Transcriptional analysis of waterlogging response in barley identifies signatures of waterlogging tolerance/sensitivity

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, the molecular mechanisms underlying this trait are mostly unknown. Here, we surveyed 21 barley varieties for the transcriptional activation of conserved hypoxia-response genes under waterlogging. We selected five varieties that showed differential induction of core hypoxia-response genes during waterlogging treatment and further characterized their phenotypic response to waterlogging stress, with the aim of categorizing them as waterlogging sensitive or tolerant varieties. RNA-sequencing to evaluate the transcriptional responses of these selected varieties to waterlogging led to the identification of a set of 98 core waterlogging-response genes in barley. We further identified groups of genes whose expression correlated with the varietal differences in waterlogging tolerance. These datasets identify potential candidates for molecular markers and/or gene targeting to improve waterlogging tolerance in barley. ### Competing Interest Statement The authors have declared no competing interest.