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.

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.HighlightThis study identifies 5 barley varieties with different tolerance to waterlogging. We provide the first RNA-seq datasets identifying both conserved and unique transcriptional responses in both waterlogging tolerant and sensitive barley varieties.

In the model plant Arabidopsis thaliana, the zinc-finger transcription factor KNUCKLES (KNU) plays an important role in the termination of floral meristem activity, a process that is crucial for preventing the overgrowth of flowers. The KNU gene is activated in floral meristems by the floral organ identity factor AGAMOUS (AG), and it has been shown that both AG and KNU act in floral meristem control by directly repressing the stem cell regulator WUSCHEL (WUS), which leads to a loss of stem cell activity. When we re-examined the expression pattern of KNU in floral meristems, we found that KNU is expressed throughout the center of floral meristems, which includes, but is considerably broader than the WUS expression domain. We therefore hypothesized that KNU may have additional functions in the control of floral meristem activity. To test this, we employed a gene perturbation approach and knocked down KNU activity at different times and in different domains of the floral meristem. In these experiments we found that early expression in the stem cell domain, which is characterized by the expression of the key meristem regulatory gene CLAVATA3 (CLV3), is crucial for the establishment of KNU expression. The results of additional genetic and molecular analyses suggest that KNU represses floral meristem activity to a large extent by acting on CLV3. Thus, KNU might need to suppress the expression of several meristem regulators to terminate floral meristem activity efficiently.