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Updated: Dec 29, 2025
mirMachine: A One-Stop Shop for Plant miRNA Annotation
Published on: May 1, 2021
Analysis of miRNAs in Two Wheat Cultivars Infected With Puccinia striiformis f. sp. tritici
Sowmya R Ramachandran1, Nicholas A Mueth1, Ping Zheng2
1Department of Plant Pathology, Washington State University, Pullman, WA, United States.
Abstract:
MicroRNAs are small RNAs that regulate gene expression in eukaryotes. In this study, we analyzed the small RNA profiles of two cultivars that exhibit different reactions to stripe rust infection: one susceptible, the other partially resistant. Using small RNA libraries prepared from the two wheat cultivars infected with stripe rust fungus (Puccinia striiformis f. sp. tritici), we identified 182 previously known miRNAs, 91 variants of known miRNAs, and 163 candidate novel wheat miRNAs. Known miRNA loci were usually copied in all three wheat sub-genomes, whereas novel miRNA loci were often specific to a single sub-genome. DESeq2 analysis of differentially expressed microRNAs revealed 23 miRNAs that exhibit cultivar-specific differences. TA078/miR399b showed cultivar-specific differential regulation in response to infection. Using different target prediction algorithms, 145 miRNAs were predicted to target wheat genes, while 69 miRNAs were predicted to target fungal genes. We also confirmed reciprocal expression of TA078/miR399b and tae-miR9664 and their target genes in different treatments, providing evidence for miRNA-mediated regulation during infection. Both known and novel miRNAs were predicted to target fungal genes, suggesting trans-kingdom regulation of gene expression. Overall, this study contributes to the current repository of wheat miRNAs and provides novel information on the yet-uncharacterized roles for miRNAs in the wheat-stripe rust pathosystem.
Insights
This study identifies novel microRNAs (miRNAs) in wheat, revealing their differential regulation in response to stripe rust infection and suggesting trans-kingdom regulation between wheat and fungi.
Area of Science:
- Plant molecular biology
- Genomics
- Agricultural science
Background:
- MicroRNAs (miRNAs) are crucial regulators of gene expression in eukaryotes.
- Understanding miRNA roles in plant-pathogen interactions is vital for crop improvement.
Purpose of the Study:
- To analyze small RNA profiles of wheat cultivars with varying stripe rust resistance.
- To identify and characterize differentially expressed miRNAs and their targets in the wheat-stripe rust pathosystem.
Main Methods:
- Small RNA sequencing of two wheat cultivars (susceptible and partially resistant) infected with *Puccinia striiformis*.
- Bioinformatic analysis to identify known, variant, and novel miRNAs.
- Differential expression analysis (DESeq2) and target prediction algorithms.
Main Results:
- Identified 182 known, 91 variant, and 163 novel wheat miRNAs.
- Discovered 23 differentially expressed miRNAs, including TA078/miR399b, showing cultivar-specific regulation.
- Predicted 145 wheat-targeting and 69 fungal-targeting miRNAs, with evidence of trans-kingdom regulation.
Conclusions:
- This research expands the wheat miRNA repository and highlights the significant role of miRNAs in the wheat-stripe rust interaction.
- Identified specific miRNAs involved in cultivar-specific responses and potential trans-kingdom regulatory mechanisms.
