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

Abstract

Background Frequent occurrence of extreme high temperature is a major threat to crop production. Increasing evidence demonstrates that long non-coding RNAs (lncRNAs) have important biological functions in the regulation of the response to heat stress. However, the regulatory mechanism of lncRNAs involved in heat response requires further exploration and the regulatory network remains poorly understood in maize. Results In this research, high-throughput sequencing was adopted to systematically identify lncRNAs in maize inbred line CM1. In total, 53,249 lncRNAs (259 known lncRNAs and 52,990 novel lncRNAs) were detected, of which 993 lncRNAs showed significantly differential expression (DElncRNAs) under heat stress. By predicting the target genes, 953 common targets shared by cis- and trans-regulation of the DElncRNAs were identified, which exhibited differential expression between the control and the heat stress treatments. Functional annotation indicated that a number of important biological processes and pathways, including photosynthesis, metabolism, translation, stress response, hormone signal transduction, and spliceosome, were enriched for the common targets, suggesting that they play important roles in heat response. A lncRNA-mediated regulatory network was constructed to visualize the molecular response mechanism in response to heat stress, which represented the direct regulatory relationships of DElncRNAs, differentially expressed miRNAs, target genes, and functional annotations. Conclusions This study lays a foundation for further elucidation of the regulatory mechanism for the response to heat stress in the maize inbred line CM1. The findings provide important information for identification of heat-responsive genes, which will be beneficial for the molecular breeding in the cultivation of heat-tolerant maize germplasm.

Genome-wide identification of long non-coding RNAs and their potential functions in radish response to salt stress

“…Furthermore, it was also noticed that certain lncRNAs were not distributed on any chromosome, suggesting that these lncRNAs may be transcriptional noise (Nojima and Proudfoot, 2022). As anticipated, lncRNAs identified in radish were found to be shorter in total length and ORFs, and they also harbored fewer exons compared to protein-coding transcripts, which coincided with previous results in other plant species (Lv et al, 2016;Yan et al, 2020;Hu et al, 2022). We also recognized 363 lncRNAs that exhibit differential expression patterns in response to salt treatments (Supplementary Table S5).…”

“…In rice, an intronic lncRNA known as RICE FLOWERING ASSOCIATED (RIFLA) plays an essential role in the flowering process mediated by OsMADS56, achieved through the formation of a complex with OsiEZ1 (Shin et al, 2022). Recent research has hinted that lncRNAs exhibit responsiveness to various stressors, including salt stress (Baruah et al, 2021;Cao et al, 2021;Liu et al, 2022a;Hu et al, 2022). For example, a total of 742 saltresponsive lncRNAs were identified in maize (Liu et al, 2022a).…”

Current perspectives of lncRNAs in abiotic and biotic stress tolerance in plants

“…Accumulating evidence has shown the importance of lncRNAs in plant responses to heat stress. Several heat stress response co-expression networks between lncRNA and mRNA have been inferred by analyzing cis-acting lncRNAs ( Bhatia et al., 2020 ; He et al., 2020 ; Hu et al., 2022 ). Consistently, many TF genes were enriched in such networks providing support for the regulatory role of lncRNAs in the regulation of TFs during heat stress response potential targets of heat stress-responsive lncRNAs (204 transcripts) have also been inferred in poplar ( Song et al., 2020 ).…”

“…In B. rapa, many of the 192 predicted target genes of the 34 DE lncRNAs identified under heat stress were also heat responsive ( Song et al., 2016a ). Comparative phenotype and transcriptome analysis of the heat-resistant elite maize inbred line under heat stress revealed 993 heat-responsive DE lncRNAs with close to a thousand predicted cis-regulated target genes that share strong co-expression ( Hu et al., 2022 ). Many important biological processes and pathways involved in heat response including stress response, hormone signaling, metabolism, photosynthesis and spliceosome were also highly enriched ( Hu et al., 2022 ).…”

Metabolic pathways engineering for drought or/and heat tolerance in cereals

“…Equally, lncRNAs potentially modulate HS responses via a ceRNA mode involving lncRNA- osa-miR1439 -regulatory gene circuits ( Chen et al., 2020 ; Zhang et al., 2022c ). In maize, 53 249 (including 259 known and 52 990 unknown) heat-responsive lncRNAs were identified, among which 993 lncRNAs showed significant differential expression under HS ( Hu et al., 2022 ). The cis - and trans - regulation mechanisms involving these differentially expressed lncRNAs shared 953 common gene targets.…”