Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants.

Muhammad S Iqbal,Idrees A Nasir,Arfan Ali,Bushra Tabassum,Bushra Rashid,Muhammad N Hafeez,Javed I Wattoo,Muhammad N Sharif

doi:10.3389/fgene.2016.00159

Abstract

Potato virus Y has emerged as a threatening problem in all potato growing areas around the globe. PVY reduces the yield and quality of potato cultivars. During the last 30 years, significant genetic changes in PVY strains have been observed with an increased incidence associated with crop damage. In the current study, computational approaches were applied to predict Potato derived miRNA targets in the PVY genome. The PVY genome is approximately 9 thousand nucleotides, which transcribes the following 6 genes:CI, NIa, NIb-Pro, HC-Pro, CP, and VPg. A total of 343 mature miRNAs were retrieved from the miRBase database and were examined for their target sequences in PVY genes using the minimum free energy (mfe), minimum folding energy, sequence complementarity and mRNA-miRNA hybridization approaches. The identified potato miRNAs against viral mRNA targets have antiviral activities, leading to translational inhibition by mRNA cleavage and/or mRNA blockage. We found 86 miRNAs targeting the PVY genome at 151 different sites. Moreover, only 36 miRNAs potentially targeted the PVY genome at 101 loci. The CI gene of the PVY genome was targeted by 32 miRNAs followed by the complementarity of 26, 19, 18, 16, and 13 miRNAs. Most importantly, we found 5 miRNAs (miR160a-5p, miR7997b, miR166c-3p, miR399h, and miR5303d) that could target the CI, NIa, NIb-Pro, HC-Pro, CP, and VPg genes of PVY. The predicted miRNAs can be used for the development of PVY-resistant potato crops in the future.

Highlights

Potato Virus Y (PVY) has emerged as one of the most alarming pathogens in potatoes around the world; it affects the yield and quality of potatoes by inducing ringspot disease (Lorenzen et al, 2006; Ali et al, 2016)
Open Reading Frame (ORF) and nucleotide distribution of PVY genome were calculated through CLC Genomics Workbench v8
MiRNA-mRNA attachment is less complicated than it is in animals and it mostly depends on a higher quality match between the target sequence and the miRNA than it does in animals (Witkos et al, 2011)

Summary

Introduction

PVY has emerged as one of the most alarming pathogens in potatoes around the world; it affects the yield and quality of potatoes by inducing ringspot disease (Lorenzen et al, 2006; Ali et al, 2016). PVY can be transmitted via vegetative propagation, seed tubers and aphids (Robert et al, 2000). Biotechnology has opened new horizons to combat PVY by introducing transgenic varieties of Solanum tuberosum (McCue et al, 2012). The infection cycle of a potyvirus begins when the viral particle enters the cell via a wound or during feeding by its vector aphid (Filipowicz and Hohn, 1996; Bailey-Serres, 1999). PVY is a positive sense, single-stranded RNA virus, belong to the Potyviridae family and genus potyvirus. The virus releases its RNA into the cell cytoplasm, and this ssRNA uses

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