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

Qing-Xin Song,Jin-Song Zhang,Biao Ma,Yun-Feng Liu,Shou-Yi Chen,Xing-Yu Hu,Wan-Ke Zhang

doi:10.1186/1471-2229-11-5

Abstract

BackgroundMicroRNAs (miRNAs) regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. miRNAs and related target genes have been widely studied in model plants such as Arabidopsis and rice; however, the number of identified miRNAs in soybean (Glycine max) is limited, and global identification of the related miRNA targets has not been reported in previous research.ResultsIn 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.ConclusionsWe 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.

Highlights

MicroRNAs regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. miRNAs and related target genes have been widely studied in model plants such as Arabidopsis and rice; the number of identified miRNAs in soybean (Glycine max) is limited, and global identification of the related miRNA targets has not been reported in previous research
Overview of small Polyadenylated RNA (RNA) library sequencing The soybean small RNA library was constructed using RNAs obtained from seeds of 15-day-old after flowering and sequenced by Solexa SBS technology
In our study, a small RNA library and a degradome library were constructed from developing soybean seeds for deep sequencing

Summary

Introduction

MicroRNAs (miRNAs) regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. miRNAs and related target genes have been widely studied in model plants such as Arabidopsis and rice; the number of identified miRNAs in soybean (Glycine max) is limited, and global identification of the related miRNA targets has not been reported in previous research. MicroRNAs (miRNAs) regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. MiRNAs and related target genes have been widely studied in model plants such as Arabidopsis and rice; the number of identified miRNAs in soybean (Glycine max) is limited, and global identification of the related miRNA targets has not been reported in previous research. MiRNAs play important roles in different developmental stages by mediating gene silencing at transcriptional and post-transcriptional levels [4,5,6]. Soybean is the most widely planted oil crop in the world; the regulation of its seed development is not well studied. Identification of new miRNAs and elucidation of their functions in seed development will help us understand the regulation of soybean lipid synthesis. Because of its ultra highthroughput, many new miRNAs with low abundance could be identified using this technology

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Discussion

Conclusion