Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

In our study, a small RNA library and a degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. GO analysis indicated that many of the identified miRNA targets may function in soybean seed development. Additionally, a soybean homolog of Arabidopsis SUPPRESSOR OF GENE SLIENCING 3 (AtSGS3) was detected as a target of the newly identified miRNA Soy_25, suggesting the presence of feedback control of miRNA biogenesis.We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library and a degradome library. Our study provides more information about the regulatory network of miRNAs in soybean and advances our understanding of miRNA functions during seed development.MicroRNAs (miRNAs) are endogenous ~21-nt noncoding RNAs derived from single-stranded RNA precursors that can form stem-loop structures [1,2]. MiRNA was first identified in Caenorhabditis elegans and subsequently found in almost all eukaryotes [3]. In higher plants, miRNAs play important roles in different developmental stages by mediating gene silencing at transcriptional and post-transcriptional levels [4-6]. Soybean is the most widely planted oil crop in the world; however, the regulation of its seed development is not well studied. The roles of miRNAs in soybean seed development remain largely unknown. Therefore, identification of new miRNAs and elucidation of their functions in seed development will help us understand the regulation of soybean lipid synthesis. Recently, the soybean genome sequence has been finished [7], which will greatly ad