Open Access Highly Accessed Research article

Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing

Hongjun Liu1, Cheng Qin12, Zhe Chen1, Tao Zuo3, Xuerong Yang4, Huangkai Zhou5, Meng Xu5, Shiliang Cao6, Yaou Shen1, Haijian Lin1, Xiujing He1, Yinchao Zhang1, Lujiang Li1, Haiping Ding7, Thomas Lübberstedt8, Zhiming Zhang1* and Guangtang Pan1*

Author Affiliations

1 Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China

2 Zunyi Institute of Agricultural Sciences, Zunyi 563102, China

3 Interdepartmental Genetics Graduate Program, Iowa State University, Ames 50011, USA

4 Animal Nutrition Institute, Sichuan Agricultural University, Ya’an 625014, China

5 BGI-Shenzhen, Shenzhen 518083, China

6 Maize Research Institute of Heilongjiang, Academy of Agricultural Sciences, Harbin 150086, China

7 Sichuan Agricultural University, Chengdu 611130, China

8 Department of Agronomy, Iowa State University, Ames 50011, USA

For all author emails, please log on.

BMC Genomics 2014, 15:25  doi:10.1186/1471-2164-15-25

Published: 14 January 2014

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.