MicroRNA Regulation Of Rice Genomes Under Abiotic Stress And During Domestication

MicroRNAs (miRNAs) are a set of endogenous noncoding small RNA molecules widely found in eukaryote, with about 21-24 nucleotides. miRNAs regulate the expression of their target genes at post-transcriptional level, and play important roles in various animal and plant developmental stages. With the fast development of the next generation sequencing technology, we can now conduct large-scale analysis on finding novel miRNAs and investigating the interaction between miRNAs and their target, also their biological functions as well. Rice is one of the most important crops in the world, as the whole genome of several Asian and African cultivated and Wild rice species have been published, rice therefore became one of the most ideal model plant for studying adaptation to environmental changes and artificial selection under the process of domestication. MiRNAs are involved in the gene regulation during multiple biological processes, such as plant growth and development, metabolism and response to stimuli et al. The study of plant miRNA would bring insight on the evolution of the miRNA involved post-transcriptional gene regulatory network and biological function, and also favor the searching for possible candidate on the study of adaptive evolution, or discovering important agronomic traits related miRNAs.We profiled the small RNA and gene expression patterns of 4 cultivated rices by RNA-seq technology,2 of which are drought tolerate lines and the other 2 are drought sensitive lines. We found that all 4 lines showed a similar miRNA expression pattern within 24 hours after the drought stress began, but over 1,500 genes are differentially expressed under stress, suggesting that miRNAs do not act differently between drought tolerate lines and drought sensitive lines. By analyzing miRNA/target pairs, we can see that miRNAs and their hardly show negative correlation in the early hours after the stress treatment. Thus, we believe that miRNAs are working in a more complicated gene regulatory network, and serve as a buffer which help the whole transcriptome to keep stable.We also conducted deep sequencing on 3 African rices, including 1 cultivated rice:Oryza glaberrima, and 2 wild rices:Oryza barthii and Oryza brachyantha. By the comparative analysis of miRNAs expression profile, we managed to find miRNAs that are possibly responsible for domestication and novel miRNAs too.In the last part of this study, we developed a method of miRNA silencing via anti oligodeoxyribonucleotides (AMOs). We designed a protocol for delivering these chemically modified antisense oligonucleotides that are complementary to mature miRNAs, which sequester target messenger RNAs (mRNAs) in competition with mature miRNAs in RISCs, leading to the blockage of miRNA functions via steric hindrance. Our results indicated that, the miRNA inhibition by AMOs is highly efficient and quite long-lasting. By getting similar results which were reported in previous works via miRNA target mimics, we believe that the inhibition of miRNA function by AMOs will be of great value as a powerful tool for elucidating biological functions of plant miRNAs and their regulatory networks in vivo.