Plant Molecular Biology Reporter

, Volume 37, Issue 5–6, pp 413–420 | Cite as

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

  • Abozar GhorbaniEmail author
  • Ahmad Tahmasebi
  • Keramatollah Izadpanah
  • Alireza Afsharifar
  • Ralf G. Dietzgen
Original Paper


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.


Alternative splicing Maize Nucleorhabdovirus Protein network Response to pathogens 



AG was supported by a fellowship from Shiraz University and Iran National Foundation of Elites. Supported also by the Queensland Department of Agriculture and Fisheries and the University of Queensland through the Queensland Alliance for Agriculture and Food Innovation.

Compliance with Ethical Standards

The manuscript has not been submitted in other Journal. This research was financial supported by Shiraz University, Iran. AG, AT, KI, RD and AA designed the study; AG performed the experiments, AG and AT analyzed the data, AG drafted the manuscript, all authors edited and approved the final version of the manuscripts.

Supplementary material

11105_2019_1169_MOESM1_ESM.xlsx (45 kb)
Supplementary table 1 Complete list of genes that were affected by alternative splicing events in MIMV-infected maize. Gene ontology terms for molecular function (F), biological processes (P) and cellular component (C) are shown. (XLSX 45 kb)
11105_2019_1169_Fig4_ESM.png (1 mb)
Supplementary figure 1

Venn diagram showing the number and percentage of genes that were affected by AS events in MIMV-infection and uninfected maize. (PNG 1056 kb)

11105_2019_1169_MOESM2_ESM.tif (24.5 mb)
High Resolution Image (TIF 25065 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Abozar Ghorbani
    • 1
    • 2
    Email author
  • Ahmad Tahmasebi
    • 3
  • Keramatollah Izadpanah
    • 1
  • Alireza Afsharifar
    • 1
  • Ralf G. Dietzgen
    • 2
  1. 1.Plant Virology Research Center, College of AgricultureShiraz UniversityShirazIran
  2. 2.Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandSt. LuciaAustralia
  3. 3.Biotechnology Institute, College of AgricultureShiraz UniversityShirazIran

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