A novel and efficient method for identifying cotton leafroll dwarf virus infection in upland cotton (Gossypium hirsutum)

We report the development of a novel and more efficient, rapid, cost‐effective and simple technique than current PCR‐based identification methods for screening cotton (Gossypium hirsutum) plants for the presence of cotton leafroll dwarf virus (CLRDV). This protocol takes advantage of the PACE (PCR Allele Competitive Extension) system and uses PCR amplification of cDNA, coupled with sequence‐specific fluorescent probes to differentiate between infected and uninfected cotton plants. This procedure has the potential for application in detection of other RNA viruses in a variety of other crops, by using primers specific for the RNA‐dependent RNA polymerase (RdRP) gene and a widely conserved housekeeping gene in the host organism; in this case, the G. hirsutum polyubiquitin gene (GhUB).