Source: Agricultural Research Service submitted to NRP
PROTEOMIC, GENOMIC, AND BIOLOGICAL CHARACTERIZATION OF EMERGING VIRUSES IN UPLAND COTTON
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1031885
Grant No.
2024-67013-41951
Cumulative Award Amt.
$294,000.00
Proposal No.
2023-07679
Multistate No.
(N/A)
Project Start Date
Mar 1, 2024
Project End Date
Feb 28, 2027
Grant Year
2024
Program Code
[A1811]- AFRI Commodity Board Co-funding Topics
Recipient Organization
Agricultural Research Service
600 E. Mermaid Lane Rm 2023
Glenside,PA 19038-8551
Performing Department
(N/A)
Non Technical Summary
Cotton leafroll dwarf virus (CLRDV), a polerovirus, is a persistent threat to cotton production in the United States. We will conduct research to understand how CLRDV is transmitted by insect vectors using molecular-based appraoches. This information will be useful for developing targeted disease management strategies. Recently, we characterized a new DNA virus from CLRDV-infected plants, cotton virus A (CotV-A, genus Caulimovirus). Sequences from this virus are also inserted into the cotton genome, referred to asendogenous virus elements. We will conduct experiments to ascertain how CotV-A may be transmitted in upland cotton. Lastly, we will use a technology called high throughput sequencing (HTS) to characterize CLRDV and CotV-A interactions in upland cotton and weed reservoirs. The impact of CotV-A on cotton production is unknown, and management strategies are nonexistent. This research is vital for the cotton industry, as we do not yet have the tools to evaluate the impacts of CotV-A on yield potential or on plants that are carrying a high viral load. Our research is critical for the industry because a new and serious pathology has increased its incidence in numerous upland cotton-producing states and the cause is unknown. Our HTS survey will inform the industry about this emerging issue and determine whether it involves CLRDV, CotV-A or additional viral agents.
Animal Health Component
10%
Research Effort Categories
Basic
80%
Applied
10%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2121710110170%
2113110110120%
2131710110110%
Knowledge Area
212 - Pathogens and Nematodes Affecting Plants; 211 - Insects, Mites, and Other Arthropods Affecting Plants; 213 - Weeds Affecting Plants;

Subject Of Investigation
3110 - Insects; 1710 - Upland cotton;

Field Of Science
1101 - Virology;
Goals / Objectives
n 2022, cotton, Gossypium spp. (Family: Malvaceae), was one of the top 10 plant commodities in the United States (US) corresponding to 13.7 million acres of production and valued at approximately $6.45 billion. Cotton leafroll dwarf virus (CLRDV) is a phloem-limited polerovirus that represents a persistent threat to cotton production in the US. Since its discovery in Alabama in 2017, CLRDV subsequently spread to almost all cotton-producing states in the US. CLRDV is transmitted by the cotton aphid, Aphis gossypii, and is the causative agent of cotton blue disease (CBD) in South America, Africa and Asia, and cotton leafroll dwarf disease (CLRDD) in the US.In this project, we will pursue the following three objectives:Objective 1. Identify and characterize the aphid proteins involved in CLRDV transmission.Objective 2. Determine biological factors regulating transmission of a newly discoveredcotton virus, CotV-A, which also has integrated sequences in the cotton genome.Objective 3. Characterize population dynamics of CLRDV, CotV-A and potential new viruses in upland cotton and weed reservoirs.These research objectives will provide a holistic understanding of CRLDV, its cotton aphid vector, interactions with CotV-A and possible interactions with other viruses found in upland cotton production fields in the US cotton belt. The objectives will be pursued in parallel and while synergistic, the success of one does not rely on the other.
Project Methods
Methods to be used in this project draw from the fields ofmolecular biology, mass spectrometry-based proteomics, vector biology, and high throughput sequencing.

Progress 03/01/24 to 02/28/25

Outputs
Target Audience:The target audience for this research includes the cotton research community, including cotton pathologists and breeders, university extension agents, cotton industry representatives, companies that produce agricultural products applied to cotton,and cotton growers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Project participants have given local seminars andparticipated in the 2025 Beltwide Cotton conference. A Cornell graduate student is working on Objective 3 of the project, which is providing training in cotton pathology, virology and computational biology.An undergrad working on the project was trained in molecular virology techniques and has applied to graduate school. How have the results been disseminated to communities of interest?Currently, we have focused on submitting peer-reviewed publications on the research. Datasets and results briefs on CLRDV sequencing have been provided to the Department of Homeland Security for use in epidemiological modeling. What do you plan to do during the next reporting period to accomplish the goals?The grant is in its infancy and I am still waiting to hire a postdoc on the project. We have identified a candidate, who is awaiting their visa processing. In the next reporting period, I hope to onboard the postdoc and continue research as outlined in our workplan.

Impacts
What was accomplished under these goals? Under objective 1, we set up co-immunoprecipitation experiments to identify proteins from Aphis gossypiithat bind to CLRDV. Three replicate immunoprecipitations were performed. These experiments are in progress and will be a focus of work in the next year of research. Under objective 2, we developed an exonuclease V protocol to identify the episomal form of CotVA. Exonuclease V should specifically degrade linear DNA and leave behind circular DNA. In further development of this protocol, we could not obtain complete degredation of cotton chromosomal DNA, thus making it impossible for the assay to distinguish between CotVA endogenous viral elements that are integrated into the genome and the episomal form of CotVA. Unfortunately, another group who requested this protocol from us in the early stages of protocol development used the protocol in an attempt to detect CotVA episomal forms and published their research using the protocol without reaching back out to us to discuss the results or their findings (https://www.mdpi.com/1999-4915/16/7/1111). This was very unfortunate because we would have shared the new information about the protocol and worked with their group to further trouble shoot the procedure. Hence, there is even further confusion in a possiblerole of CotVA in causing the new "crazy cotton" phenotype being observed in the U.S. cotton belt (https://cropprotectionnetwork.org/publications/defining-and-quantifying-the-occurrence-of-crazy-cotton-in-mid-south-cotton-production#:~:text=Although%20there%20are%20a%20variety,stem%20scarring%2Fscabbing%20). Under objective 3, when performing high throughput sequencing to characterize CotVA and CLRDV sequences from field-collected cotton samples, we observed an abundance of circular transposable elements from symptomatic cotton samples. We are testing the hypothesis that CLRDV or CotVA infection activates the "mobilome" of cotton, leading to the expression and variability of virus-associated phenotypes. The mobilome is the collection of mobile genetic elements within a genome.

Publications

  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Olmedo-Velarde A, Shakhzadyan H, Norton R, Heck M. First Report of Cotton Leafroll Dwarf Virus Infecting Upland Cotton Plants in Arizona. Plant Disease. 2025 Jan 2:PDIS-04.
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: West-Ortiz M, Olmedo-Velarde A, Stuehler Jr D, Pollock E, Alvarez-Quinto R, Wilson JR, Preising S, Larrea-Sarmiento A, Alabi OJ, Fuchs M, Heck M. Cotton Plants Presenting Symptoms Associated with Cotton Leafroll Dwarf Virus Revealed a Novel Caulimovirid, Cotton Virus A, with Endogenous Caulimovirids in Its Hosts. Phytobiomes Journal. 2025(ja).
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Olmedo-Velarde A, Shakhzadyan H, Rethwisch M, West-Ortiz MJ, Waisen P, Heck ML. Data mining redefines the timeline and geographic spread of cotton leafroll dwarf virus. Plant Disease. 2024 Jun 6(ja).