Gene network modeling and pathway analysis of maize transcriptomes in response to Maize Iranian mosaic virus

Abstract

Abstract Maize Iranian mosaic virus (MIMV, family Rhabdoviridae) is one of the factors limiting cereal production in Iran. MIMV can affect maize transcriptome, alternative splicing, circular RNAs and miRNA profiles during infection and active biological pathways in the maize cells. In the present study, we sought to find critical genes and key pathways involved in MIMV infection and analyzed gene networks, pathways and promoters using transcriptome data. We determined the hub genes involved in pathways related to the proteasome and ubiquitin. These hub genes played a key role in the response to MIMV infection. Gene ontology (GO) and pathway analysis showed that metabolic processes are most affected in MIMV infection. In addition, the results showed the important role of the cellular endoplasmic reticulum in MIMV infection. Network cluster analysis confirmed the result of GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Potential miRNAs were identified as target hub genes using the psRNATarget server. The discovered miRNAs belonged to miR166, miR167, miR169, miR395, miR399, miR408 and miR482 families, which are involved in various pathogenicity or resistance processes against MIMV or other viruses. The results of this study provide a list of hub genes, important pathways and new insights for future development of virus-resistant transgenic crops and clarify the basic mechanism of plant response. They may also be a source of information on the role of key genes and the pathway controlling the responses.