Integrated Multi-Omics Reveals DAM-Mediated Phytohormone Regulatory Networks Driving Bud Dormancy in ‘Mixue’ Pears

Pear (<i>Pyrus pyrifolia</i>) is an important deciduous fruit tree that requires a specific period of low-temperature accumulation to trigger spring flowering. The warmer winter caused by global warming has led to insufficient winter chilling, disrupting floral initiation and significantly reducing pear yields in Southern China. In this study, we integrated targeted phytohormone metabolomics, full-length transcriptomics, and proteomics to explore the regulatory mechanisms of dormancy in 'Mixue', a pear cultivar with an extremely low chilling requirement. Comparative analyses across the multi-omics datasets revealed 30 differentially abundant phytohormone metabolites (DPMs), 2597 differentially expressed proteins (DEPs), and 7722 differentially expressed genes (DEGs). Integrated proteomic and transcriptomic expression clustering analysis identified five members of the dormancy-associated MADS-box (<i>DAM</i>) gene family among dormancy-specific differentially expressed proteins (DEPs) and differentially expressed genes (DEGs). Phytohormone correlation analysis and <i>cis</i>-regulatory element analysis suggest that <i>DAM</i> genes may mediate dormancy progression by responding to abscisic acid (ABA), gibberellin (GA), and salicylic acid (SA). A dormancy-associated transcriptional regulatory network centered on <i>DAM</i> genes and phytohormone signaling revealed 35 transcription factors (TFs): 19 TFs appear to directly regulate the expression of <i>DAM</i> genes, 18 TFs are transcriptionally regulated by <i>DAM</i> genes, and two TFs exhibit bidirectional regulatory interactions with <i>DAM</i>. Within this regulatory network, we identified a novel pathway involving <i>REVEILLE 6</i> (<i>RVE6</i>), <i>DAM</i>, and <i>CONSTANS-LIKE 8</i> (<i>COL8</i>), which might play a critical role in regulating bud dormancy in the 'Mixue' low-chilling pear cultivar. Furthermore, lncRNAs <i>ONT.19912.1</i> and <i>ONT.20662.7</i> exhibit potential <i>cis</i>-regulatory interactions with <i>DAM1/2/3</i>. This study expands the DAM-mediated transcriptional regulatory network associated with bud dormancy, providing new insights into its molecular regulatory mechanisms in pear and establishing a theoretical framework for future investigations into bud dormancy control.