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. 2022 Aug 17;14(8):1803.
doi: 10.3390/v14081803.

Differential Expression of Genes between a Tolerant and a Susceptible Maize Line in Response to a Sugarcane Mosaic Virus Infection

Gustavo Rodríguez-Gómez  1 , Pablo Vargas-Mejía  1 , Laura Silva-Rosales  1
Affiliations

Differential Expression of Genes between a Tolerant and a Susceptible Maize Line in Response to a Sugarcane Mosaic Virus Infection

Gustavo Rodríguez-Gómez et al. Viruses. .

Abstract

To uncover novel genes associated with the Sugarcane mosaic virus (SCMV) response, we used RNA-Seq data to analyze differentially expressed genes (DEGs) and transcript expression pattern clusters between a tolerant/resistant (CI-RL1) and a susceptible (B73) line, in addition to the F1 progeny (CI-RL1xB73). A Gene Ontology (GO) enrichment of DEGs led us to propose three genes possibly associated with the CI-RL1 response: a heat shock 90-2 protein and two ABC transporters. Through a clustering analysis of the transcript expression patterns (CTEPs), we identified two genes putatively involved in viral systemic spread: the maize homologs to the PIEZO channel (ZmPiezo) and to the Potyvirus VPg Interacting Protein 1 (ZmPVIP1). We also observed the complex behavior of the maize eukaryotic factors ZmeIF4E and Zm-elfa (involved in translation), homologs to eIF4E and eEF1α in A. thaliana. Together, the DEG and CTEPs results lead us to suggest that the tolerant/resistant CI-RL1 response to the SCMV encompasses the action of diverse genes and, for the first time, that maize translation factors are associated with viral interaction.

Keywords: ABC transporter; Hsp90-2; RNAseq; SCMV; ZmPVIP1; ZmPiezo; eEF1α.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Symptom development and Sugarcane mosaic virus (SCMV) detection in three maize lines inoculated with SCMV isolated Veracruz 1 (SCMV-Ver1) in leaves at the same phenological stage: (A) B73 susceptible-symptomatic line, with chlorotic mosaic symptoms, and CI-RL1 and F1, without evident symptoms; (B) SCMV-Ver1-infected plants (CI-RL1, F1, and B73 from left to right). (C) Presence of the SCMV Coat Protein (CP)-cistron in three plants randomly selected from each line.
Figure 2
Figure 2
Cluster groups of transcript expression patterns (non-DEGs) in three maize lines: B73, F1 (B73 × CI-RL), and CI-RL1. (A) Group 1, with C0 to C2 clusters having high expression levels for CI-RL1; Group 2, including C3 and C4 clusters with low expression levels for CI-RL1. (B) Venn diagram of 43 selected candidate genes present in one or more expression pattern clusters. * Set of sixteen candidate genes found in only one group (Group 1 or 2).
Figure 3
Figure 3
Venn diagrams of differentially expressed genes (DEGs), showing B73 susceptible (blue), F1 progeny (red), and CI-RL1 tolerant lines (green). (A) All DEGs (p-values ≤ 0.01); (B) upregulated and (C) downregulated DEGs.
Figure 4
Figure 4
Functional enrichment network of cellular components (CCs) of differentially expressed genes (DEGs) in B73, CI-RL1, and F1 progeny. (A) Enrichment network of upregulated (B) and downregulated genes. Nodes represent an enriched CC ontology term, and edges represent the relationships between these ontologies. CC shared terms correspond to the following: B73 alone (blue); shared between B73 and F1 (orange); shared between all lines (purple); shared between CI-RL1 and F1 (pink); and those corresponding to CI-RL1 alone (green).
Figure 5
Figure 5
Bar plot of functionally up- (A) and downregulated (B) genes of the enriched biological processes (BPs) for B73 susceptible (blue), F1 progeny, (red), and CI-RL1 (in green) lines. (A) The x-axis represents the percentage of background annotated genes for each BP term.
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References

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Grants and funding

G.R. and P.V. were supported by the Consejo Nacional de Ciencia y Tecnología postgraduate scholarships (CVUs 420714 and 1024179). This research was funded through PlanTecc (IP-240 and IP-231) and Cinvestav funds, in addition to personal funding by L.S.-R.
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