MicroRNAs （miRNAs） are a class of endogenous small (about 22 nucleotides), noncoding RNAs, which play important roles in plant growth, development and stress tolerance by binding to the target sites in mRNAs. Since a single nucleotide change in miRNAs can affect the maturity and regulation of miRNA, study on the distribution of single nucleotide polymorphisms (SNPs) in miRNA gene may be of great importance for functional and evolutionary research. In order to explore the potential functional significance of SNPs in the premiRNA in rice, we analyzed the distribution of SNPs in premiRNA region and flanking region, including 5′ and 3′ flanking regions in rice. The results showed that there was no significant difference in the frequency of SNPs between the premiRNA region and its flanking region in rice, which was different from the results in other species. Further study on the frequency of SNPs across premiRNA secondary structures showed that there was no significant difference between seed region and loop region, which was thought to undergo less negative selection pressure in other species. However, in consistent with other species, the frequency of SNPs in proteincoding gene region of rice was significantly lower than that in gene flanking region, indicating that the flanking region of premiRNA may be essential for the function of miRNA. Another reseaon was the uneven distribution of SNPs in different miRNAs. Some miRNAs were less important to rice function, thus was subjected to relaxation of selective pressure, accumulating more and more mutations to become a new gene or loss of functions. However, we could not rule out the bias in the results because of the unreliable data in current SNP database.
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