A Comprehensive Transcriptomics Analysis Reveals Long Non-Coding RNA to Be Involved in the Key Metabolic Pathway in Response to Waterlogging Stress in Maize

Abstract

Waterlogging stress (WS) in a dynamic environment seriously limits plant growth, development, and yield. The regulatory mechanism underlying WS conditions at an early stage in maize seedlings is largely unknown. In the present study, the primary root tips of B73 seedlings were sampled before (0 h) and after (2 h, 4 h, 6 h, 8 h, 10 h, and 12 h) WS and then subjected to transcriptome sequencing, resulting in the identification of differentially expressed protein-coding genes (DEpcGs) and long non-coding RNAs (DElncRs) in response to WS. These DEpcGs were classified into nine clusters, which were significantly enriched in several metabolic pathways, such as glycolysis and methionine metabolism. Several transcription factor families, including AP2-EREBP, bZIP, NAC, bHLH, and MYB, were also significantly enriched. In total, 6099 lncRNAs were identified, of which 3190 were DElncRs. A co-expression analysis revealed lncRNAs to be involved in 11 transcription modules, 10 of which were significantly associated with WS. The DEpcGs in the four modules were enriched in the hypoxia response pathways, including phenylpropanoid biosynthesis, MAPK signaling, and carotenoid biosynthesis, in which 137 DElncRs were also co-expressed. Most of the co-expressed DElncRs were co-localized with previously identified quantitative trait loci associated with waterlogging tolerance. A quantitative reverse transcription-polymerase chain reaction analysis of DEpcG and DElncR expression among the 32 maize genotypes after 4 h of WS verified significant expression correlations between them as well as significant correlation with the phenotype of waterlogging tolerance. Moreover, the high proportion of hypoxia response elements in the promoter region increased the reliability of the DElncRs identified in this study. These results provide a comprehensive transcriptome in response to WS at an early stage of maize seedlings and expand our understanding of the regulatory network involved in hypoxia in plants.

Transcriptomic Analysis Revealed the Common and Divergent Responses of Maize Seedling Leaves to Cold and Heat Stresses

“…To validate the repeatability of the RNA-Seq data, eight DEGs were randomly selected for verification by qRT-PCR. The operation procedure was similar to as previously described by Yu et al [ 51 ]. Briefly, the RNA samples subjected to RNA-Seq were also used for qRT-PCR, and the total RNA was purified with RNase-free DNase (Invitrogen, Gaithersburg, MD, USA) ( Figure S1 ) following the synthesizing of single-stranded cDNA using recombinant M-MLV reverse transcriptase (Invitrogen) according to the manufacturer’s protocol.…”

The hypoxia–reoxygenation stress in plants

“…Hypoxia-responsive miRNAs, trans -acting siRNAs, and natural antisense siRNA (natsiRNA) have all been reported to regulate responses to hypoxia ( Moldovan et al, 2010 a , b ). Long non-coding RNAs (lncRNAs) are differentially expressed upon waterlogging stress ( Yu et al , 2020 ), and they also seem to regulate plant tolerance to hypoxia ( Song and Zhang, 2017 ). The hypoxia-responsive and salicylic acid (SA)-induced AtR8 lncRNA seems to be involved in activating nonexpressor of pathogenesis-related gene 1 (NPR1)-mediated and pathogenesis-related protein 1 (PR-1)-independent defense and root elongation through functional interaction with WRKY53/WRKY70 transcription factors ( Li et al , 2020 ).…”

Root Involvement in Plant Responses to Adverse Environmental Conditions

“…In Arabidopsis, a nucleus-localized lncRNA DRIR is a positive regulator, enhancing plant responses to drought and salt stress [145], and the root-specific AtR8 increases accumulation under hypoxic conditions [146]. In rice, one hundred forty four lncRNA affect root development at early stage in response to Cd stress [147], and recently it has been reported that lncRNAs are involved in the regulation of key metabolic pathways in response to water stress in maize root tips [148].…”