Micro RNA (miRNA) profiling of maize genotypes with differential response to Aspergillus flavus implies zma-miR156–squamosa promoter binding protein and zma-miR398/zma-miR394-F-box cominations involved in resistance mechanism

Authors: GANDHAM, PRASAD - LSU Agcenter; Rajasekaran, Kanniah - Rajah; Sickler, Christine; MOHAN, HARIKRISHNAN - LSU Agcenter; Gilbert, Matthew; BAISAKH, NIRANJAN - LSU Agcenter

Submitted to: Stress Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/5/2024
Publication Date: 5/10/2024
Citation: Gandham, P., Rajasekaran, K., Sickler, C., Mohan, H., Gilbert, M., Baisakh, N. 2024. Micro RNA (miRNA) profiling of maize genotypes with differential response to Aspergillus flavus implies zma-miR156–squamosa promoter binding protein and zma-miR398/zma-miR394-F-box cominations involved in resistance mechanism. Stress Biology. 4. Article 26. https://doi.org/10.1007/s44154-024-00158-w.
DOI: https://doi.org/10.1007/s44154-024-00158-w

Interpretive Summary: Maize is a major food crop worldwide. It is susceptible to infection by the saprophytic, opportunistic fungal pathogen Aspergillus flavus that produces the carcinogenic metabolite aflatoxin (AF). Therefore, there is a need to develop resistant varieties that can prevent the fungus infection and subsequently AF accumulation. Several previous studies have used various molecular approaches to identify genetic elements with potential roles in AF resistance, but there is a lack of research identifying the involvement of genetic elements such as microRNAs (miRNAs) at the gene regulation level in maize-A. flavus interaction. Other studies have suggested the important roles of miRNAs in regulating the expression of genes controlling the plant’s immune system. In this study, we compared the miRNA profiles of three maize lines (resistant TZAR102, moderately resistant MI82, and susceptible Va35) at different time points after A. flavus infection to investigate possible regulatory antifungal role of miRNAs. A total of 316 miRNAs including 41 previously unreported miRNAs were identified in response to the fungal infection across all three maize lines. Of these, 82 miRNAs were significantly differentially expressed with 39 miRNAs exhibiting temporal differential regulation irrespective of genotype. These miRNAs targeted 544 genes that are involved in diverse molecular functions of which the majority were regulatory genes. Coexpression network analysis identified 34 major hubs of miRNA-target gene pairs that may have potential role in resistance/susceptible response of maize to A. flavus. Specifically, three combinations were identified to be associated with resistance in varieties such TZAR102. These candidate small RNAs and target genes will be investigated further to develop varieties with improved AF resistance.

Technical Abstract: Maize (Zea mays), a major food crop worldwide, is susceptible to infection by the saprophytic fungal pathogen Aspergillus flavus that has the potential to produce the carcinogenic metabolite aflatoxin (AF). Several studies have used “-omics” approaches to identify genetic elements with potential roles in AF resistance, but there is a lack of research identifying the involvement of small RNAs such as microRNAs (miRNAs) in maize-A. flavus interaction. Previous research has suggested the important roles of miRNAs in regulating the expression of genes controlling the plant’s immune system. In this study, we compared the miRNA profiles of three maize lines (resistant TZAR102, moderately resistant MI82, and susceptible Va35) at 8 h, 3 d, and 7 d after A. flavus infection to investigate possible regulatory antifungal role of miRNAs. A total of 316 miRNAs (275 known and 41 putative novel) belonging to 115 miRNA families were identified in response to the fungal infection across all three maize lines. Of these, 82 unique miRNAs were significantly differentially expressed with 39 miRNAs exhibiting temporal differential regulation irrespective of genotype. The miRNAs targeted 544 genes (mRNAs) involved in diverse molecular functions of which majority were transcription factors (TF), such as squamosa promoter binding protein (SBP), F-box, GRAS, myeloblastosis, nuclear transcription factor Y subunit A-3, and auxin response factors. The two most notable biological processes involved in plant immunity, namely cellular responses to oxidative stress (GO:00345990) and reactive oxygen species (GO:0034614) were significantly enriched in the resistant line TZAR102. Coexpression network analysis identified 34 hubs of miRNA-mRNA pairs that may have potential role in resistance/susceptible response of maize to A. flavus. Specifically, zma-miR156- SBP and zma-miR398/zma-miR394-F-box combinations were identified in the resistance-associated modules.