The Genetic Polymorphism, Expression And Evolution Of MIRNA Genes During Rice Domestication

Rice is one of staple crops and outstanding model plants. Cultivar of rice (O. sativa) evolved from O. rufipogon and differentiated into two subspecies, japonica and indica. The formation and the genomes of crops were influenced deeply by domestication. At the genotype level, the reduction of nucleotide diversity was caused by domestication bottleneck. For some crucial loci/genes, the allele frequency spectrum could be skewed due to selective pressure and linkage disequilibrium could be increased because of the selective sweeps. The endogenous small RNA is a kind of regulation element which exists globally in almost all life forms and plays universal function. Based on the biogenesis and regulating process, small RNA could be divided into 2 groups:microRNAs and small interfering RNAs. Transcripts of MIRNA genes could form the hairpin secondary structures and process into mature miRNAs about 20nt cleaved by DCL to interfere the target genes. MiRNAs could regulate certain percentage genes based on recent researches. High throughput sequencing develop rapidly recent years facilitate the small RNA research and make research on small RNAs the hotspot this decade. Fifteen genes were identified as domestication genes in rice which were mainly transcription factors, a kind of protein-coding gene. The function of non-coding small RNAs in crop domestication is still unclear.This work researched domestication selection of miRNAs in rice, using resequencing data, miRNA microarray data and high throughput small RNA sequencing data by methods of population genetics and bioinformatics. Main results achieve here were:(1) the investigation of the genetic diversity of 94 small RNA loci was carried out and plenty of mutations were detected at some loci in cultivar, for example,12 mutations were found in 11 mature miRNA loci (about 12.5% of investigated), which indicated significant higher level of mutations in miRNA and other type of small RNAs in cultivar. Four small RNA loci were potential loci under domestication selection. This research indicated that MIRNA genes could also be the targets of domestication selection and may play as important roles during domestication or improvement as the coding genes. (2) the expression profiles of miRNAs were compared between cultivar and wild rice with microarray and high thoughput sequencing data. More miRNAs were up-regulated during domestication and the variance of expression of some miRNAs reduced in cultivar. No obvious relationship between miRNA expression and the abundance of cleavage fragments of target genes were observed as reported by previous studies. Multi-patterns of regulation of miRNAs may be responsible for this observation. (3) We identified several candidates of wild rice specific MIRNA genes. Comparison with the homologs of cultivar inferred that pseudogenes caused by frame-change mutations maybe a mechanism of miRNA emerging. Meanwhile, the MIRNA genes could loss in cultivar during domestication under selection constraints. Further analysis is carrying on with the coming data of whole genome resequencing data of wild rice.Taken together, this work carried out on the small RNAs with important regulatory function, analyzed the expression and the dynamic of evolution of miRNA during domestication, concluded with non-coding small RNAs were also the target of domestication selection, finally revealed the important roles of small RNAs during evolution or the formation of crop varieties as regulation factors, which may guide the researchers in genetics and crop breeding at such aspects.