Genome-Wide Study on Cultivar-Specific and Stripe Rust Responsive Mirnas in Triticum aestivum

Wheat represents approximately 30% of the world’s grain production with more than 200 million hectares under cultivation. Productivity of the crop is mainly governed by genetic and environmental factors influencing growth and development. Understanding the genetic factors that regulate these processes will help in developing varieties with better yield potential and disease resistance. A major regulartor of eukaryotic gene expression are microRNAs that control myriad of physiological processes from development to plant stress responses. Using 12 small RNA libraries prepared from two wheat cultivars infected with stripe rust fungus (Puccinia striiformis), we identified 43 previously-known miRNAs, 50 variants of known miRNAs and 93 candidate novel miRNAs. RNA sequencing revealed 20 cultivar-specific miRNAs, 6 miRNAs differentially expressed between the two cultivars and 4 miRNAs responsive to stripe rust infection. These results were validated using RT-PCR and qRT-PCR. Using different target prediction algorithms,145 miRNAs were predicted to target wheat genes, while 69 miRNAs were found to target fungal genes. Of the fungal targets a majority coded for small, secreted, cellular proteins, suggesting a trans-kingdom regulation of gene expression potentially involved in the cultivar-specific resistance to stripe rust. Overall, this study contributes to the current repository of wheat miRNAs and provides novel information on the yet uncharacterized roles for miRNAs in wheat host-pathogen interactions.