Location: Crop Diseases, Pests and Genetics Research
2025 Annual Report
Objectives
Grapes and citrus are major crops in California with an estimated value of $8.7 billion per year. Inputs for protection against pathogens and insect pests can be significant, and often environmentally friendly control strategies are lacking. To address the plant disease management challenges confronted by grape and citrus producers in California, research will focus on the following four objectives and associated sub-objectives.
Objective 1: Create novel grapevine and citrus pathogen identification and disease diagnosis methods.
Subobjective 1A: Develop novel species identification techniques for Xylella fastidiosa (Xf) and fungal pathogens of grapevines including utilizing FAME profiling and phenotype microarrays.
Subobjective 1B: Improve diagnostics of citrus pathogens through field deployable technologies such as isothermal amplification, robotics, and artificial intelligence.
Subobjective 1C: Develop sensitive and accurate detection systems for grape and citrus pathogens using genomic information.
Objective 2: Elucidate vector feeding and movement behaviors associated with transmission and spread of Xylella fastidiosa.
Subobjective 2A: Compare vector probing behaviors of blue-green sharpshooter (BGSS), with or without Xf, on Pierce’s disease (PD)-resistant or -susceptible grapevines.
Subobjective 2B: Develop an electropenetrography (EPG)-based Resistance Index (EPG-RI) to rapidly detect grapevine resistance to Xf inoculation behaviors of vectors.
Subobjective 2C: Determine the role of glassy-winged sharpshooter (GWSS) nymphs in spreading Xf within vineyards.
Subobjective 2D: Develop a flexible individual-based model to evaluate implications of results from studies conducted during completion of this project on pathogen spread.
Objective 3: Develop vibrational control methods for grapevine pests for integration into vineyard management practices.
Subobjective 3A: Evaluate female BGSS re-mating receptivity and communication.
Subobjective 3B: Determine efficacy of natural tremulatory signals in disrupting mating of the BGSS.
Subobjective 3C: Assess BGSS male attractiveness to playback of female vibrational signals.
Subobjective 3D: Develop methods for transmission of GWSS and BGSS disruptive signals to crops and ground vegetation.
Objective 4: Develop sustainable management tactics for pests and diseases of grapevine and citrus.
Subobjective 4A: Develop formulations to improve the use of region-specific biological control strains of Trichoderma spp. as a disease management tool for combating bacterial and fungal diseases of grapevines.
Subobjective 4B: Determine susceptibility of vine mealybug (VMB) to soil-applied imidacloprid.
Subobjective 4C: Target bacterial endosymbionts for control of VMB.
Subobjective 4D: Evaluate sub-lethal effects of soil-applied imidacloprid on GWSS fecundity, survival, and movement behavior.
Subobjective 4E: Determine distribution and genetic diversity of citrus tristeza virus (CTV) in citrus in California and assess the environmental/economic impact for future deployment of genetically-engineered (GE)-CTV.
Approach
The approach is to synergistically exploit weak links between main components of grapevine and citrus pathosystem (pathogen, vector, plant) and insect pests to induce an unstable or neutral interaction that can lead to disruption of destructive processes affecting grape and citrus production. First, disease management requires accurate, sensitive, and cost-effective diagnostic tests to identify causal agents. The most recent genomic information will be used to improve pathogen detection methods that are based on DNA sequences, whereas studies of pathogen phenotypes will lead to development of novel complimentary diagnostic methods. Second, developing plant disease management strategies requires a fundamental understanding of pathogen spread. Mathematical models will be used to evaluate the role of environmental factors on pathogen spread and to simulate management approaches. Experiments will compare insect vector feeding behaviors on resistant and susceptible plants and evaluate the role of juvenile stages in pathogen spread. Third, management of insect-transmitted pathogens requires novel sustainable methods for suppressing vector population growth. Methods to disrupt mating by interfering with insect vector behaviors will be developed. A final objective will assess current control methods to minimize risk of insecticide resistance, develop novel molecular technology targeting vector endosymbionts, identify biological control agents of fungal cankers, and evaluate safety and efficacy of genetically-engineered viruses to manage citrus diseases. The research will benefit grape and citrus growers by addressing current needs and developing novel technology to meet the demand for sustainable farming practices.
Progress Report
This report documents FY 2025 progress for project 2034-22000-014-000D, “Development of Applied Management Systems for Diseases of Perennial Crops with Emphasis on Vector-Borne Pathogens of Grapevine and Citrus”, which began in February 2022.
In support of Objective 1, work continued on development of novel pathogen identification and disease diagnosis methods. Toward Sub-objective 1A, ARS researchers in Parlier, California, continued to test nutritional requirements of multiple grapevine fungal pathogens for evaluation of pathogen aggressiveness, as well as pathogen sensitivity to fungicidal compounds. Data generated from these analyses can be incorporated into integrated pest management programs to ensure optimal fungal pathogen control. For Sub-objective 1B, ARS researchers in Parlier, California, and Beltsville, Maryland, conducted multi-laboratory validation testing of a new molecular detection method for Spiroplasma citri, the pathogen causing citrus stubborn disease. The new method works directly on crude citrus sap, and results can be read using a handheld lateral flow device that can be deployed in the field. A 100% match of results was achieved from the two laboratories, validating the new molecular method in comparison with previously used quantitative polymerase chain reaction (qPCR) methods that require full laboratory facilities. This research improves diagnostics for citrus pathogens by making pathogen testing faster and less constrained by available laboratory resources. Under Sub-objective 1C, researchers continued to explore available Xylella fastidiosa genome sequences for targets to improve X. fastidiosa strain detection. A virulence-related hemagglutinin adhesin gene was found to have high and varied copy number that could be used to increase detection sensitivity and differentiate between strains of different host origins. In support of Sub-objective 1D, researchers worked towards developing new rapid and sensitive molecular diagnostic methods for detection of grapevine leafroll-associated virus 3 (GLRaV-3) in vineyards. New methods can detect viral nucleic acids from a single temperature incubation and are currently undergoing optimization for high reproducibility. Additionally, researchers evaluated molecular testing protocols (Reverse Transcriptase-PCR) for early detection of GLRaV-3 in table and raisin grape germplasm. The efficacy and accuracy of GLRaV-3 early detection by RT-PCR was verified by late-season detection using enzyme-linked immunosorbent assay (ELISA).
Under Objective 2, progress was made towards understanding insect vector feeding and movement behaviors related to transmission of the bacterial pathogen X. fastidiosa in grapevines. For Sub-objective 2A, ARS researchers in Parlier, California, measured and statistically analyzed blue-green sharpshooter feeding behaviors on Pierce’s disease-susceptible or -resistant grapevines using electropenetrography (EPG). Results showed that insects performed more behaviors associated with pathogen inoculation on disease-susceptible grapevines. For Sub-objective 2B, researchers performed principal component analysis of insect feeding behavior data measured with EPG. This analysis found that pathogen inoculation-associated behaviors performed by insect vectors can be represented by four principal components, allowing for consolidation of complex measurements into a simplified index for clear comparison of insect feeding on different plants. In support of Sub-objective 2C, researchersconducted studies describing movement of glassy-winged sharpshooter nymphs in relation to the spread of X. fastidiosa between plants. Under Sub-objective 2D, researchers created detailed simulation models that tracked the spread of an insect-transmitted plant pathogen through an agricultural region. Model simulations were run on SCINet high performance computing infrastructure and provide detailed information on how pathogens are likely to spread.
In support of Objective 3, progress was made in developing methods for transmission of disruptive vibrational signals to crops and ground vegetation to interfere with pest communication. Previous research suppressed glassy-winged sharpshooter mating during field trials, with vibrational emitters transmitting disruptive signals through the wires used in vineyard trellis system. While trellised vineyards are equipped for transmission of disruptive vibrations through wires, citrus plantings in California are composed of stand-alone trees with minimal contact between trees. Because citrus is an important host of glassy-winged sharpshooters, knowledge of properties of signal transmission in citrus trees is required to extend vibrational control to citrus orchards. Research under Sub-objective 3D showed that 1) the disruptive signal was strongly detected near the emitter and signal intensity diminished away from the emitter, 2) lower frequencies had a greater intensity than higher frequencies, and 3) smaller citrus trees vibrated more than larger trees, creating a larger signal intensity at the emitter. Collectively, results revealed that the disruptive signals were detectable throughout the citrus trees, which will allow further analysis to be done in the field with glassy-winged sharpshooter to better understand signal dynamics. Also in support of Sub-objective 3D, transmission of disruptive vibrational signals for glassy-winged sharpshooter and blue-green sharpshooter to ground cover plants present within vineyards was evaluated in a vineyard at the ARS in Parlier, California. Playback experiments were conducted and analysis of signal intensities recorded in grapevines and ground vegetation are underway.
Under Objective 4, progress was made on developing sustainable management tactics for pests and diseases of grapevine and citrus. For Sub-objective 4A, ARS researchers in Parlier, California, continued testing novel fungal biological control agents from California vineyards for efficacy in management of grapevine trunk diseases and important insect pests such as mealybugs and sharpshooters. Field applications of the biological control agents significantly reduced fungal canker pathogen infections of pruning wounds in vineyards, in some cases more effectively than commercial fungicides. Additionally, new potential bacterial biological control agents were tested against vine mealybugs in laboratory assays.
In support of Sub-objective 4D, ARS researchers in Parlier, California, evaluated the effects of sub-lethal doses of imidacloprid on glassy-winged sharpshooter development. This information is important for understanding the impacts of insecticides on pest populations beyond direct lethal effects. Under Sub-objective 4E, ARS researchers propagated several new viral-vector constructs that express plant defense proteins. These constructs are a second generation of improved viral vectors developed for increasing plant defenses against the pathogen ‘Candidatus Liberibacter asiaticus’ which causes Huanglongbing (HLB) disease in citrus. This research supports the development of genetically engineered viral vectors for use in plant disease mitigation, and assessment of environmental and economic impacts of this technology for control of HLB. This work is in collaboration with Texas A&M AgriLife Research under subordinate agreement 58-2034-2-017.
Additional research progress was made on monitoring the movement of three-cornered alfalfa hoppers, a known vector of grapevine red blotch virus, between alfalfa fields and vineyards, as well as continued studies using machine learning to count insects on photographs taken of yellow panel sticky traps. This research will facilitate monitoring of insect vectors in agricultural areas, and surveillance for invasive pests. Additionally, ARS researchers in Parlier, California, made progress on screening grape germplasm for genetic resistance to vine mealybug.
Accomplishments
1. Biological control innovation combats grapevine trunk diseases. Grapevine fungal trunk diseases impacting grape production worldwide and in the U.S. require costly vineyard replacement every 10-15 years. Novel biological control agents, including beneficial fungi, could provide long-term disease control as an effective alternative to existing agrochemicals. ARS researchers in Parlier, California, discovered Trichoderma fungal strains from Californian vineyards with biological control activity against grapevine fungal trunk diseases. Six of these new biological control fungal strains provided disease control equivalent or better than a commercial synthetic fungicide when applied to grapevine pruning wounds in the field. A partnership to transfer these strains to an industry partner could develop innovative fungal biopesticide alternatives for grape growers in the U.S. to control grapevine trunk diseases.
2. Early virus detection to protect table and raisin grape germplasm. Grapevine leafroll disease (GLRD) is one of the most devastating viral diseases in most grape-growing regions worldwide. The most effective GLRD control strategies include planting certified virus-free grapevines and removing virus-infected vines as soon as possible. Early virus detection in vineyards is critical for this strategy, but can be challenging with existing detection methods, especially when screening a wide range of plant varieties, such as germplasm collections. ARS scientists in Parlier, California, tested a table and raisin grape germplasm collection for grapevine leaf roll associated virus 3 (GLRaV-3) using common standardized molecular detection protocols and found that in some genotypes, virus infection can be detected much earlier in the season compared with non-molecular testing methods. Although early detection was not equally sensitive in all grape varieties, molecular detection was highly accurate as all detected infections were later confirmed using alternate methods. This information provides important guidance for GLRD management in table and raisin grape vineyards and will facilitate timely removal of virus-infected vines for improved disease suppression.
3. Improved citrus pathogen detection by novel molecular methods. Spiroplasma citri (Sc), the causal agent of citrus stubborn disease, causes significant losses to citrus production in warm, semi-arid citrus growing regions including California. Low concentration and erratic distribution of Sc in tissues makes its detection difficult in citrus plants. ARS scientists in Parlier, California, and Beltsville, Maryland, validated a new detection method known as CRISPR/Cas for detection of Sc in crude citrus plant extracts. This innovative methodology performed equally with existing molecular detection methods and produced results that can be read using field-deployable dip stick devices, reducing both time to results and testing costs. This novel method improves field testing capacity for Sc in orchards to facilitate citrus stubborn disease management.
4. Citrus greening disease control with improved production of plant defense proteins. U.S. agriculture lacks sustainable control measures for citrus greening disease caused by the pathogen ‘Candidatus Liberibacter asiaticus’ (CLas), which is responsible for more than a 70% loss of citrus production in Florida and threatens citrus production in California. ARS scientists in Parlier, California, tested seven new plant viral vectors expressing spinach defensin, a protein that boosts citrus immune response to target CLas. These viral vectors showed greater stability and higher defense protein expression compared with previous versions of this technology during propagation in citrus plants. These results are critical for the Environmental Assessment and Environmental Impact Study needed for field release of this technology for citrus greening mitigation in California.
5. Ground cover planting in vineyards can increase pollinator presence, suppress weeds, and improve water retention. Specialty crop agriculture could be enhanced with ground cover plants in the interrow spaces of vineyards that provide several benefits including recruitment of pollinators and beneficial insects, weed suppression, and improved water retention. However, detailed evaluation is necessary to guide vineyard management recommendations because benefits may vary depending on the type of ground cover planted and the vineyard management system. ARS scientists in Parlier, California, evaluated different ground cover plant species for beneficial impacts in a table grape vineyard. Vineyards rows planted with lacy phacelia in the interrow space had 76 times more honeybee presence, an 86% reduction in weed biomass, and a 15% increase in soil water retention compared with vineyards planted with rye or left bare. This information is critical to inform vineyard management decisions to improve crop production, quality, and profitability while reducing inputs.
6. Improved high-consequence crop pathogen identification using whole genome sequencing. Xylella fastidiosa (Xf) is a bacterial plant pathogen that causes significant diseases in many economically important crops such as grape, almond, pecan, and blueberry. Accurate identification of specific Xf strains is important for disease management because strains vary in their ability to cause disease in different crops. ARS scientists in Parlier, California, used whole genome sequences of over 100 Xf isolates from different host plant species and geographical origins to develop a molecular detection protocol that differentiates specific strains based on the sequence of the hemagglutinin adhesin gene. This approach improved Xf detection at the strain level, which is crucial for accurate disease management decisions in areas where multiple crops are grown in close proximity.
Review Publications
Backus, E.A., Shugart, H. 2024. The vector regulation hypothesis: Dynamic competition between pathogen and vector behaviors constrains Xylella fastidiosa biofilm development in sharpshooter foreguts. Applied and Environmental Microbiology. 90. Article e01102-24. https://doi.org/10.1128/aem.01102-24.
Wallis, C.M., Baumgartner, K. 2025. Fatty acid methyl ester (FAME) profiling for species-specific characterization and detection of fungal pathogens that cause tree and grapevine truck diseases. Mycologia. 117(2):319-330. https://doi.org/10.1080/00275514.2024.2439753.
Burbank, L.P., Strickland, J.A. 2025. Genome sequences of chitinase-producing Streptomyces, Bacillus, and Paenibacillus bacterial isolates from vine mealybugs (Planococcus ficus). Microbiology Resource Announcements. 14. Article e01281-24. https://doi.org/10.1128/mra.01281-24.
Aguin-Pombo, D., Boavida, C., Valdiviesso, T., Trindade, C., Backus, E.A., Mateus, C. 2024. Empoasca fabalis DeLong (Hemiptera: Cicadellidae) in European sweet potatoes: Records, leaf damage, and Auchenorrhyncha insights. Phytoparasitica. 52. Article 66. https://doi.org/10.1007/s12600-024-01176-0.
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.
Viravathana, P., Burbank, L.P., Jablonska, B., Sun, Q., Roper, M.C. 2024. A membrane localized RTX-like protein mediates physiochemical properties of the Pantoea stewartii subsp. Stewartia cell envelope that impact surface adhesion, cell surface hydrophobicity and plant colonization. BMC Microbiology. 24. Article 369. https://doi.org/10.1186/s12866-024-03516-w.
Sisterson, M.S., Uchima, S.Y. 2025. Effects of soil-applied imidacloprid on behavior of Plannococcus ficus. Journal of Economic Entomology. 118(3):1215-1224. https://doi.org/10.1093/jee/toaf077.
Clement, R.A., Lee, H., Manoukis, N.C., Pacheco, Y.M., Ross, F., Sisterson, M.S., Owen, C.L. 2025. Addressing biological invasions in agriculture with big data in an informatics age. Agriculture. 15(11):1157. https://doi.org/10.3390/agriculture15111157.
Peng, H., Zhai, Y. 2025. Grapevine CYP734A15 is a brassinosteroid-inactivating cytochrome P450 enzyme. Biochemical and Biophysical Research Communications. 775. Article 152128. https://doi.org/10.1016/j.bbrc.2025.152128.