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

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

JOURNAL=Frontiers in Genetics

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2016.00159

DOI=10.3389/fgene.2016.00159

ISSN=1664-8021

ABSTRACT=<p><italic>Potato virus Y</italic> has emerged as a threatening problem in all potato growing areas around the globe. <italic>PVY</italic> reduces the yield and quality of potato cultivars. During the last 30 years, significant genetic changes in <italic>PVY</italic> 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 <italic>PVY</italic> genome. The <italic>PVY</italic> genome is approximately 9 thousand nucleotides, which transcribes the following 6 genes:<italic>CI, NIa, NIb-Pro, HC-Pro, CP, and VPg</italic>. A total of 343 mature miRNAs were retrieved from the miRBase database and were examined for their target sequences in <italic>PVY</italic> 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 <italic>PVY</italic> genome at 151 different sites. Moreover, only 36 miRNAs potentially targeted the <italic>PVY</italic> genome at 101 loci. The <italic>CI</italic> gene of the <italic>PVY</italic> 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 <italic>CI, NIa, NIb-Pro, HC-Pro, CP</italic>, and <italic>VPg</italic> genes of <italic>PVY</italic>. The predicted miRNAs can be used for the development of <italic>PVY</italic>-resistant potato crops in the future.</p>