Genome-Wide Analysis of Alternative Splicing in Zea mays during Maize Iranian Mosaic Virus Infection

Maize Iranian mosaic virus (MIMV) infects several gramineous plants and is an economically important nucleorhabdovirus in Iran. Maize responds to MIMV infection at the transcriptional level. Alternative splicing (AS) is a mechanism that generates multiple mRNAs from a single pre-mRNA, often encoding protein isoforms with functional differences. We carried out genome-wide analysis of AS responses to MIMV in maize seedlings and identified genes involved in this molecular response. The AS events we investigated included skipped exons, alternative 3′ splice site, alternative 5′ splice site, mutually exclusive exons, and retained introns. In total 10,881 maize genes showed AS, of which 601 genes were involved in response to MIMV-infection and 186 were found only in uninfected maize. AS was identified in some of the genes that are involved in disease resistance or pathogenicity pathways. We demonstrated that in MIMV-infects maize, host genes that are involved in symptom development, virus multiplication, resistance to pathogens and host-pathogen interaction are affected by AS mechanism. Gene network analysis showed that ten genes represent the hubs for the protein network in maize and that they are involved in response to pathogen attack and include 26S proteasome, 14–3-3-like protein A, Rop family, mitogen-activated protein kinase, ubiquitin and serine/threonine-protein kinases. In conclusion, we showed that AS occurs as a transcriptional regulatory mechanism in maize response to MIMV infection and we identified genes that have the key roles in pathogenicity pathways that were differentially spliced in infected seedlings.