Location: Soil Dynamics Research
2024 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
Fiscal Year 2024 saw advances across each objective of the project with major progress made in understanding the vector abundance and dynamics across different cotton production environments. Two different aphid species were ruled out from cotton virus transmission. An additional species was identified as a possible vector of cotton leafroll dwarf virus (CLRDV), but more studies are needed to confirm this role. These findings coupled with information about length of transmission times combined with other host species being identified will contribute to both agronomic and disease management plans in the future, which are evolving with these recent research findings. Current projects related to high throughput sequencing of virus infected plants as well as the refinement of symptom expression across cotton cultivars and reliability of an infectious clone for future experiments are continuing. Another project is designed to identify molecular factors of CLRDV that suppress host defense response, which can explain why different strains cause a wide range of disease symptoms and severity. This information will help identify host factors that play a role during virus infection that can contribute to development of resistant varieties. Experiments related to alternative host plants and herbicide damage are continuing, as well as efforts focused on prioritizing aphid resistance within collaborative breeding efforts. Additional projects to acquire diverse germplasm and planting of a genome wide association study designed to determine plant defense candidate genes specific to cotton leaves was initiated. In addition, we are expanding the scope of our project to include additional cotton pests. Four manuscripts focused on aphid characterization and population dynamics in the Southeast United States, as well as virus suppression of defense mechanisms were published. Project funds available to collaborators resulted in five graduate students recently completing their degrees with another seven students working on ongoing CLRDV projects in various disciplines. The efforts of collaborators (a postdoc, graduate students, and PI’s) resulted in 17 presentations at international, national, and regional conferences. In addition, the hiring process for a Research Entomologist has been completed. This new researcher came onboard after our current project was certified, but this person is familiarizing themselves with our current research efforts, providing leadership on appropriate projects, and developing additional projects that will complement our existing research efforts.
Accomplishments
1. Seasonal dynamics of aphid flights and cotton leafroll dwarf virus spread in Alabama. Cotton leafroll dwarf virus (CLRDV) is an introduced virus of cotton in the United States (U.S.). The only vector known to transmit this virus to cotton is the cotton aphid, however, there are several other species of aphids reported to colonize cotton in the southeastern U.S. Little is known regarding annual population dynamics of these species in the southeastern U.S. or the timing of CLRDV spread to cotton plantings. Researchers at Auburn University, which are collaborators of ARS researchers at Auburn, Alabama, monitored the population dynamics of cotton feeding aphid species along with the spread of CLRDV at different locations in Alabama. During this study, CLRDV spread at all locations occurred when the cotton aphid was actively dispersing in the field. Multiple CLRDV spread events suggest spread is occurring widely in the environment. During the cotton growing season the cotton aphid was the most abundant species. However, early season spread at sites in south and central Alabama, when the cotton aphid was not abundant, but the corn root aphid was, suggests additional aphid vectors are possible and warrants further research on the corn root aphid. This study provides basic information regarding spread and management of CLRDV by identifying when virus spread occurs along with characterizing dispersal of known and potential aphid vectors.
2. A newly isolated cotton infecting Polerovirus with cryptic pathogenicity encodes a weak suppressor of RNA silencing. Cotton is a major crop grown globally. One of the main diseases of cotton is caused by a viral pathogen, cotton leafroll dwarf virus (CLRDV). CLRDV is transmitted by aphids and replicates within phloem tissue. Substantial economic losses from CLRDV have occurred in South American countries. CLRDV strains in the United States show cryptic pathogenicity, making it hard to diagnose and detect in the field. Researchers at Auburn University, which are collaborators of ARS researchers at Auburn, Alabama, investigated the viral suppressor of RNA silencing (VSR) of CLRDV strains in the United States and demonstrated its weakness as a VSR compared to other CLRDV strains in South America. Genetic differences within the functional domain of the protein may be the cause of such a difference, and the potential emergence of more damaging strains of CLRDV could follow. This work contributes to the development of better management strategies by understanding the pathogenicity and host immune response.
3. The spatiotemporal distribution, abundance, and seasonal dynamics of cotton-infesting aphids in the southern United States. Cotton leafroll dwarf virus (CLRDV) can cause yield loss in cotton. Eight species of aphids have been reported to feed on cotton, but the cotton aphid is the only known CLRDV vector in the U.S. Little is known about their distribution, abundance, and seasonal dynamics in the southern United States Researchers at Auburn University, which are collaborators of ARS researchers at Auburn, Alabama, worked with researchers from Clemson University, Mississippi State University, North Carolina State University, Texas A&M, Virginia Tech, University of Florida, University of Georgia, and University of Tennessee to monitor populations of aphids that infest cotton fields throughout the southern U.S., where CLRDV has been previously reported. The cotton aphid and corn root aphid were the most abundant species collected. Several other species were detected in this study, but they were detected at low levels. This study documents seasonal variation of aphids associated with cotton over a two-year period and can serve as baseline data of cotton-infesting aphid species in the southern United States.
4. Plant virus transmission during seed development and implications to plant defense system. Most plants produce seed for reproduction and plant viruses have evolved to use that seed for their dispersal. The presence of plant pathogenic viruses in seed is a major worldwide concern for producers and seed companies because undetected viruses in the seed can cause a significant threat to yield in many economically important crops. ARS researchers at Auburn, Alabama, along with cooperators at Auburn University and Warsaw University, Poland, have provided an overview of the current knowledge of plant virus transmission during seed development. Transmission of plant viruses occurs directly through the embryo or indirectly by getting in pollen. Infection of plant viruses during early seed development can result in structural or genetic changes that cause poor seed quality and low yields due to the virus present during seedling development. Understanding the spread of plant viruses during seed development will help identify sources of introduction, reduce spread, decrease disease severity, and facilitate the future of plant disease management through seed in many crops.
Review Publications
Escalante, C., Sanz-Seaz, A., Jacobson, A., Otulak-Koziel, K., Koziel, E., Balkcom, K.S., Zhao, C., Conner, K. 2024. Plant virus transmission during seed development and implications to plant defense system. Frontiers in Plant Science. 15:1385456. https://doi.org/10.3389/fpls.2024.1385456.
Akinyuwa, M., Price, B., Martin, K., Kang, S. 2023. A newly isolated cotton-infecting Polerovirus with cryptic pathogenicity encodes a weak suppressor of RNA silencing. Frontiers in Agronomy. 5:1235168. https://doi.org/10.3389/fagro.2023.1235168.
Mahas, J., Mahas, J., Ray, C., Kesheimer, A., Steury, T., Conzemius, S., Crow, W., Gore, J., Greene, J., Kennedy, G., Kerns, D., Malone, S., Paula-Moraes, S., Roberts, P., Stewart, S., Taylor, S., Toews, M., Jacobson, A.L. 2023. The spatiotemporal distribution, abundance, and seasonal dynamics of cotton-infesting aphids in the southern U.S. Insects. 14(7):639. https://doi.org/10.3390/insects14070639.
Mahas, J., Ray, C., Kesheimer, A., Conner, K., Jacobson, A. 2023. Seasonal dynamics of aphid flights and cotton leafroll dwarf virus spread in Alabama. Insects. 14(7):604. https://doi.org/10.3390/insects14070604.
Akinyuwa, M., Price, B., Kang, S. 2024. Characterization of the proteins encoded by a recently emerged cotton-infecting Polerovirus. Virus Genes. https://doi.org/10.1007/s11262-024-02086-3.
