A comprehensive analytical method ‘Regulatome’ revealed a novel pathway for aerenchyma formation under waterlogging in wheat

Waterlogging is a major abiotic stress restricting crop yield globally, and aerenchyma formation is one of the most important adaptive strategies in waterlogging-tolerant plants. However, the conservation of this process remains poorly understood, and additional pathways are yet to be identified. Here, physiological, anatomical, transcriptomic, and metabolomic analyses were conducted on wheat seedlings under normal and waterlogging conditions. Waterlogging caused growth inhibition and physiological damage, as well as induced aerenchyma formation in roots. A total of 10,346 differentially expressed genes and 3,419 differential metabolites were identified in roots. In addition to the AP2/ERF (APETALA2/ETHYLENE RESPONSIVE FACTOR) gene family, integrating analyses also revealed the role of LOB/AS2 (LATERAL ORGAN BOUNDARIES/ASYMMETRIC LEAVES2) in aerenchyma formation under waterlogging. It was revealed that the classical pathway of aerenchyma formation mediated by ethylene response, as well as synergy of calcium ion and reactive oxygen species, was deeply conserved in both monocots and eudicots during 160 million years of evolution through gene co-expression networks of cross-species. The newly introduced concept 'Regulatome' supported the classical pathway of aerenchyma formation, with a proposed model of the jasmonic acid signalling pathway involved in waterlogging, suggesting its usefulness in gene identification and function exploration. These findings provide a novel insight into the regulatory mechanisms of aerenchyma formation and breeding approaches for developing wheat cultivars with high waterlogging tolerance.