Co-expression network analysis of the H3K27me3/H3K4me3-modified genes correlated with chilling accumulation in apple dormant flower buds

Bud dormancy in woody perennials is essential for survival during winter and ensures robust plant development. For apple (Malus × domestica), the short-term chilling induces bud dormancy in autumn, prolonged chilling leads to dormancy release and shift to a quiescent state in winter, and a subsequent warm period promotes bud break and blooming in spring. Although several studies suggested epigenetic regulation through histone modifications contributes to bud dormancy regulation, limited information is available. To explore the involvement of H3K27me3/H3K4me3 modifications in gene expressions underlying dormancy progress, we first searched for the co-expression networks correlated with the accumulated chilling temperatures, namely the chill unit (CU), which was calculated based on the Utah model, and the ambient temperatures, namely the monthly mean temperature (MMT). We found four co-expression modules that were significantly correlated with the CU and MMT. Then, we examined the genes with significantly varying H3K27me3/H3K4me3 levels responding to temperature changes. We identified that the genes reported to integrate abscisic acid (ABA) and auxin metabolic and signaling pathways, showed varying H3K4me3 levels. These results suggest that histone modification affects dormancy phase transition possibly through integrating temperature cues on the expression changes of genes in ABA and auxin metabolic and signaling gene networks.