Real-time quantitative PCR assay for the quantification of virus and satellites causing leaf curl disease in cotton in Pakistan

Cotton leaf curl disease (CLCuD) is the major biotic constraint to cotton production in Pakistan and northwestern India. The disease is caused by monopartite begomoviruses in association with a specific DNA satellite, Cotton leaf curl Multan betasatellite. The virus-betasatellite complex is also frequently associated with another DNA satellite-like molecule; an alphasatellite. A quantitative real-time PCR (qPCR) assay to detect all three components of the monopartite begomovirus/betasatellite/alphasatellite complex which causes CLCuD was established. This was used to investigate the relationship between symptoms and virus/satellite titre. Not surprisingly the analysis showed that, overall, there was a reasonable correlation between symptom severity and virus/satellite titre − more severe symptoms usually being associated with more virus/satellite. However, cotton plants were identified with no or very mild symptoms with relatively high virus/satellite titres and plants with severe symptoms but relatively low virus/satellite titres. This may be attributed to the resistance/susceptibility of the cotton variety − tolerant plants being able to sustain a relatively high virus/satellite titre whilst exhibiting mild symptoms. The usefulness of this qPCR procedure in the screening for resistance in cotton against CLCuD is discussed.