Selection of target sequences as well as sequence identity determine the outcome of RNAi approach for resistance against cotton leaf curl geminivirus complex

Cotton leaf curl is a serious disease of cotton and several other malvaceous plant species that is transmitted by the whitefly Bemisia tabaci [1]. The disease is, at this time, endemic throughout Pakistan and western India [2,3]. Affected cotton plants exhibit a range of symptoms that include leaf curling, stunted growth and a poor yield of cotton fibre [1,4]. Additionally, affected plants may develop leaf-like outgrowths from the veins on the underside of leaves. The disease is caused by a geminivirus complex that involves several distinct begomoviruses (genus Begomovirus, family Geminiviridae) that interact with a disease-specific DNA satellite, Cotton leaf curl Multan betasatellite (CLCuMB) [3,5-7].The geminiviruses are a rapidly emerging group of plant viruses, which can be attributed to various factors, including increased insect vector populations, the presence of alternate hosts and recombination among viruses [8,9]. Geminiviruses are plant-infecting viruses with circular single-stranded (ss)DNA genomes of 2.5-5.6 kb [10]. Whitefly-transmitted geminiviruses are classified in the genus Begomovirus which encompasses many of the agriculturally most destructive geminiviruses. All begomoviruses native to the New World have bipartite genomes, with components known as DNA A and DNA B. In the Old World, although a few bipartite begomoviruses have been identified, the majority of begomoviruses have genomes consisting of a single component, homologous to the DNA A component of the bipartite viruses [11,12]. A small number of truly monopartite begomoviruses have been characterized, such as Tomato leaf curl virus and Tomato yellow leaf curl Sardinia virus (TYLCSV) [13,14]. However, the majority of monopartite begomoviruses are associated with addition ssDNA components, known as betasatellites and alphasaltellites [15]. The betasatellites are symptom modulating satellites which, in some cases, are required by their helper begomoviruses to systemically infect the plants fr