Identification and characterization of heat-responsive miRNAs and their regulatory network in maize

Abstract

Background: MicroRNAs (miRNAs) are a class of small non-coding RNAs, which have been demonstrated to play essential roles in plant growth and development, and in responses to abiotic stress. Heat stress is one of the most serious stresses that affecting crop yield and quality, however, the related regulatory mechanisms of miRNAs remains poorly understanding in maize.Results: In this study, a total of 340 miRNAs, including 215 known and 125 novel members, were identi ed from maize seedlings under heat stress (MH) and control conditions (MC) using high-throughput sequencing approach. The 215 known miRNAs can be further divided into 40 different families, and 21-nt miRNAs were found to be most abundant among the known miRNAs. Thirty-ve miRNAs, including 26 known and 9 novel members, were signi cantly different expressed between MC and MH libraries. Furthermore, 174 target genes were predicted to be cleaved by 115 miRNAs using degradome sequencing.Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for these targets to explore the biological function and pathways involved. Based on the relationships of miRNAs, target genes and the enriched results, a regulatory network was constructed for the miRNAs and their respective target genes, and 16 signi cantly differently expressed miRNAs (DEMs) were involved in the network.Conclusions: The results revealed novel insights into the roles of miRNAs in heat stress response and provided a useful foundation for understanding the regulatory mechanisms of heat-responsive miRNAs in maize.

Identification and characterization of heat-responsive lncRNAs in maize inbred line CM1

“…Increasing evidence indicates that all protein-coding genes, miRNAs and lncRNAs have important biological functions in various abiotic stress responses. In our previous study, 35 DEMs were identified in CM1 under heat stress and their target mRNAs were predicted using degradome sequencing [ 38 ]. The regulatory relationships of these 35 DEMs and the detected DElncRNAs were further predicted in the present study.…”

“…To construct a regulatory network in the response to heat stress in the maize inbred line CM1, the GO and KEGG annotations for the common target genes shared by cis - and trans -acting lncRNAs were used to explore the potential biological functions of DElncRNAs. In addition, 35 significantly differentially expressed miRNAs (DEMs) identified in our previous study [ 38 ], were used to predict the regulatory relationships between DEMs and DElncRNAs using psRNATarget software [ 39 ]. On the basis of these results, Cytoscape software was used to construct a lncRNA-mediated regulatory network to visualize the regulatory relationships of DElncRNAs, DEMs, target genes, and the significantly enriched GO terms and KEGG pathways ( p -value < 0.05).…”

Identification of miRNAs and their target genes associated with improved maize seed vigor induced by gibberellin

“…Recently, increasing number of miRNAs related with plant seeds have been identified and functionally studied in plants, such as Arabidopsis ( Mehdi et al, 2021 ), rice ( Parmar et al, 2020 ), maize ( Zhao et al, 2022 ) and Brassica napus ( Jiang et al, 2021 ). MiR159, targeting two abscisic acid (ABA)-positive regulators MYB33 and MYB101, was proved to play a vital role in the seed germination process ( Reyes and Chua, 2007 ).…”