Transcriptome analysis of barley (Hordeum vulgare L.) under waterlogging stress, and overexpression of the HvADH4 gene confers waterlogging tolerance in transgenic Arabidopsis

Abstract

Background Waterlogging is one of the major abiotic stresses in barley and greatly reduces grain yield and quality. To explore the mechanism controlling waterlogging tolerance in barley, physiological, anatomical and transcriptional analyses were performed in two contrasting barley varieties, viz. Franklin (susceptible) and TX9425 (tolerant). Results Compared to Franklin, TX9425 had more adventitious roots and aerenchymas and higher antioxidant enzyme activities. A total of 3064 and 5693 differentially expressed genes (DEGs) were identified in TX9425 after 24 h and 72 h of waterlogging treatment, respectively, while 2297 and 8462 DEGs were identified in Franklin. The results suggested that TX9425 was less affected by waterlogging stress after 72 h of treatment. The DEGs were enriched mainly in energy metabolism, hormone regulation, reactive oxygen species (ROS) scavenging, and cell wall-modifying enzymes. Alcohol dehydrogenase (ADH) plays an important role in response to waterlogging stress. We found that HvADH4 was significantly upregulated under waterlogging stress in TX9425. Transgenic Arabidopsis overexpressing HvADH4 displayed higher activity of antioxidant enzymes and was more tolerant to waterlogging than the wild type (WT). Conclusions The current results provide valuable information that will be of great value for the exploration of new candidate genes for molecular breeding of waterlogging tolerance in barley.

Transcriptional signatures associated with waterlogging stress responses and aerenchyma formation in barley root tissue

“…The aerenchyma percentage increased significantly in both tested cultivars after one day of treatment, and it was further enhanced after three days of waterlogging, suggesting that this sampling window is suitable for the capture of gene expression changes associated with aerenchyma formation. Furthermore, while in general there is a relatively limited number of datasets representing barley root response to waterlogging, the time points between 1 and 3 d were also used by several recently published studies exploring response to waterlogging (Borrego-Benjumea et al, 2020; Luan et al, 2023). Using the same timepoints therefore may facilitate comparisons between gene expression response to waterlogging observed across several datasets, different experimental set ups and cultivars.…”

“…The gene expression changes observed at both time points, in both cultivars, highlighted GO terms associated with redox state management, metabolic adaptations and stress responses, suggesting that these processes play a key role in waterlogging response in barley (Figure 6). These GO terms have previously been linked to waterlogging responses in barley in other transcriptomic analyses (Borrego-Benjumea et al, 2020; Luan et al, 2023; Miricescu et al, 2023). In the first global transcriptomic study of barley root tissue under waterlogging stress, Borrego-Benjumea et al (2020) similarly identified enriched GO terms in the upregulated gene set for metabolism (carbohydrate, glycolytic and nucleoside), general enrichment for “oxidoreductase activity” and “response to chemical” related GO terms in Yerong root tissue subjected to 72 h waterlogging stress.…”

“…The root system, as the first line of defence against soil waterlogging, undergoes metabolic and anatomical adaptations supporting survival of the whole plant, and therefore should be studied as a priority when early waterlogging stress responses are considered (Herzog et al, 2016; Langan et al, 2022). However, relatively limited resources are currently available in terms of transcriptomic (Borrego-Benjumea et al, 2020; Luan et al, 2023), proteomic or metabolomic datasets (Andrzejczak et al, 2020; Luan et al, 2018a; Luan et al, 2022) characterizing responses of barley root tissue to waterlogging stress or hypoxia. Here, we used a combination of plant phenotyping and transcriptomics (RNA-seq) to further our understanding of waterlogging responses in barely root tissue, with particular focus on elucidation of pathways and genes modulating formation of root aerenchyma, a key anatomical adaptation for waterlogging tolerance (Mustroph, 2018).…”

“…For example, Borrego-Benjumea et al (2020) carried out whole root tissue transcriptional profiling under waterlogging stress and a larger scale study examined waterlogging-induced root transcriptomic signatures in 21 barley cultivars that led to isolation of 98 core waterlogging response genes (Miricescu et al, 2023). Root transcriptome profiling (Luan et al, 2023), and combination of genome-wide association studies (GWAS) and root transcriptome profiling (Luan et al, 2022), also led to identification of several barley waterlogging associated genes that were further functionally validated in Arabidopsis thaliana .…”

Exploring the Potential of Multiomics and Other Integrative Approaches for Improving Waterlogging Tolerance in Plants

“…Transcriptome analysis in G. max after waterlogging stress showed a set of differentially expressed genes related to ET signaling, energy metabolism, and fermentation pathways [ 141 ]. During waterlogging stress in wheat plants, a transcriptome analysis was performed which showed a number of differentially expressed genes associated with oxidoreductase activity and biological response to ABA and SA [ 40 ].…”