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.
Highlights
Small RNAs are small, mobile noncoding RNA molecules that regulate gene expression and inhibit translation
Louise exhibits an infection type (IT) of 2–3 while Penawawa has miRNAs in Wheat Stripe-Rust Pathosystem a rating of 6–8 when rated based on a 0–9 scale (Carter et al, 2009)
Despite the widespread use of high-temperature adult plant resistance (HTAP) resistance in the field, little is known about its mechanism for disease resistance
Summary
Small RNAs (sRNAs) are small, mobile noncoding RNA molecules that regulate gene expression and inhibit translation. The RNA silencing mediated by microRNAs. miRNAs in Wheat Stripe-Rust Pathosystem helps regulate myriad physiological processes such as plant growth, development, reproduction, and stress responses (Kulcheski et al, 2011; Parent et al, 2012; Qiu et al, 2016). Upon infection with viruses and Pseudomonas syringae DC3000, levels of miR482 were reduced, with a consequent increase in NBS-LRR genes and resistance to disease (Shivaprasad et al, 2012) These genes serve as phasiRNA-generating loci that produce secondary siRNAs involved in suppression of many other NLR genes (Zhai et al, 2011; Li et al, 2012; Fei et al, 2013; Fei et al, 2015). A target for miRNA tae-miR9664 was confirmed using 5’ RNA Ligase-Mediated Rapid Amplification of cDNA Ends (5’RLM-RACE), and the corresponding target was found to be differentially expressed between the two cultivars tested
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