| Rice (Oryza sativa) is one of monocot plants. As a cereal grain, it is the most important staple food for a large part of the world's human population. It is the grain with the second-highest worldwide production, after maize. Since being artificially cultivated, the economic traits, especially the stress tolerance of rice, have been closely considered by people.Stress refers to those environmental factors which adversely affect plant growth and development. When the stress exceeds the tolerence ability of plants, Stress can cause the plant irreversible damage. Stress consists of biotic stress and abiotic stress:biotic stress is a series stresses, such as grazing, trampling, which are caused by human, animal or microbe and so on; Abiotic stress, such as light stress, salt stress and drought stress, which are caused by temperature, radiation, salt, water or other abiotic factors. With long-term of evolution, plant abtained a series of abilities, by which plant can servive from varias stresses.Plant responses to stress by regulating the expression of specific genes. Therefore, most researchers have paid more attentions to the regulation of stress response genes. Gene expression regulation is generally divided into transcriptional regulation and post-transcriptional regulation. In the post-transcriptional regulation, mRNA non-coding regions (including the 5'UTR and 3'UTR) play an important role. miRNAs (MicroRNA) are a class of endogenous small (-22 nucleotides), non-coding RNAs, which play important roles in plant growth, development and stress tolerance by binding to the target sites in 3'UTR of mRNAs. It is an effective process to study the regulation of stress response genes that studies on motifs within 3'UTR and on miRNA that can target to those motifs.We have extracted 3'UTR and CDS sequences of the protein coding genes of rice by Perl scripts. Then, we annotationed and divided all the genes into two groups according to whether they are stress response generally. We put these data into MySQL database. Motifs presented in 3'UTR region were predicated using the above datasets. Those motifs specific located in 3'UTR region of stress response gene or non-stress response geng were obtained through the comparision of stress responsive gene with non-stress responsive genes, CDS with UTR regions.MiRNAs bind to motifs within 3'UTR region and regulate gene expression level. The study of miRNA and miRNA SNP can improve the research in the roles of miRNA in stress response.In order to explore the potential functional significance of SNPs in the pre-miRNA in rice, we analyzed the distribution of SNPs in pre-miRNA region and flanking region,including 5'flanking region and 3'flanking region,in rice. The results showed that there is no significant difference of the frequency of SNPs between the miRNA gene region and its flanking region, which was different from the result in other species. Further study on the frequency of SNPs frequency across pre-miRNA showed that there is no significant difference of the frequency of SNPs between seed region and loop region, which was thought to undergo less negative selection pressure in other species. However, in consistent with the result in other species, the frequency of SNPs in gene region was significantly lower than that in gene flanking region. The feature of SNP distribution in pre-miRNA may be related to its uneven distribution among.Part of the miRNA is very important to rice function,thus subjected to strong negative selection, resulting in low frequency SNP.The other part of the miRNA genes undergoing the pressure relax of negative selection because of artificial selection, or artificial cultivation, and eventually become a new gene or loss of function. accumulated more mutation. However, we could not exclude the possibility thatour results might be biased based on the unreliable data in current SNPs database. |
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