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

Abstract

BackgroundIn 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.ResultsWe 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.ConclusionsThis 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.

Development of Incompletely Fused Carpels in Maize Ovary Revealed by miRNA, Target Gene and Phytohormone Analysis

“…The length of the sRNAs ranged from 18 to 25 nt, and in both the IFC and CFC libraries, the 24 nt category was most abundant (average of 51.07%; Figure 2A). This is consistent with the typical lengths of plant sRNAs reported in other studies (Liu et al, 2014; Hackenberg et al, 2015). Of the known miRNAs, 21-nt miRNAs were most abundant (59.7%) (Figure 2B), representing the dominant size of mature miRNAs in plants.…”

“…Recent studies have reported the role of miRNAs in determining gene expression during maize ear and kernel development (Liu et al, 2014; Xin et al, 2015). However, few studies have examined miRNA expression during ovary growth, in particular, during carpel fusion.…”

“…In this study, we used high-throughput sequencing to detect miRNA activity at the moment of incomplete carpel fusion could being morphological distinguished, and identified their targets through degradome analysis, which was previously used to identify miRNA-mRNA target pairs in tomato, maize and grapevine (Pantaleo et al, 2010; Karlova et al, 2013; Liu et al, 2014). Subsequently, the results were validated by quantitative RT-PCR (qRT-PCR) analysis of ovary formation and growth development in IFC and CFC ovaries.…”

Transcriptome Profiling of Wheat Inflorescence Development from Spikelet Initiation to Floral Patterning Identified Stage-Specific Regulatory Genes

“…The digital gene expression libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biosystems), following the manufacturer's recommendations. Small RNA libraries were prepared as described previously (Liu et al, 2014a).…”

Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses

“…Many known miRNAs and their targets are conserved across different plant species (Montes et al, 2014). In maize, many conserved miRNA targets have been experimentally confirmed (Shen et al, 2013;Zhai et al, 2013;Zhao et al, 2013;Liu et al, 2014), but a few exceptions exist, for example those of miR168 and miR399. MiRNAs are members of multiple regulatory networks controlling plant development, and many miRNA families also play roles in stress responses and tolerance (for review, see Sunkar et al, 2012).…”