The submergence tolerance regulator SUB1A differentially coordinates molecular adaptation to submergence in mature and growing leaves of rice (Oryza sativa L.).

A typical adaptive response to submergence regulated by SUB1A, the ethylene-responsive transcription factor gene, is the restricted elongation of the uppermost leaves. However, the molecular and physiological functions of SUB1A have been characterized using entire shoot tissues, most of which are mature leaves that do not elongate under submergence. We aimed to identify leaf-type-specific and overlapping adaptations coordinated in SUB1A-dependent and -independent manners. To this end, we compared the transcriptomic and hormonal responses to submergence between mature and growing leaves using rice genotypes with and without SUB1A. Monosaccharide, branched-chain amino acid, and nucleoside metabolism, associated with ATP synthesis, were commonly activated in both leaf types regardless of genotype. In both leaf types, pathways involved in carbohydrate and nitrogen metabolism were suppressed by SUB1A, with more severe restriction in growing leaves that have a greater energy demand if SUB1A is absent. In growing leaves, accumulation of and responsiveness to growth-regulating hormones were properly modulated by SUB1A, which correlated with restricted elongation. In mature leaves, submergence-induced auxin accumulation was suppressed by SUB1A. This study demonstrates that different sets of hormonal pathways, both of which are modulated by SUB1A, contribute to distinct adaptive responses to submergence in mature and growing rice leaves.