Ramachandran Sowmya R, Mueth Nicholas A, Zheng Ping, Hulbert Scot H
Department of Plant Pathology, Washington State University, Pullman, WA, United States.
Department of Horticulture, Washington State University, Pullman, WA, United States.
Front Plant Sci. 2020 Jan 10;10:1574. doi: 10.3389/fpls.2019.01574. eCollection 2019.
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 ( f. sp. ), 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.
微小RNA是在真核生物中调控基因表达的小RNA。在本研究中，我们分析了两个对条锈病感染表现出不同反应的小麦品种的小RNA图谱：一个易感品种，另一个是部分抗性品种。利用从感染条锈病菌（f. sp.）的两个小麦品种中制备的小RNA文库，我们鉴定出182个先前已知的miRNA、91个已知miRNA的变体以及163个候选的新型小麦miRNA。已知的miRNA位点通常在小麦的所有三个亚基因组中都有拷贝，而新型miRNA位点往往特定于单个亚基因组。对差异表达的微小RNA进行的DESeq2分析揭示了23个表现出品种特异性差异的miRNA。TA078/miR399b在感染反应中表现出品种特异性的差异调控。使用不同的靶标预测算法，预测有145个miRNA靶向小麦基因，而有69个miRNA靶向真菌基因。我们还证实了TA078/miR399b和tae-miR9664及其靶标基因在不同处理中的相互表达，为感染期间miRNA介导的调控提供了证据。已知和新型miRNA均被预测可靶向真菌基因，这表明存在基因表达的跨物种调控。总体而言，本研究为当前的小麦miRNA文库做出了贡献，并提供了关于miRNA在小麦-条锈病病理系统中尚未明确的作用的新信息。
