Genome-wide Identification Of Domestication-related MiRNAs In Rice And The Obtainment Of OsmiR821Transgenic Rice Plants

The origination and domestication of Asia cultivated rice is a popular and interesting issue thathas highly attracted the attentions of the scientists who work on rice and evolutionary biology. Recently,a mounts of researches demonstrated that artificial selection should have imposed on the whole ricegenome. However, to date, only a few of domesticated genes including protein-coding genes andregulatory miRNA genes have been reported in rice. Based on the591rice miRNA precursors and thehigh-quality SNP data produced from the high-throughput re-sequencing of tens to hundreds of ricegenotypes, we have firstly identified and analyzed the domestication-related rice miRNA genes（DR-miRNAs）at the genome-wide level, using the combinations of population genetics, evolutionarybiology, bioinformatics and molecular biology approaches. The results show that364out of the591pre-miRNAs contain single nucleotide polymorphisms（SNPs）that may significantly affect the stabilityof hairpin structures of232and99miRNAs, as well as their target genes spectrum;190out of591miRNA loci show non-neutral evolutionary pattern in domesticated rice, of which29loci have clearsignatures of positive selection, indicating that these loci should be under strong natural and/or artificialselection during rice evolution. Interestingly, some DR-miRNAs and their specific target genes maybecome the common human selective targets during domestication. There are18and11DR-miRNAsfalling into the intergenic and intronic regions, respectively, of which5DR-miRNAs are located in thechromosomal regions that have undergone large-scale segmental duplications. The target genes ofDR-miRNAs that are enriched in the binding and catalytic activity functional categories may mainlyparticipated in the cellular and metabolic processes. Notably, we have generated transgenic rice plantscarrying the over-expression and repression vectors of DR-miR821b/c to investigate their biologicalfunctions. The biological function of DR-miR821b is further investigated by site-directed mutation ofthe3SNPs within its precursor sequence sequentially. Based on the results addressed above, we furtherclarify that miRNAs, like protein-coding genes, should act as one of important evolutionary forces fordriving rice evolution during domestication. The results presented here not only provide the useful clue,basal theory, and crucial genes for rice improvements or molecular breeding, but may also deepen ourinsights into understanding the processes and mechanisms of rice domestication.