Development of a Precise and Sensitive Loop‐Mediated Isothermal Amplification ( LAMP ) Assay for the Detection of Ganoderma lucidum , the Causative Agent of Basal Stem Rot in Coconut

Abstract

Basal stem rot, also known as Ganoderma wilt, ranks among the most destructive and fatal diseases impacting coconut palm productivity in India. Early, accurate detection, followed by appropriate interventions, is essential to prevent indiscriminate fungicide use and effectively control basal stem rot epidemics. Though sensitive, DNA‐based PCR methods are not amenable to on‐site diagnosis as they require laboratory infrastructure. In recent years, interest has been growing in developing alternative techniques, for example, DNA‐based point‐of‐care (POC) diagnostics. We developed loop‐mediated isothermal amplification (LAMP) assays based on visual fluorescence detection and real‐time LAMP for specific, highly sensitive, and rapid detection of Ganoderma lucidum by targeting the small subunit ribosomal RNA gene. The detection threshold for the assay developed was less than 10 min. The LAMP assay was specific for G. lucidum in coconut, and no cross‐reaction was observed with Phytophthora palmivora or Trichoderma harzianum . This technique was also applied to detect G. lucidum in infected coconut tissue samples. This method can rapidly detect G. lucidum and has great potential for application in low‐resource settings.