Location: Foreign Disease-Weed Science Research
2024 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, the last needed DNA sequence from multiple strains of Xylophilus ampelinus have recently been received after some delays; work can now progress rapidly on genome assembly and RPA assay development. Under Sub-objective 1B, pathogen sequencing and characterization, several viruses were detected in RNA sequence from leaves of a fruit tree species with virus-like symptoms, even though no viral diseases are known for this particular species. Additional sequencing and characterization are in process. There was no progress on Sub-objective 1C, generating antibodies for the poleroviruses maize yellow mosaic virus and cotton leafroll dwarf virus, due a critical vacancy in the virologist position. For Sub-objective 1D, new strains of Rathayibacter toxicus from Australia were added to the ICPB.
Objective 2 focuses on the relationship between pathogen biology and disease expression. For Sub-objectives 2A and B, which focus on determining the function of various viral proteins and RNAs, no progress was made because of repairs needed in the greenhouse building where research will be performed and because of a critical vacancy in the virologist position. For Sub-objective 2C, proteome data from X. fastidiosa grown on rich and minimal media is being analyzed. Transcriptome data is still being acquired after which analysis will begin. Several different inoculation methods for X. ampelinus have been tested for Sub-objective 2D; it appears that a leaf-puncture method is the most reproducible. Under Sub-objective 2E, homologous recombination knockout constructs are being transformed into R. toxicus for the creation of needed mutants. 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 repairs needed in the greenhouse building where research will be performed and because of a critical vacancy in the virologist position.
Accomplishments
1. Almond is a transmission-competent host of plum pox virus. Plum pox virus (PPV) causes devastating disease in stone fruit and is widely present in most commercial stone fruit production areas except those in the United States. There are conflicting reports in the scientific literature about whether almond is susceptible or may have some natural immunity to PPV. ARS researchers in Frederick, Maryland, and Kearneysville, West Virginia, have demonstrated that almond can be infected by a specific isolate of PPV. Even though viral titers were approximately 100-fold lower in almond than in the more susceptible peach, aphids can transmit PPV from almond to peach. These results have profound implications for efforts to keep PPV out of the United States and specifically for stone fruit production in California, where almonds are often grown close to peaches, plums, and apricots. Monitoring stone fruits for PPV infection should include testing almonds and should PPV ever be detected in California, almond trees will need to be removed along with all other known hosts of PPV.
Review Publications
Stone, A.L., Damsteegt, V.L., Smith, O.P., Stewart, L.R. 2024. Global phylogenic analysis of soybean dwarf virus isolates and their associations with aphid vectors and severe disease in soybeans. Virology. 591:109984. https://doi.org/10.1016/j.virol.2024.109984.
Rogers, E.E., Stone, A.L., Burchard, E.A., Sherman, D.J., Dardick, C.D. 2024. Almond can be infected by Plum Pox Virus-D isolate Penn4 and is a transmission-competent host. Plant Disease. https://doi.org/10.1094/PDIS-09-23-1910-SC.