Development and application of rapid molecular assays for cotton pathology.

Abstract

Several endemic co on diseases cause yield and economic losses in many Australian co on growing regions. Exotic diseases also present significant biosecurity risks. Traditional mycology methods can take days to weeks for a diagnosis and standard PCR methods for viral diseases can still take 1-2 days to complete. Rapid diagnostics such as new Loop-mediated isothermal amplification (LAMP) provide an opportunity to provide diagnostics within 1-2 hours from sampling symptomatic issue. This can provide a significant me saving in the lab and greatly reduce turnaround me to advise affected growers, leading to better management outcomes.

We have targeted pathogens that are either emerging, pose a biosecurity threat or may be difficult to distinguish from other diseases by symptoms alone. We have developed LAMP assays for endemic diseases co on bunchy top virus 1 and 2 (CBTV-1, -2), Eutypella sp., Fusarium Fov, and Ramularia pseudoglycines affecting co on, We have also developed diagnostics for the exotic co on leafroll dwarf virus (CLRDV) for incursion preparedness.

These LAMP assays are already proving useful for rapid turnaround diagnostics for CBT samples which increased in incidence in many areas in the 2022-23 season. We are beginning to apply the Eutypella LAMP to search for alternative hosts and pathogen reservoirs in the environment. The Ramularia LAMP was used to confirm infections in WA cotton, not reported in that region for several decades.