Elucidating the molecular responses to waterlogging stress in onion (Allium cepa L.) leaf by comparative transcriptome profiling

Abstract

IntroductionWaterlogging is a major stress that severely affects onion cultivation worldwide, and developing stress-tolerant varieties could be a valuable measure for overcoming its adverse effects. Gathering information regarding the molecular mechanisms and gene expression patterns of waterlogging-tolerant and sensitive genotypes is an effective method for improving stress tolerance in onions. To date, the waterlogging tolerance-governing molecular mechanism in onions is unknown.MethodsThis study identified the differentially expressed genes (DEGs) through transcriptome analysis in leaf tissue of two onion genotypes (Acc. 1666; tolerant and W-344; sensitive) presenting contrasting responses to waterlogging stress.ResultsDifferential gene expression analysis revealed that in Acc. 1666, 1629 and 3271 genes were upregulated and downregulated, respectively. In W-344, 2134 and 1909 genes were upregulated and downregulated, respectively, under waterlogging stress. The proteins coded by these DEGs regulate several key biological processes to overcome waterlogging stress such as phytohormone production, antioxidant enzymes, programmed cell death, and energy production. The clusters of orthologous group pathway analysis revealed that DEGs contributed to the post-translational modification, energy production, and carbohydrate metabolism-related pathways under waterlogging stress. The enzyme assay demonstrated higher activity of antioxidant enzymes in Acc. 1666 than in W-344. The differential expression of waterlogging tolerance related genes, such as those related to antioxidant enzymes, phytohormone biosynthesis, carbohydrate metabolism, and transcriptional factors, suggested that significant fine reprogramming of gene expression occurs in response to waterlogging stress in onion. A few genes such as ADH, PDC, PEP carboxylase, WRKY22, and Respiratory burst oxidase D were exclusively upregulated in Acc. 1666.DiscussionThe molecular information about DEGs identified in the present study would be valuable for improving stress tolerance and for developing waterlogging tolerant onion varieties.

Transcriptomic and Metabolomic Analyses Reveal the Response Mechanism of Ophiopogon japonicus to Waterlogging Stress

“…In the context of waterlogging stress, different plant varieties can exhibit significant impacts on metabolic pathways and gene transcription levels. For instance, flood-tolerant onions demonstrated a higher prevalence of downregulated genes [ 37 ], while cotton displayed a robust response involving antioxidant enzyme genes and transcription factor genes after 20 days of waterlogging [ 14 ]. Similarly, waterlogging stress induced notable changes in gene expression and metabolites in CMD.…”

“…In addition, the mechanism of plant response to waterlogging stress is also closely related to plant species and duration of flooding. For example, onion ( Allium cepa L.) showed significant changes in the phenylalanine metabolic pathway, pathogenesis-related proteins, and energy production after 72 h of waterlogging treatment [ 37 ]. Cotton ( Gossypium hirsutum L.) showed a significant increase in several metabolites including sinapyl alcohol, adenosine, and galactaric acid after 10–20 days of waterlogging [ 14 ].…”

Transcriptome Analysis Reveals POD as an Important Indicator for Assessing Low-Temperature Tolerance in Maize Radicles during Germination

“…The increase in POD activity removes excess ROS and free radicals from plants, thereby reducing damage to plant tissues from stressful environments [64,65]. In the existing study, some terms enriched to GO, such as response to oxidative stress (GO: 0006979), peroxidase activity (GO: 0004601), and hydrogen peroxide catabolic processes (GO: 0042744), are associated with plant stress tolerance [66,67]. In tobacco subjected to cold domestication, some DEGs and differential metabolites (which have regulatory roles in phenylpropanoid biosynthesis) are involved in low-temperature defence processes [68].…”