Abstract
BackgroundCircular RNAs (circRNAs) are known to play an important role in the regulation of gene expression in eukaryotes. Photo-thermosensitive genic male sterile (PTGMS) is a very important germplasm resource in two-line hybrid rice breeding. Although many circRNAs have been identified in rice (Oryza sativa L.), little is known about the biological roles of circRNAs in the fertility transition of the PTGMS rice line.ResultsIn the present study, RNA-sequencing libraries were constructed from the young panicles of the Wuxiang S sterile line rice (WXS (S)) and its fertile line rice (WXS (F)) at three development stages with three biological replicates. A total of 9994 circRNAs were obtained in WXS rice based on high-throughput strand-specific RNA sequencing and bioinformatic approaches, of which 5305 were known circRNAs and 4689 were novel in rice. And 14 of 16 randomly selected circRNAs were experimentally validated with divergent primers. Our results showed that 186 circRNAs were significantly differentially expressed in WXS (F) compared with WXS (S), of which 97, 87 and 60 circRNAs were differentially expressed at the pollen mother cell (PMC) formation stage (P2), the meiosis stage (P3) and the microspore formation stage (P4), respectively. Fertility specific expression patterns of eight circRNAs were analysis by qRT-PCR. Gene ontology (GO) and KEGG pathway analysis of the parental genes of differentially expressed circRNAs (DECs) revealed that they mainly participated in various biological processes such as development, response to stimulation, hormonal regulation, and reproduction. Furthermore, 15 DECs were found to act as putative miRNA sponges to involved in fertility transition in PTGMS rice line.ConclusionIn the present study, the abundance and characteristics of circRNAs were investigated in the PTGMS rice line using bioinformatic approaches. Moreover, the expression patterns of circRNAs were different between WXS (F) and WXS (S). Our findings primarily revealed that circRNAs might be endogenous noncoding regulators of flower and pollen development, and were involved in the fertility transition in the PTGMS rice line, and guide the production and application of two-line hybrid rice.
Highlights
Circular RNAs are known to play an important role in the regulation of gene expression in eukaryotes
We found an enrichment of this Gene ontology (GO) term at the The pollen mother cell (PMC) formation stage (P2) and The meiosis stage (P3) stages to a greater extent than at the The microspore formation stage (P4) stage, suggesting that the process of fertility transition is more complex during the PMC formation and meiosis stages
Compared with the P3 and P4 stages, one parental gene (OsRR1) was involved in the plant hormone signal transduction pathway at the P2 stage. These results revealed the parental genes of differentially expressed circRNAs (DECs) in the fertility transition involved in development, stimulationresponse, hormonal regulation and reproduction, implying that Circular RNAs (circRNA) may play important roles in the fertility transition of Photo-thermosensitive genic male sterile (PTGMS) rice by the metabolic pathway and hormone signaling pathway
Summary
Circular RNAs (circRNAs) are known to play an important role in the regulation of gene expression in eukaryotes. Circular RNAs (circRNAs) comprise a pervasive and vital class of noncoding RNAs characterized by a singlestranded covalently closed ring structure [1, 2]. They are mainly derived from a back-splicing event in which an upstream 5′ splice acceptor is linked to a downstream 3′ splice donor [3,4,5]. In the 1970s, Sanger et al [8] provided the first evidence for the presence of circRNAs in some plant viroids Despite their detection for decades, circRNAs used to be considered rare in eukaryotic cells or disregarded as splicing errors or reverse transcription (RT)-PCR artifacts. Due to the advance of high-throughput sequencing and high-efficiency bioinformatics methods [9,10,11,12], understanding of the widespread and diverse circRNAs has improved substantially in a variety of organisms [13,14,15,16,17]
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