Abstract
BackgroundLong non-coding RNAs (lncRNAs) play important roles in response to abiotic stresses in plants, by acting as cis- or trans-acting regulators of protein-coding genes. As a widely cultivated crop worldwide, maize is sensitive to salt stress particularly at the seedling stage. However, it is unclear how the expressions of protein-coding genes are affected by non-coding RNAs in maize responding to salt tolerance.ResultsThe whole transcriptome sequencing was employed to investigate the differential lncRNAs and target transcripts responding to salt stress between two maize inbred lines with contrasting salt tolerance. We developed a flexible, user-friendly, and modular RNA analysis workflow, which facilitated the identification of lncRNAs and novel mRNAs from whole transcriptome data. Using the workflow, 12,817 lncRNAs and 8,320 novel mRNAs in maize seedling roots were identified and characterized. A total of 742 lncRNAs and 7,835 mRNAs were identified as salt stress-responsive transcripts. Moreover, we obtained 41 cis- and 81 trans-target mRNA for 88 of the lncRNAs. Among these target transcripts, 11 belonged to 7 transcription factor (TF) families including bHLH, C2H2, Hap3/NF-YB, HAS, MYB, WD40, and WRKY. The above 8,577 salt stress-responsive transcripts were further classified into 28 modules by weighted gene co-expression network analysis. In the salt-tolerant module, we constructed an interaction network containing 79 nodes and 3081 edges, which included 5 lncRNAs, 18 TFs and 56 functional transcripts (FTs). As a trans-acting regulator, the lncRNA MSTRG.8888.1 affected the expressions of some salt tolerance-relative FTs, including protein-serine/threonine phosphatase 2C and galactinol synthase 1, by regulating the expression of the bHLH TF.ConclusionsThe contrasting genetic backgrounds of the two inbred lines generated considerable variations in the expression abundance of lncRNAs and protein-coding transcripts. In the co-expression networks responding to salt stress, some TFs were targeted by the lncRNAs, which further regulated the salt tolerance-related functional transcripts. We constructed a regulatory pathway of maize seedlings to salt stress, which was mediated by the hub lncRNA MSTRG.8888.1 and participated by the bHLH TF and its downstream target transcripts. Future work will be focused on the functional revelation of the regulatory pathway.
Highlights
Long non-coding RNAs play important roles in response to abiotic stresses in plants, by acting as cis- or trans-acting regulators of protein-coding genes
NLncCirSmk starts with the quality control of raw FASTQ files from paired sequencing data, going through optional trimming and Ribosome RNA (rRNA) filtering, alignment and assembly, identification of Long non-coding RNAs (lncRNAs) and novel Messenger RNAs (mRNAs), and expression analysis
Predicted lncRNA targets responding to salt stress To further address the roles of the 742 potential salt stress-responsive differentially expressed lncRNAs (DELs), we identified from all the differentially expressed mRNAs (DEMs) the potential cis- and trans- target transcripts
Summary
Long non-coding RNAs (lncRNAs) play important roles in response to abiotic stresses in plants, by acting as cis- or trans-acting regulators of protein-coding genes. As a widely cultivated crop worldwide, maize is sensitive to salt stress at the seedling stage It is unclear how the expressions of protein-coding genes are affected by non-coding RNAs in maize responding to salt tolerance. The molecular regulatory networks of these genes have not been fully elucidated It is still obscure how the expression of protein-coding genes is affected by non-coding RNA in maize [20].Long noncoding RNA (lncRNA) is a type of non-coding RNA that has ≥ 200 nucleotides in length. HuancaMamani et al identified in a hyper-arid maize line 1,710 putative lncRNAs responsive to the combined stress of salt and boron, which showed an unusual higher expression relative to protein-coding genes under the stress conditions [25]. The reports on saltresponsive lncRNAs are still being discovered in maize
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