Micro RNAs (miRNAs) are a class of small non-coding RNAs with post-transcriptional gene regulation responsibilities. In plants, miRNAs regulate development of leaves, roots, shoots, and flowers through targeting families of transcription factors and through targeting genes in the signal transduction and hormone pathways involved in plant growth and development. In addition to plant development, miRNAs are also involved in biotic and abiotic stress responses (Mallory & Vaucheret, 2006; Zhang, Pan, & Anderson, 2006), Plant disease and environmental stress reduce crop yield, which is a global problem as reduced crop yield struggles to meet world food production demand. With the majority of our world population's diet being composed of grains, there is a critical need to understand the epigenetic influence of miRNAs in cereal crops, especially in Avena sativa. There is currently no annotated miRNAs in oat. The role of miRNAs in post-transcriptional regulation in plants is only beginning to be understood. MiRNA annotation in large, complex, un-sequenced genomes is challenging due to the lack of existing software and pipelines that incorporate sequence and structure-based approaches to effectively predict miRNAs. Integrating computational and molecular biology techniques, this study provides the first annotated miRNA library in hexaploid oat using a pipeline for annotation of miRNAs in the absence of a reference genome for use in other large, complex genomes. As an allopolyploid, the annotation of miRNAs in a diploid, tetraploid, and synthetic hexaploid exists as the first investigation of genome specific miRNAs. This study also proposes a new model to explain the conditioning of the hulless trait in oat by miR172, enabling hulless oats to be bred more efficiently to fulfill the needs of an emerging market. In its entirety, this work improves the sequencing resources of oat and provides the framework for further inquiries into the effect of miRNAs on plant genomes.
