Abstract
The “competing endogenous RNA (ceRNA) hypothesis” has recently been proposed for a new type of gene regulatory model in many organisms. Anther development is a crucial biological process in plant reproduction, and its gene regulatory network (GRN) has been gradually revealed during the past two decades. However, it is still unknown whether ceRNAs contribute to anther development and sexual reproduction in plants. We performed RNA and small RNA sequencing of anther tissues sampled at three developmental stages in two maize lines. A total of 28,233 stably transcribed loci, 61 known and 51 potentially novel microRNAs (miRNAs) were identified from the transcriptomes. Predicted ceRNAs and target genes were found to conserve in sequences of recognition sites where their corresponding miRNAs bound. We then reconstructed 79 ceRNA-miRNA-target gene regulatory networks consisting of 51 known miRNAs, 28 potentially novel miRNAs, 619 ceRNA-miRNA pairs, and 869 miRNA-target gene pairs. More than half of the regulation pairs showed significant negative correlations at transcriptional levels. Several well-studied miRNA-target gene pairs associated with plant flower development were located in some networks, including miR156-SPL, miR159-MYB, miR160-ARF, miR164-NAC, miR172-AP2, and miR319-TCP pairs. Six target genes in the networks were found to be orthologs of functionally confirmed genes participating in anther development in plants. Our results provide an insight that the ceRNA-miRNA-target gene regulatory networks likely contribute to anther development in maize. Further functional studies on a number of ceRNAs, miRNAs, and target genes will facilitate our deep understanding on mechanisms of anther development and sexual plants reproduction.
Highlights
Anther development is a crucial biological process for male fertility and sexual reproduction in plants
To perform genome-wide identification of competing endogenous RNA (ceRNA) and investigate their potential functions in maize anther development, transcribed loci should first be identified in transcriptomes
To further identify the conserved and significant functional interactions among ceRNAs, miRNAs, and target genes, the transcribed loci shared between lines L7 and L30 were selected for the step analysis
Summary
Anther development is a crucial biological process for male fertility and sexual reproduction in plants. All the GMS genes investigated previously, and their regulatory relationships, together comprise a gene regulatory network (GRN) of anther development that mainly consists of transcription factors (TFs) and their regulated target genes. MiRNAs have been reported to be involved in plant flowering and the subsequent anther developmental pathways by repressing the transcriptional or translational activities of target genes in GRNs [8,9,10]. Gene regulatory models in anther development mainly include two types: (1) trans-acting factors that interact with cis-regulatory elements, and (2) miRNA-mediated repression of target gene expression
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