Genomes-based loop-mediated isothermal amplification assay for rapid and specific detection of walnut pathogen Xanthomonas arboricola pv. juglandis

Xanthomonas arboricola pv. juglandis (Xaj) causes walnut bacterial blight (WBB), significantly impacting walnut (Juglans regia L.) production. This work aimed to develop a loop-mediated isothermal amplification (LAMP) assay for the rapid, sensitive, and specific detection of Xaj. Utilizing next-generation sequencing data, we identified a unique 524 nt region in Xaj and designed three primer sets. The Xaj_K13041 primer set demonstrated 100% specificity, detecting Xaj DNA at concentrations as low as 0.1 pg/µL (2 copies per tube) within 40 min, outperforming existing PCR methods. The LAMP assay was validated on DNA from infected walnut fruits, showing good performance compared to established methods and effective detection for future field conditions. The assay’s reliability, speed and low cost make it suitable for phytosanitary services. This work presents the first LAMP-based assay for Xaj detection, providing a valuable tool for early and accurate identification, essential for managing WBB and ensuring stable walnut crop production.