Identification and characterization of microRNAs in the developing maize endosperm

•We identified expression patterns of ninety five known miRNAs in developing endosperm.•Seventy known miRNAs that showed significantly differential expression may play an important role in endosperm development.•Eighteen novel miRNAs identified and grouped into 11 families may play an important role in endosperm development.•We had identified 12 corresponding miRNAs* of these novel miRNAs.

MicroRNAs (miRNAs) are non-coding RNAs that are approximately 20–22 nucleotides long. miRNAs have been shown to be important regulators that control a large variety of biological functions in eukaryotic cells. To investigate the roles of miRNAs in maize endosperm development, two small RNA libraries of maize endosperm at two developmental stages were sequenced. A total of 17,773,394 and 18,586,523 small RNA raw reads were obtained, respectively. Further analysis identified and characterized 95 known miRNAs belonging to 20 miRNA families. In addition, 18 novel miRNAs were identified and grouped into 11 families. Potential targets for 5 of the novel miRNA families were successfully predicted. We had also identified 12 corresponding miRNAs* of these novel miRNAs. In summary, we investigated expression patterns of miRNA in maize endosperm at key developmental stages and identified miRNAs that are likely to playing an important role in endosperm development.