Genome-Wide Analysis of microRNAs Associated with Flower Development in Rice

MicroRNAs (miRNAs) are non-coding small RNAs that regulate target gene expression at the posttranscriptional level. Plant miRNAs have been identified that contribute to a variety of biological process, including flower development. Functional studies examining Arabidopsis miRNAs have identified several miRNAs that play crucial roles in flower development by repressing key regulatory genes in floral organ identity. Although these miRNAs are well conserved in rice, their role in rice flower development had not been well characterized. To better understand the role of rice miRNAs in flower development, small RNA libraries were constructed from rice floral organs as well as panicle tissues from different stages. We also constructed PARE (Parallel Analysis of RNA Ends) degradome libraries from anther and pistil. Both small RNA and PARE libraries were deeply sequenced by Illumina technology and analyzed to identify differentially regulated miRNAs and to investigate their target cleavage functions. From the small RNA libraries, we identified most of previously-reported rice miRNAs as well as tens of new miRNAs using a computational pipeline. Of these, about 20% of miRNAs were preferentially expressed in a specific floral organ. Analysis of PARE data revealed the cleavages of target RNAs in the particular floral organ where these miRNAs are expressed. We have identified more than 170 miRNAs that were differentially expressed during panicle development. Of these, some miRNA variants showed differential expression patterns in different stages. Additional studies are underway to investigate the association of floral-organ-preferential miRNAs and differentially-expressed miRNA variants with the expression of their target genes.