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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Publications at this Location » Publication #412620
Research Project: Basic and Applied Approaches for Pest Management in Vegetable Crops

Location: Vegetable Research

Title: Loop-mediated Isothermal Amplification (LAMP) assay for robust and reliable detection of Xanthomonas axonopodis pv. vasculorum

Author
item MARABELLA, MITCHELL - University Of Hawaii
item HOWARD, JULIA - University Of Hawaii
item BHANDARI, SANTOSH - University Of Hawaii
item DO, SALLY - University Of Hawaii
item MONTOYA-PIMOLWATANA, MAYA - University Of Hawaii
item DOU, YICHEN - University Of Hawaii
item DOBHAL, SHEFALI - University Of Hawaii
item ARIZALA, DARIO - University Of Hawaii
item MONTESINOS, STEFANIA - University Of Hawaii
item Andreason, Sharon
item OCHOA-CORONA, FRANCISCO - Oklahoma State University
item BINGHAM, JON-PAUL - University Of Hawaii
item ODANI, JENEE - University Of Hawaii
item JENKINS, DANIEL - University Of Hawaii
item MA, LI MARIA - Oklahoma State University
item FLETCHER, JACQUELINE - Oklahoma State University
item STACK, JAMES - Kansas State University
item ARIF, MOHAMMAD - University Of Hawaii

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: The bacterial plant pathogen Xanthomonas axonopodis pv. vasculorum, which causes gumming disease in sugarcane, is a significant threat to global sugar production. Despite its economic implications, a field-deployable diagnostic tool is not available. In this study, a field-ready diagnostic method was developed, and its specificity and sensitivity were validated by extensive testing. This new tool will be of interest to plant diagnosticians, sugarcane growers, and the scientific community.

Technical Abstract: Xanthomonas axonopodis pv. vasculorum (Xav), the causative agent of sugarcane gumming disease, represents a significant threat to global sugarcane production due to its systemic and destructive nature. Despite the economic implications, a field-deployable, Xav-specific diagnostic tool has not been developed. This study developed a loop-mediated isothermal amplification (LAMP) assay targeting the pelL gene, unique to Xav strains, as a rapid and precise diagnostic assay. The selection of the pelL gene was informed by comprehensive in silico analyses of Xav genomes and related Xanthomonas species and other close relatives. Validation against the NCBI GenBank database and internally sequenced genomes confirmed the gene's exclusivity to Xav. Subsequent primers for both endpoint PCR and LAMP assays were designed using pelL gene region. The LAMP assay underwent extensive testing against inclusivity and exclusivity panels. The exclusivity panel, comprising 93 strains from related species, other bacterial genera, and host genomes, demonstrated the assay's specificity with no false positives or negatives. The assay exhibited a detection limit of 1 pg, and its effectiveness was unimpeded by crude pre-DNA interference from the host plant, sugarcane. Further validation through multi-device and multi-operator testing underscored the assay's 100% reproducibility and robustness. Application to infected plant samples resulted in the successful detection of all infected specimens, without any false positives or negatives. This novel LAMP assay is a highly accurate and reliable tool for Xav detection, with promising applications in routine diagnostics, biosecurity measures, microbial forensics, and epidemiological research.