Genome-wide identification and analysis of miRNA-related single nucleotide polymorphisms (SNPs) in rice

MiRNAs are key regulators in the miRNA-mediated regulatory networks. Single nucleotide polymorphisms (SNPs) that occur at miRNA-related regions may cause serious phenotype changes. To gain new insights into the evolution of miRNAs after SNP variation, we performed a genome-wide scan of miRNA-related SNPs, and analyzed their effects on the stability of miRNAs structure and the alteration of target spectrum in rice.

We find that the SNP density in pre-miRNAs is significantly higher than that in the flanking regions, owing to the rapid evolution of a large number of species-specific miRNAs in rice. In contrast, it is obvious that deeply conserved miRNAs are under strong purifying selection during evolution. In most cases, the SNPs in stem regions may result in the miRNA hairpin structures changing from stable to unstable status; And SNPs in mature miRNAs have great potential to have either newly created or disrupted the miRNA-target interactions. However, the total number of gained targets is over 2.5 times greater than that are lost after mutation. Notably, 12 putative domestication-related miRNAs have been identified, where the SNP density is significantly lower.

The present study provides the first outline of SNP variations occurred in rice pre-miRNAs at the whole genome-wide level. These analyses may deepen our understanding on the effects of SNPs on the evolution of miRNAs in the rice genome.