Skip to main content
Article
Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing
BMC Genomics
  • Hongjun Liu, Sichuan Agricultural University
  • Cheng Qin, Sichuan Agricultural University
  • Zhe Chen, Sichuan Agricultural University
  • Tao Zuo, Iowa State University
  • Xuerong Yang, Sichuan Agricultural University
  • Huangkai Zhou, BGI-Shenzhen
  • Meng Xu, BGI-Shenzhen
  • Shiliang Cao, Academy of Agricultural Sciences
  • Yaou Shen, Sichuan Agricultural University
  • Haijian Lin, Sichuan Agricultural University
  • Xiujing He, Sichuan Agricultural University
  • Yinchao Zhang, Sichuan Agricultural University
  • Lujiang Li, Sichuan Agricultural University
  • Haiping Ding, Sichuan Agricultural University
  • Thomas Lubberstedt, Iowa State University
  • Zhiming Zhang, Sichuan Agricultural University
  • Guangtang Pan, Sichuan Agricultural University
Document Type
Article
Publication Date
1-1-2014
DOI
10.1186/1471-2164-15-25
Abstract

Background

In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana. In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages. Results

We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed. Conclusions

This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development.

Comments

This article is published as Liu, Hongjun, Cheng Qin, Zhe Chen, Tao Zuo, Xuerong Yang, Huangkai Zhou, Meng Xu et al. "Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing." BMC genomics 15, no. 1 (2014): 25. doi: 10.1186/1471-2164-15-25. Posted with permission.

Creative Commons License
Creative Commons Attribution 4.0 International
Copyright Owner
Liu et al.
Language
en
File Format
application/pdf
Citation Information
Hongjun Liu, Cheng Qin, Zhe Chen, Tao Zuo, et al.. "Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing" BMC Genomics Vol. 15 Iss. 25 (2014)
Available at: http://works.bepress.com/thomas-lubberstedt/37/