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.
Highlights
In plants, microRNAs 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
Overview over small RNA library sequencing To study the involvement of regulatory miRNAs in the complex process of ear development, we profiled miRNA accumulation during ear development in the maize inbred line B73
We identified 122 miRNAs (96 conserved + 26 non-conserved) and 64 miRNA star (miRNA*), they showed a diverse range of abundance, and only a few miRNA families dominated in the miRNA library and microarray assay data
Summary
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. Maize produces two distinct inflorescences, commonly referred to as the tassel and the ear. In this respect, it differs from other grasses such as rice and wheat. Small RNA-guided post-transcriptional regulatory mechanisms play important roles in many aspects of plant biology, including metabolism [5], hormone responses [6], epigenetic control of transposable elements [7], and responses to biotic stress [8] and abiotic stress [9]. Identification of miRNAs and their targets in diverse species has been a major focus in recent years
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