Integrative investigation of root-related mRNAs, lncRNAs and circRNAs of ‘Muscat Hamburg’ (Vitis vinifera L.) grapevine in response to root restriction through transcriptomic analyses

Abstract Background Root restriction is a physical and ecological cultivation mode which restricts plant roots into a limited container to regulate vegetative and reproduction growth by reshaping root architecture. However, little is known about related molecular mechanisms. To uncover the root-related regulatory network of endogenous RNAs under root restriction, transcriptome-wide analyses of mRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) involved in root development was performed. Results In this study, a total of 26588 mRNAs, 1971 lncRNAs and 2615 circRNAs were identified in root of annual ‘Muscat Hamburg’ grapevine by the next generation sequencing, respectively. The expression profile of mRNAs, lncRNAs and circRNA were further confirmed by the quantitative real-time PCR (qRT-PCR). Gene ontology enrichment analysis showed that a majority of the differentially expressed mRNAs, lncRNAs and circRNAs were annotated to the categories of cellular process, metabolic process, cell part, binding and catalytic activity. In addition, the regulatory network of endogenous RNAs was then constructed by the prediction of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA, implying that these RNAs play significant regulatory roles for root architecture shaping in response to root restriction. Conclusion Our results, for the first time, integrated the regulatory network of competitive endogenous RNAs (ceRNAs) functions of lncRNA and circRNA, and provided a basis for studying the potential functions of non-coding RNAs during root development of grapevine.