Transcriptional analysis in multiple barley varieties identifies signatures of waterlogging response

Abstract

Waterlogging leads to major crop losses globally, particularly for waterlogging‐sensitive crops such as barley. Waterlogging reduces oxygen availability and results in additional stresses, leading to the activation of hypoxia and stress response pathways that promote plant survival. Although certain barley varieties have been shown to be more tolerant to waterlogging than others and some tolerance‐related quantitative trait loci have been identified, the molecular mechanisms underlying this trait are mostly unknown. Transcriptomics approaches can provide very valuable information for our understanding of waterlogging tolerance. Here, we surveyed 21 barley varieties for the differential transcriptional activation of conserved hypoxia‐response genes under waterlogging and selected five varieties with different levels of induction of core hypoxia‐response genes. We further characterized their phenotypic response to waterlogging in terms of shoot and root traits. RNA sequencing to evaluate the genome‐wide transcriptional responses to waterlogging of these selected varieties led to the identification of a set of 98 waterlogging‐response genes common to the different datasets. Many of these genes are orthologs of the so‐called “core hypoxia response genes,” thus highlighting the conservation of plant responses to waterlogging. Hierarchical clustering analysis also identified groups of genes with intrinsic differential expression between varieties prior to waterlogging stress. These genes could constitute interesting candidates to study “predisposition” to waterlogging tolerance or sensitivity in barley.

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

“…Likewise, short term waterlogging stress in Franklin and TX9425 barley cultivars, revealed higher representation of terms in metabolism modulation, catalytic activity and oxidation-reduction processes (Luan et al, 2023). This, together with observed significant overlap with core transcriptional response to waterlogging defined for barley by Miricescu et al (2023) (Table S4A, 4B), places this research within the established literature on general transcriptomic responses in barley to waterlogging.…”

“…However, while there were large differences in basal (control) gene expression between Franklin and Yerong at both 24 and 72 h, they provided putative explanation for only between 9 and 26 % of cultivar specific differences in gene expression in response to waterlogging (Figure S3). The transcriptional signature induced by waterlogging stress in this study was also compared to the list of core waterlogging-response genes recently identified by Miricescu et al (2023), revealing a significant overlap and strong association between the response observed for both cultivars and at both time points (Table S4A), with the same direction of regulation (Table S4B) . Collectively, generated data underscore that both core and cultivar specific responses to waterlogging stress exist and need to be further dissected to elucidate transcriptional signatures related to waterlogging tolerance and sensitivity.…”

“…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.…”

“…(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. In this study, we explored the transcriptional signatures associated with responses to waterlogging in barley root tissue, focusing specifically on aerenchyma formation.…”

“…However, recent progress in this area has been observed in terms of characterization of gene expression changes and proteomic profiling associated with response to waterlogging in barley roots (Borrego-Benjumea et al, 2020; Luan et al, 2018a), facilitated by the availability of a chromosome-scale assembly of the barley genome (Mascher et al, 2017, 2021) and a high-resolution barley transcriptome (Coulter et al, 2022). 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 .…”