Identification of microRNAs and Their Target Genes Explores miRNA-Mediated Regulatory Network of Cytoplasmic Male Sterility Occurrence during Anther Development in Radish (Raphanus sativus L.).

Wei Zhang,Yang Zhang,Everlyne M Muleke,Yang Xie,Yan Wang,Ronghua Wang,Liwang Liu,Liang Xu,Xianwen Zhu

doi:10.3389/fpls.2016.01054

Wei Zhang, Yang Zhang + Show 7 more

Open Access

https://doi.org/10.3389/fpls.2016.01054

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Abstract

MicroRNAs (miRNAs) are a type of endogenous non-coding small RNAs that play critical roles in plant growth and developmental processes. Cytoplasmic male sterility (CMS) is typically a maternally inherited trait and widely used in plant heterosis utilization. However, the miRNA-mediated regulatory network of CMS occurrence during anther development remains largely unknown in radish. In this study, a comparative small RNAome sequencing was conducted in floral buds of CMS line ‘WA’ and its maintainer line ‘WB’ by high-throughput sequencing. A total of 162 known miRNAs belonging to 25 conserved and 24 non-conserved miRNA families were isolated and 27 potential novel miRNA families were identified for the first time in floral buds of radish. Of these miRNAs, 28 known and 14 potential novel miRNAs were differentially expressed during anther development. Several target genes for CMS occurrence-related miRNAs encode important transcription factors and functional proteins, which might be involved in multiple biological processes including auxin signaling pathways, signal transduction, miRNA target silencing, floral organ development, and organellar gene expression. Moreover, the expression patterns of several CMS occurrence-related miRNAs and their targets during three stages of anther development were validated by qRT-PCR. In addition, a potential miRNA-mediated regulatory network of CMS occurrence during anther development was firstly proposed in radish. These findings could contribute new insights into complex miRNA-mediated genetic regulatory network of CMS occurrence and advance our understanding of the roles of miRNAs during CMS occurrence and microspore formation in radish and other crops.

Highlights

MicroRNAs are a type of endogenous noncoding small RNAs of ∼21–24 nucleotides that are known to be important negative regulators of gene expression at transcriptional and post-transcriptional level by mediating mRNA degradation or translational repression (Voinnet, 2009)
To identify known and potential novel miRNAs involved in anther development and Cytoplasmic male sterility (CMS) occurrence, we constructed two small RNA libraries from the floral buds of ‘WA’ and ‘WB’ line
The findings suggested that these miRNAs may play critical roles during anther development in radish

Summary

Introduction

MicroRNAs (miRNAs) are a type of endogenous noncoding small RNAs of ∼21–24 nucleotides that are known to be important negative regulators of gene expression at transcriptional and post-transcriptional level by mediating mRNA degradation or translational repression (Voinnet, 2009). High-throughput sequencing now is widely used and has been proven to be an excellent application for the identification of plant miRNAs. As a class of negative regulators, miRNAs have been identified and characterized during anther development in several plant species, including Arabidopsis (Chambers and Shuai, 2009), Oryza sativa (Wei et al, 2011; Yan et al, 2015), Gossypium hirsutum (Wei et al, 2013), Brassica juncea (Yang et al, 2013), and B. rapa (Jiang et al, 2014). A large number of miRNAs during anther development have been isolated and identified in many crop species, the miRNA-mediated regulatory network of CMS occurrence during anther development remain to be clarified in root vegetable crops

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