Abstract
Among biotic stresses afflicting potato plants, viruses are the most damaging and are
responsible for large economic losses worldwide. Co-infections with multiple viruses
are common in potato, with an enhanced disease impact being observed in affected
plants. RNA interference (RNAi) provides an applied methodology to selectively
reduce the expression of targeted genes through the expression of sequence-specific
short interfering RNAs (siRNAs). This silencing mechanism can be implemented to
induce resistance against multiple viruses in transgenic plants through the endogenous
delivery of siRNA cassettes. The current study was aimed to identify the efficient
siRNA execution sites in dominating viral genomes to simultaneously target both DNA
and RNA viruses in potato. To achieve this objective, we followed a computational
approach to identify the viral silencing targets by comparative pairwise sequence
analysis of different isolates of Potato leafroll virus (PLRV; + single-stranded (ss)
RNA virus) and Tomato leaf curl New Delhi virus (ToLCNDV; ssDNA virus). The
identified consensus sequences [300bp of PLRV-coat protein (CP); 180bp of
ToLCNDV-precoat protein (AV2)] were further used as template sequences to predict
the likely siRNAs execution sites and to characterize their putative thermodynamic
attributes. The identified template sequences were computationally tested for
triggering a siRNA-mediated targeting of viral genomes and proved to be highly
efficient and site-specific. This methodology could be applied for engineering an
RNAi-mediated virus resistance in transgenic plants with commercial applications.
Amir Hameed, Shabih Fatma, Muhammad Noman, Temoor Ahmed, Javed Iqbal Wattoo. (2018) A computational approach to execute siRNA generating hotspots targeting dual DNA and RNA viral infections in potato, Asian Journal of Agriculture and Biology, Volume 6, Issue 1.
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