Sequence Variation And Selection Of MicroRNAs In Rice

Non-coding microRNAs (21-24 nt) widely exist in many organisms and play an important role in post-transcriptional regulation in plants. Domestication selection is the most important evolutionary force the crop genomes. The notable feature of the known domestication genes is that they mainlly encode transcription factors which regulate other protein-coding genes. Whether microRNAs, regulators of transcription factors, are targets of domestication selection has not yet been determined. In this study, we detected expression profiles of 516 microRNAs between cultivar and wild rice and then estimated the genetic diversity and neutrality of microRNAs which expressed differently in the two populations. The main results are as follows:1. Of the 516 microRNAs, 14 have distinguished expression patterns between cultivar and wild rice. In the 14 loci, miR396f and miR396d expressed differently in indica and japonica subgroups.2. The significant genetic diversity reductions of DNA polymorphism at mature miRNA compared to pre-miRNA and up- and down-stream was found, which suggested that purifying selection is the predominant evolutionary force that shaped miRNAs in rice. Relative to the wild rice, the intraspecific polymorphism and interspecific divergence at both miRNA mature sequence and pre-miRNA (including up- and down-stream) were lower on cultivar rice.3. Single nucleotide polymorphisms (SNPs) were found at the mature sequences of miR399a and miR164c. Large amount of SNPs and indels were also found at pre-miRNA, upstream and downstream sequence of the 14 small RNAs.4. Four loci, miR164c, miR164d, miR164e and miR399j, were considered as candidates of domestication gene because significant positive selection by at least one of three neutrality tests (Tajima's D, Fay and Wu's H and HKA) were detected in the cultivar population but not in the wild population. miR399d and miR1862d on which significant positive selection were found might have experienced the nature selection. Based on the above results, microRNAs could play an important role in the rice domestication and/or improvement and should not be ignored in the effort to identify the molecular basis for the events.