Geminiviruses are economically important plant pathogens and are characterized by twinned isometric particles containing single-stranded (ss)DNA genomes of 2.5-3.0 kb  that replicate through double-stranded (ds)DNA intermediates by a rolling-circle mechanism . The family Geminiviridae is divided into four genera, (Begomovirus, Mastrevirus, Curtovirus and Topocuvirus) that encompass viruses that differ in genome organization as well as their insect vectors. Begomoviruses are transmitted by the whitefly Bemisia tabaci and have either monopartite or bipartite genomes. Monopartite begomoviruses are often associated with circular, ssDNA satellites that are collectively referred to as betasatellites (formerly known as DNA β). Betasatellites have recently been found to be associated with some bipartite begomoviruses and are required by some of their helper begomoviruses to induce bona fide disease symptoms in plants. Numerous economically important diseases and even the earliest recorded plant viral disease are now known to be caused by begomovirus/betasatellite complexes [3, 4].
Betasatellites are widespread in the Old World, where monopartite begomoviruses are known to occur. Numerous distinct betasatellites, from various economically important hosts and diverse locations, have been cloned and have been found in most cases to contribute significantly to disease symptoms . Analysis of betasatellite sequences reveals a highly conserved organization consisting of an adenine-rich region and a region of sequence highly conserved between all betasatellites (known as the satellite conserved region [SCR]). The SCR contains a potential hairpin structure with the loop sequence TAA/GTATTAC that has similarity to the origins of replication of geminiviruses and nanoviruses. Betasatellites encode only a single gene, known as the bC1, located on the complementary-sense strand, is conserved in position and size in all betasatellites [6, 7].
Chilli leaf curl betasatellite (ChLCB) is associated with chilli leaf curl disease (ChLCuD), a significant constrain to chilli production across the Indian subcontinent [8, 9]. Saeed et al.  demonstrated that tobacco plants transformed with the βC1 of Cotton leaf curl Multan betasatellite (CLCuMB) under the control of the Cauliflower mosaic virus 35S promoter, or with a dimer of CLCuMB, exhibited severe disease-like phenotypes, while plants transformed with a mutated version of the βC1 appeared normal. Qazi et al.  showed that expression of CLCuMB βC1 from a Potato virus X vector induced symptoms typical of cotton leaf curl disease (CLCuD) in the absence of the helper begomovirus. These results demonstrated that CLCuMB βC1 is the major determinant of symptoms of the CLCuD complex .
The interactions between plants and viruses are complex and involve several types of responses that may or may not cause disease in the host . In compatible interactions, the invading virus is able to infect and replicate within a susceptible plant to cause disease. Alternatively, the host may trigger innate immunity mechanisms that restrict virus movement and prevent disease onset. In both situations, viral pathogens severely disturb plant growth and development, due to their effect on cellular metabolism . Viral infection produces a plethora of symptoms derived from biochemical and metabolic changes in cells, tissues and even in the whole plants which are susceptible and hypersensitive resistant hosts. Huang et al.  and Sui et al.  demonstrated that plant viruses cause severe impact on host gene expression and protein activity due to the activation of a set of genes and the inactivation of others. The gene expression profile in the host plant changes according to the timing and localization of the infection, as the virus spreads from cell to cell away from the site of inoculation [14, 15].
The present studies are aimed at identifying host genes and pathways that are induced by ChLCB βC1. This may be achieved using differential RNA display technology. This technique is based on "differential display reverse transcriptase polymerase chain reaction" (DDRT-PCR), first described by Liang and Pardee . This method has the advantage of technical simplicity, a lower bias against rare messages and a requirement of only small quantities of starting mRNA. Several modifications of the original technique have been reported with some solutions to the key problems identified by some authors . Stress responses have been studied using DDRT-PCR in C. elegans and S. cerevisiae [18–20]. DDRT-PCR has been applied in many laboratories to identify genes involved in signal cascades.
The identification of host genes affected by ChLCB βC1 may provide useful insights into virus-host interactions and provide targets for novel control strategies. By differential display analysis we have identified N. tabacum genes differentially regulated in response to the transient expression of ChLCB βC1 protein. Subsequently the effects of βC1 expression on each gene identified were verified by quantitative real time PCR analysis.