Genome-wide identification of MADS-box genes and their roles in regulating flower bud dormancy by integrating endogenous hormones and environmental temperature in Rhododendron

MADS-box transcription factors are crucial regulators of plant growth and environmental adaptation. However, their roles in the bud dormancy of woody plants, particularly in Rhododendron , remain poorly understood. This study aimed to comprehensively identify the MADS-box gene family in Rhododendron delavayi and investigate its regulatory functions during dormancy. Through genome-wide analysis, we identified 97 MADS-box genes ( RdMADS ) and revealed that dispersed duplication served as the primary driver for family expansion, accompanied by purifying selection. Phylogenetic classification and conserved motif analysis provided insights into their potential functional divergence. Transcriptome profiling across five dormancy stages unveiled a complex regulatory network, demonstrating that RdMADS genes interact extensively with hormone signaling pathways (ABA and GA biosynthesis/signaling) and cold response components. Notably, we identified a non-canonical, CBF -independent cold response mechanism centered on the RdHSFA1D - RdHSP70 module. Furthermore, RdPP2CA was pinpointed as a putative hub mediating crosstalk between ABA, GA, and cold signaling pathways. Key RdMADS genes, including SVP ( RdMADS45 ) and FLC ( RdMADS84 ), were confirmed as core regulators within this network, orchestrating the dormancy cycle. Our findings systematically decipher the molecular framework of MADS-box genes in Rhododendron bud dormancy, providing novel theoretical foundations and valuable genetic resources for future research on perennial plant dormancy and breeding applications.