RESEARCH ARTICLES CURRENT SCIENCE, VOL. 121, NO. 10, 25 NOVEMBER 2021 1316 *For correspondence. (e-mail: naveed.shahid@ue.edu.pk) In silico plum pox virus silencing via host-retrieved miRNAs in peach plant Muhammad Naveed Shahid 1, *, Syeda Shehnaz 1 , Muhammad Shehzad Iqbal 2,5 , Aneela Shabbeer 1 , Adil Jamal 3 and Sana Khalid 4 1 Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan 2 Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan 3 Science and Research College of Nursing, Ummal Qura University, Makkah, Kingdom of Saudi Arabia 4 Department of Botany, Lahore College for Woman University, Lahore, Pakistan 5 Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan Peach (Prunus persica) is a deciduous, edible, stone fruit producing plant, belonging to the family Rosaceae. The plant is prone to various pathogens and one of them is the plum pox virus (PPV). This is a lethal virus of peach plant causing pox disease of plum. Its attack results in 83%–100% yield loss in highly susceptible varieties of peach plant. The complete genome of PPV is 9791 base pairs with positive-sense single strand. The full-length genome of PPV encodes a large poly- protein initially, which cleaves proteolytically into ten mature proteins – coat protein, helper component pro- teinase, P1, P3, viral genome-linked protein, 6K1, 6K2, cylindrical inclusion protein, cylindrical inclusion pro- tein b and NIa-pro-proteins. The objective of this study is to identify such sites in the PPV genome which can be targeted by PPV-derived miRNAs through target prediction computational tools/algorithms. A total of 214 mature miRNAs were chosen from the miRNA data- base to check their complementarity with the PPV genome. Minimum free energy, folding energy, seed pairing, target-site accessibility, pattern recognition and multiple target sites were the parameters considered for target prediction algorithms. Two out of 214 miRNAs were predicted as potential against plum pox virus by three of four tools used for target prediction. Thus, the results encourage generating transgenic, PPV-resi- stant peach plants by expression of predicted miRNAs. Keywords: miRNAs, peach plant, plum pox virus, yield loss, target prediction algorithms. PEACH (Prunus persica) is a temperate, deciduous, edi- ble, stone fruit-producing plant. Prunus is an important genus in the family Rosaceae which comprises of differ- ent fruit varieties 1 . Peach is an important commercial and agronomical plant as it provides vitamins, fibres, antioxi- dants and minerals for a healthy diet (http://faostat. fao.org/). The genus Prunus is infected by various viral attacks and one of the most devastating among them is the plum pox disease (PPV), also known as pox disease of plum. This disease is transmitted in stone fruits through PPV, a member of the family Potyvirideae 2 . PPV is a sin- gle-stranded, positive-sense, filamentous virus. Its genome size is estimated as 9.9 kb and is 750 nm long 3 . Its trans- mission results in premature fruit drop and decreased fruit quality, resulting in agronomic and economic loss 4 . The vi- rus attack also results in 83%–100% yield loss in peach production 5,6 . Numerous strategies have been developed to control the multiplication of the virus in peach plants. Breeding programmes and genetic engineering approaches have also been used to develop resistance against PPV. These strat- egies do not provide complete information for resistance due to the specific nature of virus strain, long juvenile seedling period 5 and unnecessary degradation of RNA- silencing pathways 7–9 . Computational strategy is another technique to control this disease. Plants respond to dis- tinctive abiotic stress and viral infection. These are con- trolled both at the transcriptional and post-transcriptional levels. At the post-transcriptional level, quality controller miRNAs are utilized 10 . miRNAs are small, 21–22 nucleo- tides, endogenous and non-coding RNAs that regulate gene expression in plants and animals through their pro- teolytical activities. They bind to their complementary sequences in target regions of the viral genome and re- press the transcription or cleave the transcript 11 . Peach plant has 180 mature miRNAs and 214 precursors (miRNA database). To identify miRNAs in peach plants which have the potential to inhibit infection through mRNA cleavage, five target prediction algorithms were used. The aim of the present study is to identify the best host-retrieved potential miRNAs that can develop resis- tance against PPV using computational techniques. The predicted miRNAs can be a source to inhibit infection by cleaving the mRNA. Materials and methods Mature miRNAs of Prunus persica In many living organisms miRNAs are endogenous, non- coding and small sequences of RNA that regulate gene