRDV) is known to affect cotton yield, but when first discovered, its prevalence and severity across regions remained largely unknown. To address this, university collaborators of the ARS Auburn, Alabama location in ten states grew a uniform set of cultivars to evaluate symptom expression across genotypes and environmental conditions. Data on incidence and severity were collected by a single observer, ensuring consistency, and compiled over a span of three years across 15 distinct locations. Results revealed CLRDV presents as a regional concern, with the highest incidence consistently observed in the Southern Coastal Plain. In contrast, northern sites showed minimal and in certain years, no signs of incidence. Severity levels varied among cultivars, indicating a genotypic component to CLRDV response and suggesting a potential control avenue through breeding-based resistance. While symptom expression differed across environments, no consistent patterns emerged, reinforcing that CLRDV cannot be reliably diagnosed based on visual observation alone. Therefore, this study confirmed that molecular diagnosis is more accurate compared to observing symptoms for CLRDV detection across the southern cotton growing region, which will benefit development of future CLRDV mitigation research.
2. Cotton stalk management and a cover crop provided minimal control for cotton leafroll dwarf virus (CLRDV). CLRDV inoculum sources include cotton stalks from the prior crop year. Some form of stalk destruction has been recommended as part of a comprehensive strategy to protect US cotton production from CLRDV. Stalk destruction methods (SDM)s can vary from mowing stalks (least aggressive) to multiple surface tillage operations (most aggressive) that can reduce soil health benefits in conservation-oriented agriculture across the southeastern Cotton Belt. ARS scientists in Auburn, Alabama and Raleigh, North Carolina with Auburn Univ. collaborators found SDMs with and without a cover crop were not effective at reducing CLRDV incidence. A primary reason is that other CLRDV inoculum sources exist that contribute to in-season CLRDV infections. Planting a cover crop also did not provide soil health benefits following an aggressive SDM in the short-term. However, showing growers that using aggressive SDMs was unnecessary to reduce CLRDV incidence helps to preserve soil health benefits, while future efforts to identify agronomic practices that reduce CLRDV incidence continue.
3. Microbial community profiles of cotton aphids collected from South Alabama. The cotton aphid is a globally distributed pest that feeds on many economically important crops and is known for transmitting numerous plant diseases. However, little is known about the microbial communities it harbors in aphid populations from South Alabama -- a major cotton-growing region in the United States. ARS researchers in Auburn, Alabama, along with collaborators from Auburn University, investigated the microbial community of cotton aphids collected from this region and identified a broad diversity of bacteria, fungi, and viruses. These microbial cohabitants form complex relationships with the aphids: some may act as pathogens, others may benefit the aphids, and some could be vectored by aphids to plants. The genetic data acquired in this study improves understanding of locally transmitted aphid-borne plant diseases, supports development of biological control strategies using aphid-associated pathogens, and contributes to the enhancement of the cotton aphid genome assembly.
4. Identification of candidate plant-manipulating effector genes in the cotton aphid. To successfully colonize plant hosts, aphids secrete a range of saliva proteins into plant tissues during feeding. These proteins, known as effectors, manipulate plant defenses to facilitate feeding and colonization. To investigate how the cotton aphid uses these effectors, ARS scientists in Auburn, Alabama, and Parlier, California, in collaboration with researchers at Auburn University, applied an integrative bioinformatics pipeline to predict effector-encoding genes. This analysis identified 351 candidate effector genes in the cotton aphid and demonstrated that many are associated with plant feeding and host colonization. The study provides new insights into the molecular mechanisms underlying aphid–plant interactions and identifies potential genetic targets for developing novel pest management strategies.
Review Publications
Frazier, S., Brown, S.M., Read, Q.D., Jacobson, A.L., Conner, K., Escalante, C., Balkcom, K.S. 2024. Cotton stalk management and a cover crop produce minimal effects on cotton leafroll dwarf virus. Agronomy Journal. 117(1):e70002. https://doi.org/10.1002/agj2.70002.
Zhao, C., Escalante, C., Jacobson, A.L., Balkcom, K.S., Conner, K.N., Martin, K.M. 2025. Metatranscriptomic and metagenomic analyses of cotton aphids (Aphis gossypii) collected from cotton fields in Alabama, USA. Frontiers in Insect Science. 5:1461588. https://doi.org/10.3389/finsc.2025.1461588.
Koebernick, J.C., Hagan, A.K., Zaccaron, M., Escalante, C., Jacobson, A.L., Bowen, K.L., Strayer-Scherer, A., Heilsnis, B., Brown, S., Sikora, E.J., Allen, T.W., Faske, T.R., Bourland, F., Greene, J.K., Huseth, A., Kelly, H., Kemerait, R.C., Kerns, D., Mulvaney, M., Price, P.P., Small, I., Taylor, S., Wang, H., Conner, K. 2024. Monitoring the distribution, incidence, and symptom expression associated with cotton leafroll dwarf virus in the southern United States using a sentinel plot system. PhytoFrontiers. 4(4):671–681. https://doi.org/10.1094/PHYTOFR-02-24-0008-R.
Zhao, C., Mueller, N., Owens, I., Bansal, R., Jacobson, A.L. 2025. Identification of candidate host-manipulating effector genes in Aphis gossypii (Hemiptera: Aphididae) using a combination of transcriptome, genome, and differential gene expression data. Journal of Insect Science. 25(3):11. https://doi.org/10.1093/jisesa/ieaf053.