Rhododendron hainanense Merr. is a tropical flowering shrub valued for its strong orna-mental and medicinal properties; however, its horticultural application is limited by its susceptibility to waterlogging disasters. The AP2/ERF transcription factor family plays crucial roles in plant growth, development, and responses to biotic and abiotic stresses; however, its regulatory mechanism in response to waterlogging stress remains unclear. This study conducted a genome-wide analysis of the AP2/ERF transcription factor family in R. hainanense, identifying 142 RhAP2/ERFs genes distributed across 13 chromosomes and classified into five subfamilies. Conserved motif analysis confirmed the characteristic AP2 domain structure. Gene duplication events revealed 16 segmental duplication pairs, indicating a potential role in adaptive evolution. Cis-element and protein interaction analyses suggested involvement in abiotic stress responses. Transcriptome and qRT-PCR results under waterlogging stress showed significant up-regulation of RhERF9 and RhERF95, with RhERF9 expression increasing 130-fold after 3 days, implying a positive regulatory role for the RhERF9 protein in early waterlogging response. Tissue-specific expression highlighted RhERF9’s strong induction in roots, associated with aerenchyma formation and hypoxia adaptation. The identified candidate AP2/ERF genes in R. hainanense play important roles in abiotic stress resistance and lay a foundation for future applications in breeding and horticulture.

Rhododendron hainanense Merr. is a tropical flowering shrub with high ornamental and medicinal value, but high temperatures are a limiting factor for its landscape application. The bHLH transcription factor family regulates plant growth and development and is crucial for responses to various stresses; however, its mechanism for regulating high-temperature stress remains unclear. This study conducted a whole-genome analysis of R. hainanense, identifying 117 RhbHLH members with complete domains, unevenly distributed across 12 chromosomes. Using Arabidopsis thaliana (L.) Heynh. as a reference, the 117 RhbHLH genes were systematically categorized into 21 subfamilies. Conserved sequence analysis showed that motifs 1 and 2 form the characteristic bHLH domain, while motifs 3–6 exhibit significant conservation. Analysis of gene duplication events indicated that R. hainanense has eight pairs of segmental duplications, suggesting their role in potential adaptive evolution. Transcriptomic studies revealed that genes such as RhbHLH107 and RhbHLH49 were highly expressed in response to high temperatures, suggesting their involvement in regulating heat stress. Furthermore, the RhbHLH gene showed a strong correlation with common metabolites like flavonoids and jasmonic acid under high temperatures, indicating that these genes may participate in regulating jasmonic acid and flavonoids to mediate plant stress responses. This study lays the foundation for further research on the role of the bHLH gene family in plant heat tolerance and provides a basis for future applications in breeding and horticulture.

Heat stress severely impairs normal plant growth and yield, which significantly limits the horticultural and productive application of most Rhododendron species. In contrast, Rhododendron hainanense exhibits considerable heat tolerance due to its unique growing environment; however, the molecular mechanisms underlying its response to heat stress remain poorly understood. In this study, R. hainanense plants were subjected to heat stress treatment. Combined transcriptomic and metabolomic analyses identified 5454 differentially expressed genes and 152 differential metabolites. The results demonstrated that heat stress significantly induced the accumulation of flavonoids in R. hainanense. Notably, derivatives of myricetin, quercetin, and kaempferol were abundantly accumulated, suggesting their potential role in aiding plant defense against heat stress. The significant up-regulation of specific Rh4CL and RhFLS genes under high-temperature stress, coupled with the substantial accumulation of their flavonoid products (myricetin, quercetin, and kaempferol), indicates a potential role for these metabolites in the thermotolerance of Rhododendron hainanense. These findings provide novel insights into the heat stress response and flavonoid biosynthesis regulation in R. hainanense, highlighting the critical role of flavonoids in plant adaptation to heat stress. This study offers valuable references for the genetic improvement of Rhododendron cultivars with high stress resistance.