Recombinant variants of cotton leaf curl Multan virus is associated with the breakdown of leaf curl resistance in cotton in northwestern India.

Cotton leaf curl disease (CLCuD), caused by a begomovirus species complex, is a major constraint to cotton (Gossypium hirsutum) production in northwestern India. During 2006 to 2010, a surveillance was conducted to monitor the spread of CLCuD in Haryana and Rajasthan. Six different field symptoms, upward curling, downward curling, enation, vein thickening, severe curling and mild curling were documented. Six isolates associated with these symptom types were tested positive in PCR to cotton leaf curl Rajasthan virus. The isolates were successfully transmitted through whitefly (Bemisia tabaci) at the rate up to 73.3% to the resistant cotton cultivar, RS2013. All these six isolates were further characterised based on the complete nucleotide sequences of the viral genome and the associated betasatellites. These virus isolates shared highest sequence identity (86-99%) with the cotton leaf curl Multan virus (CLCuMuV) and the associated betasatellites also shared highest sequence identity (78-92%) with cotton leaf curl Multan betasatellite (CLCuMuB). Based on the sequence identity and phylogenetic analysis of the viral genome and betasatellite, these isolates were identified as variants of CLCuMuV. Recombination analysis revealed significant recombination events in these isolates with the other cotton infecting begomoviruses. The isolate, Mo-Raj-2 has been identified as a resistant breaking strain having a major recombination in the coding regions of both viral genome and betasatellite. The natural occurrence of disease symptoms, transmission of the virus isolates through whitefly and complete genome analysis of the virus revealed the association of recombinant variant of CLCuMuV with the breakdown of resistance in cotton in Rajasthan and Haryana, the major cotton belt of India. © Indian Virological Society 2020.