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ARS Home » Southeast Area » Auburn, Alabama » Soil Dynamics Research » Research » Research Project #438156

Research Project: GxExM Systems Approach to Crop Disease Management

Location: Soil Dynamics Research

2022 Annual Report

The new research will initially focus on managing the cotton leaf roll dwarf virus (CLRDV), also known as “cotton blue disease.” The project will have the following objectives: 1. Identify alternative (other than cotton) plant hosts for CLRDV which may contribute to its spread within cropping systems in the US cotton belt. 2. Understand seasonal population dynamics of insect vectors responsible for the spread of CLRDV within the landscape and their interactions with disease- or insect-tolerant germplasm. 3. Identify agronomic practices and management strategies for diverse germplasm for reducing risk of virus spread, disease expression, and yield loss caused by CLRDV.

The funds will be used to study the key epidemiological factors responsible for spread of cotton leaf roll dwarf virus (CLRDV) in cotton. Research will be undertaken on crop management to investigate production practices that minimize crop susceptibility to the disease, which include cultivar selection, crop health inputs, rotation, and cover crop selection as well as establish the relationship between symptom onset, host growth stage, and losses in lint yield and quality. Key epidemiological mechanisms for both the virus and the vector will be identified. On the cotton production landscape, aphid vector host selection along with dispersal and colonization patterns will be studied. This will allow strategies to be tested for alternative and sustainable management practices. It will build on the current field knowledge and strengthen the tools necessary to mitigate yield impacts at the grower level. Laboratory, field and controlled environment experiments will be utilized to build on the current knowledge to better understand the impact that winter crop production and common management practices have on virus and vector epidemiology. In addition, germplasm response to the virus in terms of symptomology and genotypic response will be addressed in order to identify resistance to either the vector or the virus providing a GxExM approach to this research.

Progress Report
In FY 2022, collaborations were strengthened between the National Soil Dynamics Lab and Auburn University to identify management strategies to minimize risk of cotton leaf roll dwarf virus (CLRDV). A series of projects focused on developing a season long integrated management plan are ongoing. These strategies pertain to specific questions designed to address interactions between CLRDV and plant health, fertility requirements, herbicide injury, and other biotic stresses, while also quantifying on-farm incidence. Preliminary results from agronomic management studies indicated traditionally recommended control strategies like cotton stalk destruction were ineffective at controlling CLRDV the following year. Other efforts this year resulted in a qPCR protocol being established, an infectious clone developed, and successful CLRDV transmission in a controlled environment with aphids in the lab. These aspects are extremely pertinent to breeding programs as testing for genetic resistance is achievable in controlled experiments and not restricted to only a field setting. The completion of a three-year multi state sentinel plot study confirmed that virus symptoms alone cannot adequately confirm virus incidence. The study did highlight regional differences for incidence and severity which will be further investigated in the future. Funds received have been allocated to purchase field and laboratory equipment to enhance research infrastructure capability associated with viral disease work in cotton. Furthermore, funds were allocated to hire a new Postdoctoral Fellow that allows for the initiation of new virology centered projects. Additional funds received for 2023 will be utilized to expand basic science aspects of the project with an emphasis on vector biology. This integral component will complement existing projects, in particular the entomology and virology objectives.

1. Cotton leafroll dwarf virus (CLRDV) detection across Florida, North Carolina, and South Carolina. Cotton leafroll dwarf virus sentinel plots were established by ARS researchers in Auburn, Alabama, across the cotton belt in 2019. As a result, CLRDV was detected for the first time in Florida, North Carolina, and South Carolina through these plots by collaborators at Auburn University. North Carolina State University, Clemson University, and the University of Florida worked with NSDL to confirm virus detection numbers and prepare the first reports of CLRDV in Florida, North Carolina, and South Carolina, respectively. Clemson University and the University of Florida also conducted additional surveys within their respective states to further determine the distribution of the virus. These reports improve our understanding of CLRDV distribution across the cotton belt and clarify relationships among CLRVD isolates present in the U.S.

2. Cotton aphid management and planting date have no effect on cotton leafroll dwarf virus incidence. This is the first study to research management strategies of cotton leafroll dwarf virus (CLRDV) in the Southeastern U.S. Initial management strategies examined by ARS researchers in Auburn, Alabama, and collaborators at Auburn University and the University of Georgia to reduce the spread of CLRDV included the use of insecticides and adjusting planting dates. Flights of cotton aphids (a vector for the virus) and timing of virus spread were also monitored to determine when virus infection occurred. However, neither management strategy examined reduced virus spread. Total aphid numbers were reduced, but not eliminated with insecticide sprays, allowing for virus spread. Three distinct periods (early-, mid-, and late-season) during the growing season were detected for virus spread. Most virus spread occurred when collection traps indicated high cotton aphid populations. These results show that insecticide spays should not be used to specifically control CLRDV because they cannot completely eliminate the aphid vector. The three main vector flight periods and corresponding disease spread events identified during the growing season indicate areas for future studies to potentially reduce virus incidence.

3. Interdisciplinary team addresses cotton leafroll dwarf virus (CLRDV) in Alabama. A multi-state and interdisciplinary team was formed to address and research extension needs of CLRDV, an emerging cotton disease with high potential negative impact for U.S. cotton production. Once CLRDV was identified by ARS researchers in Auburn, Alabama, and Auburn University collaborators immediately formed an interdisciplinary working group composed of plant breeders, plant pathologists, entomologists, and agronomists. Since then, researchers from ten other states have joined the CLRDV research group – Virginia Tech University, North Carolina State University, Clemson University, University of Georgia, University of Florida, Mississippi State University, University of Arkansas, Louisiana State University, University of Tennessee, and Texas A&M University. The formation of this group allowed initial research on CLRDV to be coordinated efficiently and deploy resources effectively to address stakeholder’s needs across the US cotton belt. The CLRDV group continues to produce and share new and relevant information with the scientific community and cotton producers to mitigate potential negative impacts of CLRDV.

4. A guide to grafting for CLRDV transmission. A new virus in cotton (Cotton leafroll dwarf virus, CLRDV) required the need to graft plants to evaluate resistance. A graft is the union of tissue from two separate plants and requires good tissue contact to be successful. Several studies have reported grafting cotton; however, the details surrounding the types of grafts, age, and environment are not described in detail. Therefore, several different graft types, and the need for humidity were investigated by ARS researchers in Auburn, Alabama, and collaborators at Auburn University. The T-graft was chosen as the most successful because it provided the highest tissue contact. Once established, the T-graft was used to test virus transmission. A transmission rate of 70% for CLRDV was obtained, regardless of graft success. These results represent the first guide to grafting cotton; therefore, this research benefits anybody that needs to graft cotton, particularly with respect to testing any virus resistance in breeding programs.

5. Genome analysis of cotton leafroll dwarf virus (CLRDV). CLRDV is an emerging cotton virus in the southeastern U.S. with potential for devastating yield losses across susceptible cultivars. However, despite the potential detrimental economic impact for the U.S. cotton industry, no information is available on the genetic diversity and population structure of the virus. ARS researchers in Auburn, Alabama, in collaboration with researchers from the University of Georgia and Auburn University, studied the genetic diversity of the virus population by examining near complete genome sequences of six isolates from Georgia and one from Alabama. Georgia Isolates were >94% identical with other isolates from the USA and South America. Isolates from Georgia and Alabama showed genetic characteristics similar to resistant-breaking ‘atypical’, less aggressive genotypes found in South America. A Texas isolate was similar to a more aggressive ‘typical’ genotype of CLRDV. This improved understanding of CLRDV population structure and genetic diversity will help develop integrated disease management strategies and facilitate resistance breeding efforts to reduce negative impacts of CLRDV in the USA cotton belt.

Review Publications
Conner, K.N., Sikora, E., Koebernick, J., Zaccaron, M. 2022. Interdisciplinary team addresses cotton leafroll dwarf virus in Alabama. Journal of Extension. 60(2). Article 9.
Heilsnis, B., Koebernick, J., Jacobson, A., Conner, K.N. 2021. A guide to grafting for cotton (Gossypium Hirsutum L.) virus transmission and the successful transmission of cotton leaf roll dwarf virus. Journal of Cotton Science. 25:222-228.
Iriarte, F., Dey, K., Small, I., Conner, K., O'Brien, G.K., Johnson, L., Savery, C., Carter, E., Sprague, D., Nichols, R., Wright, D., Mulvaney, M., Paret, M. 2020. First report of cotton leafroll dwarf virus in Florida. Plant Disease. 104(10):2744.
Mahas, J.W., Hamilton, F.B., Roberts, P.M., Ray, C., Miller, G.L., Sharman, M., Conner, K., Bag, S., Blythe, E., Toews, M., Jacobson, A.L. 2022. Investigating the effects of planting date and Aphis gossypii management on reducing the final incidence of Cotton leafroll dwarf virus. Pest Management Science. 158.
Thiessen, L., Schappe, T., Zaccaron, M., Conner, K., Koebernick, J., Jacobson, A., Huseth, A. 2020. First report of cotton leafroll dwarf virus in cotton plants affected by cotton leafroll dwarf disease in North Carolina. Plant Disease. 104(12):3275.
Wang, H., Greene, J., Mueller, J., Conner, K., Jacobson, A. 2020. First report of cotton leafroll dwarf virus in cotton fields of South Carolina. Plant Disease. 104(9):2532.
Tabassum, A., Bag, S., Suassuna, N.D., Conner, K.N., Chee, P., Kemerait, R.C., Roberts, P. 2021. Genome analysis of cotton leafroll dwarf virus reveals variability in the silencing suppressor protein, genotypes and genomic recombinants in the USA. PLoS ONE. 16(7):e0252523.