Aerial Root Growth and Development Mechanism of Flowering Cherry ‘Gotenba zakura’ (Prunus incisa) and Its Relationship with Waterlogging Tolerance

Flowering cherry is a renowned ornamental woody plant valued for its landscape applications and economic benefits in gardens. However, waterlogging during the rainy season in some areas causes death and heavy losses. Fortunately, we have found that the flowering cherry ‘Gotenba zakura’ (Prunus incisa Thunberg) is capable of generating aerial roots when subjected to heavy rains and prolonged floods. In this study, we conducted an associated analysis to explore the core regulating network of the aerial root growth mechanism in flowering cherry ‘Gotenba zakura’ by combining phenotypic observations, physiological assays, and transcriptome comparisons across five distinct stages. Through the analysis of the heatmap of DEGs (Differentially Expressed Genes) and the gene co-expression network (GCN), we identified genes that may play critical roles under waterlogging stress. The gene network indicates that aerial roots enhance waterlogging tolerance through ROS degradation, endogenous hormone induction, and energy production. This discovery provides a solid foundation for understanding the waterlogging tolerance of flowering cherry and offers molecular evidence for selecting promising rootstocks for breeding, aimed at improving waterlogging tolerance through grafting.