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

The frequency of extreme precipitation events is predicted to increase owing to climate change, leading to soil waterlogging and crop yield losses, particularly in the case of susceptible species, such as barley (Hordeum vulgare). Aerenchyma formation is a key morphological adaptation to waterlogging stress and hypoxic conditions; however, its genetic regulation in barley remains largely unresolved. The aim of this study was to address this knowledge gap and characterize the transcriptional signatures associated with the waterlogging stress response and aerenchyma formation in barley roots.

Two barley cultivars (Franklin and Yerong) were subjected to waterlogging stress, followed by analysis of phenotypic traits, including root aerenchyma formation, and transcriptomic profiling of root tissue. Differential gene expression analysis and gene regulatory network construction were carried out using generated RNA-sequencing datasets.

Performed analyses identified genes transcriptionally responsive to 24 and 72 h of waterlogging in both cultivars and highlighted metabolic adaptations, regulation of reactive oxygen species signalling and management of stress responses as key elements of the waterlogging response in barley roots. Large intra-individual variation was observed for root aerenchyma formation. This variation was exploited to identify 81 candidate aerenchyma-associated genes and ascertain pathways involved in aerenchyma formation. Furthermore, network analyses suggested that the DNA damage response gene DRT100 and the cell wall-modifying genes XTH16 and XTH15 are regulatory hub genes in aerenchyma formation.

This study provides new insights into transcriptional signatures associated with waterlogging responses and aerenchyma formation in barley roots. The identified candidate aerenchyma-associated genes offer new targets for future research and breeding efforts aimed at enhancing waterlogging tolerance in this crop species.