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.
Highlights
Waterlogging is one of major abiotic stresses that limits the productivity of terrestrial plants and has increasingly and frequently occurred in recent years due to global climate change [1,2]
A total of 330 differentially expressed PCgenes (DEpcGs), including genes coding for enzymes involved in glycolysis and fermentation (Zm00001d028759 encoded Pyruvate decarboxylase; Zm00001d037689 encoded hexokinase7) and ethylene signaling related genes (Zm00001d027622 encoded the C3HC4-type RING finger protein), were detected at all time points, and time point-specific differentially expressed genes (DEGs) numbered more than 70 in each sample
The transcriptomic response involved in waterlogging conditions has been studied in previous works [10,11,45], there are few investigations focusing on early response, especially for the regulatory Long non-coding RNA (lncRNA) that participate in low-oxygen metabolism
Summary
Waterlogging is one of major abiotic stresses that limits the productivity of terrestrial plants and has increasingly and frequently occurred in recent years due to global climate change [1,2]. Oxygen deprivation is the key feature of waterlogging stress, as plants alter their metabolism, physiology, and development to acclimatize to the low levels of oxygen [3]. The cause of these changes is the. Long non-coding RNA (lncRNA) is defined as a transcript that is longer than 200 nucleotides (nt) in length and lacks coding potential. These RNAs have been reported to affect the expression of other genes [16]. Thousands of lncRNAs have been identified in many plant species, such as Arabidopsis [17,18], rice (Oryza sativa) [19,20], maize (Zea mays L.) [21], cotton (Gossypium spp.) [5], and castor bean (Ricinus communis) [22], with the rapid development of deep RNA-seq techniques
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