Location: Foreign Disease-Weed Science Research
2025 Annual Report
Objectives
Objective 1: Develop genomic sequence resources and broad range nucleic acid and antibody-based diagnostics for novel emerging and invasive vectored plant pathogens. (NP303, C1, PS1A, PS1B)
Sub-objective 1.A: Development of rapid diagnostics for bacterial blight of grapevine caused by Xylophilus ampelinus.
Sub-objective 1.B: Identify and characterize emergent and invasive plant viruses and bacteria with potential for agronomic damage, and develop genome sequence resources.
Sub-objective 1.C: Develop immunodiagnostic reagents and field-deployable diagnostic assays for specific and sensitive detection of exotic, emergent, and quarantine plant viruses.
Sub-objective 1.D: Collect and characterize foreign and emerging bacterial plant pathogens.
Objective 2: Investigate the relationship of pathogen biology and ecology to disease expression of novel emerging and invasive vectored plant pathogens. (NP303, C2, PS2A, PS2B)
Sub-objective 2.A: Investigate virus determinants of resistance-breaking.
Sub-objective 2.B: Analyze virus protein expression and function in pathogenicity in single and mixed infections.
Sub-objective 2.C: Identify proteins and genes involved in virulence during X. fastidiosa subsp. pauca infection of citrus.
Sub-objective 2.D: Test susceptibility of New World Vitis species and hybrids to bacterial blight of grapevine caused by Xylophilus ampelinus.
Sub-objective 2.E: Genetic determinants of toxin production in Rathayibacter toxicus.
Objective 3: Understand the role of the vector in pathogen retention and transmission of viruses and bacteria. (NP303, C2, PS2B, PS2D)
Sub-objective 3.A: Develop sequence data resources for selected insect vectors and utilize data for refined taxonomic identification assays.
Sub-objective 3.B: Evaluate virus transmission determinants and test candidate molecules for transmission disruption.
Approach
Using specialized containment facilities, we will research key questions to assist in detecting and managing emerging, foreign, and invasive viral and bacterial diseases which threaten U.S. agriculture. Our research aims are to 1) develop sequence data, collections, and needed diagnostic tools for new pathogens; 2) elucidate basic molecular biology of virulence, toxicity, and pathogenicity of target pathogens; and 3) develop tools to characterize important vector populations and methods to block virus transmission. Target diseases include: foreign bacterial blight of grapevine, caused by Xylophilus ampelinus; citrus variegated chlorosis, caused by Xyllella fastidiosa; foreign and emergent maize lethal necrosis (MLN), caused by mixed infections of potyviruses in combination with the rapidly emerging maize chlorotic mottle virus (MCMV) driven by its corn thrips (Frankliniella williamsi) vector; U.S.-emergent cotton leafroll dwarf disease, caused by cotton leafroll dwarf virus (CLRDV); foreign disease caused by maize yellow mosaic virus (MaYMV/MYDV-RMV2); foreign rice tungro disease and other waikavirus-caused diseases; and foreign annual ryegrass toxicity (ARGT) livestock poisoning caused by the Select Agent Rathayibacter toxicus. Our research plan also includes the flexibility to respond to new pathogens that may emerge. Research will result in the development of sequence data, diagnostic tools, pathogen collections, and basic biological information about pathogenicity, toxicity and resistance-breaking, as well as tools to assess corn thrips populations and block spread of cotton leafroll dwarf disease.
Progress Report
The goals of Objective 1 are to develop sequence resources and diagnostics for novel emerging and invasive vectored plant pathogens. Under Sub-objective 1A, DNA sequences from Xylophilus ampelinus have been assembled into draft genomes and recombinase polymerase amplification (RPA) primers and probes have been developed. Specificity, inclusivity, and exclusivity testing of the RPA assay is in progress. Under Sub-objective 1B, sequencing was continued to determine if a virus was causing the virus-like symptoms observed on mango in Florida. Total RNA from 188 accessions held in the USDA-ARS mango germplasm collection was sequenced. Metatranscriptomic analysis using Phytopipe revealed that the most prominent viruses are Mangifera indica latent virus (MILV), Mangifera indica totivirus 1 (MiTV1) and an unclassified species in the Tombusviridae family. Reverse transcription polymerase chain reaction (RT-PCR) assays are being used to validate these findings and correlate virus presence with disease symptoms. In work related to Objective 1, sequences of plum pox virus (PPV) isolates obtained during the eradication efforts in the U.S. were examined. Phylogenetic analysis revealed that there were at least five separate introductions of PPV into the U.S.
Objective 2 focuses on the relationship between pathogen biology and disease expression. For Sub-objectives 2A and B, which aim to determine the function of various viral proteins and RNAs, no progress was made because of a critical vacancy in the virologist position. For Sub-objective 2C, proteome and transcriptome data from X. fastidiosa grown on rich and minimal media are being analyzed. Sweet orange inoculations have begun. Grapevines have been inoculated with X. ampelinus for Sub-objective 2D. Infected plants are being monitored for symptom development, and PCR, RPA, and culturing are being used to detect X. ampelinus. Under Sub-objective 2E, efforts to transform R. toxicus have not yet succeeded. In work related to Objective 2, numerous alternative host species for cacao mild mosaic virus (CaMMV) have been identified.
Objective 3 examines the role of vectors in pathogen retention and transmission of viruses and bacteria. For Sub- objectives 3A (developing sequence resources for selected vectors) and 3B (examining virus transmission determinants and their disruption), no progress has been made due to the virologist vacancy.
Accomplishments
1. Protecting U.S. olive production with data-driven risk assessments for olive quick decline syndrome. Protecting the health and sustainability of the U.S. olive industry—valued at over $500 million annually—requires proactive defenses against emerging global threats such as olive quick decline syndrome (OQDS), caused by Xylella fastidiosa subspecies pauca. While this destructive bacterium has not yet reached the U.S., it has killed millions of trees in southern Italy, and closely related subspecies are already widespread in domestic agriculture. To evaluate the risk to California’s olive sector, ARS researchers in Parlier, California and Frederick, Maryland, tested three widely cultivated olive varieties—Manzanillo, Sevillano, and Mission—and confirmed their susceptibility to OQDS. They also found that California’s primary insect vector, the glassy-winged sharpshooter, can transmit subspecies pauca. These findings provide critical insight into host and vector dynamics and now inform national risk assessments, surveillance efforts, and disease preparedness plans. ARS stakeholders—including growers, regulators, and industry groups—are better equipped to implement early warning strategies and protect orchards, helping preserve the economic and agricultural value of U.S. olive production.
NP component C2, problem statement (PS) 2A
2. Advancing mango disease diagnostics through virome profiling of USDA-ARS germplasm. Maintaining disease-free planting material is critical to sustaining mango production, which contributes over $100 million annually to the U.S. agricultural economy. That effort is now at risk due to a newly observed viral disease of unknown origin affecting mango trees. In response, ARS scientists at Frederick, Maryland and Miami, Florida, and at Animal and Plant Health Inspection Service, Plant Protection and Quarantine (APHIS-PPQ) at Beltsville, Maryland, used high-throughput RNA sequencing to analyze the virome of trees in the Miami, Florida, mango germplasm collection—the most diverse in the world. This research revealed a broad community of viruses, including many previously uncharacterized species. Using this information, scientists developed targeted virus detection tools to enable comprehensive screening of the collection and to pinpoint the disease-causing agent. These advances expand our understanding of mango viral diversity and help prevent the distribution of infected material. ARS stakeholders—including breeders, producers, and global collaborators—are now better equipped to protect U.S. mango resources, strengthen disease diagnostics, and ensure the resilience of both domestic and international germplasm exchange networks. NP component C1, problem statement (PS) 1A
3. Improving cacao farm biosecurity by detecting alternative CaMMV hosts. Cacao farms thrive in environments free from viral threats, where growers can sustain yields and incomes while contributing to a stable global chocolate supply. In the U.S., cacao production—though relatively small in scale—generates over $70 million in economic value annually, supporting specialty agriculture in regions like Puerto Rico and Hawaii. However, this potential is threatened by cacao mild mosaic virus (CaMMV), an emerging disease that causes branch dieback and reduced yields. To reduce the risk of spread, ARS scientists in Frederick, Maryland, tested plants growing near infected cacao and confirmed that several widely cultivated ornamental and fruit species also carry CaMMV. This expanded understanding of the virus’s host range reveals how nearby vegetation may contribute to virus transmission. As a result, stakeholders are updating planting guidance to avoid introducing or maintaining known host species in high-risk areas. This new knowledge strengthens cacao disease management, reduces the potential for virus movement into new plantings, and helps safeguard the productivity and long-term resilience of U.S. cacao farms. NP component C2, problem statement (PS) 2C
Review Publications
Rogers, E.E., Sechler, A.J. 2025. Draft genome sequences of two Xylella fastidiosa subsp. pauca strains isolated from citrus. Microbiology Resource Announcements. https://journals.asm.org/doi/10.1128/mra.01046-24.
Rogers, E.E., Stone, A.L., Sherman, D.J. 2025. Phylogenetic reconstruction from sequences of plum virus samples collected in the United States point to multiple, independent introductions. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-09-24-0097-SC.
Murray, T.D., Damaso Duarte, A., Luster, D.G., Mckirdy, S., Rogers, E.E., Schroeder, B.K., Subbotin, S.A. 2025. Seed gall nematodes and their association with toxigenic bacteria. Annual Review of Phytopathology. https://doi.org/10.1146/annurev-phyto-121823-033153.
Puig, A.S., Medina Rodriguez, V., Keith, L.M., Dunwell, J., Ullah, I. 2025. Fruit and ornamental plants are natural hosts of cacao mild mosaic virus (CaMMV). PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-10-24-0108-R.
Keith, L.M., Brill, E., Matsumoto Brower, T.K., Puig, A.S. 2024. First report of cacao mild mosaic virus associated with cacao in Hawai‘i, USA. Plant Disease. 108:3424. https://doi.org/10.1094/PDIS-07-24-1517-PDN.
Burbank, L.P., Rogers, E.E., Sechler, A.J., Magdaleno, M.A., Krugner, R. 2024. Experimental infection of California ripe olive cultivars with Xylella fastidiosa subspecies pauca De Donno and acquisition by glassy-winged sharpshooter. PhytoFrontiers. 4(4):722-727. https://doi.org/10.1094/PHYTOFR-04-24-0037-R.
Culver, J., Vallar, M., Burchard, E.A., Kamens, S., Lair, S., Qi, Y., Collum, T.D., Dardick, C.D., El-Mohtar, C., Dawson, W., Rogers, E.E. 2025. Citrus phloem specific transcriptional profiling through the development of a citrus tristeza virus expressed translating ribosome affinity purification system. Plant Methods. 21(49). https://doi.org/10.1186/s13007-025-01368-7.
Puig, A., Umaharan, P. 2024. Cacao mild mosaic virus (CaMMV) and Cacao yellow vein banding virus (CYVBV): genus Badnavirus. In: End, M.J., Daymond, A.J., Hadley, P, editors. Technical Guidelines for the Safe Movement of Cacao Germplasm. Revised from the FAO/IPGRI Technical Guidelines No. 20 (Fifth Update 2024). Global Cacao Genetic Resources Network (CacaoNet). Rome (Italy): Bioversity International, p 35-42. ISBN: 978-92-9255-328-9