Flowering is a necessary condition and basis for yield in the life cycle of woody fruit trees.  Although there has been considerable interest in the regulatory mechanisms underlying floral induction and flowering, the associated epigenetic modifications remain poorly characterized.  We identified genome-wide DNA methylation changes and the transcriptional responses in axillary buds of ‘Qinguan’ (QA) and ‘Fuji’ (FA) varieties with contrasting flowering behaviors.  The DNA methylation levels were 19.35, 62.96 and 17.68% in FA, and 19.64, 62.49 and 17.86% in QA in the CG, CHG and CHH contexts, respectively.  The number of hypermethylated and hypomethylated differentially methylated regions (DMRs) in different regions contributed to significantly up- and downregulated gene expression.  DNA methylation can positively or negatively regulate gene expression depending on the CG, CHG and CHH contexts and their locations in different regions.  Additionally, the huge differences in transcription of MIKC^c-type MADS-box genes, and multiple flowering genes in multiple flowering pathways (i.e., light, aging, GA and sugar) by changing DNA methylation, contributed to contrasting flowering behaviors in both QA and FA.  Specifically, the floral meristem identity genes (i.e., FT, LEAFY, AP1 and SOC1) exhibited significantly higher expression in QA than FA, but the floral repressors (i.e., SVP, AGL15, and AGL18) showed the opposite trend.  Significant differences in multiple hormone levels were due to differentially expressed genes (DEGs) and their DMRs in hormone synthesis pathways, leading to both contrasting axillary bud outgrowth and flowering behaviors.  These findings reflect the diversity in the epigenetic regulation of gene expression and may be helpful for elucidating the epigenetic regulatory mechanism underlying the axillary bud flowering in apple.

Metabolite–microbe interactions are pivotal hubs for maintaining crop productivity under abiotic stress, and silicon (Si) fertilization has been widely recognized for enhancing plant stress tolerance. However, the mechanisms by which Si mediates rhizosphere metabolic reprogramming and microbial regulation to synergistically improve crop drought resilience remain unclear. Here, a two-year field experiment (2023–2024) was conducted using upland rice cultivar “Hanyou 73”. Treatments included well-watered conditions (CK), drought stress (D), and four Si application rates under drought (DS1-DS4, 25, 50, 75, and 100 kg ha^-1, respectively). We systematically investigated the coupled effects of Si on rhizosphere metabolites, microbial communities, and plant stress responses. Drought stress disrupted oxidative homeostasis, reduced photosynthetic capacity, and inhibited carbon and nitrogen metabolism, resulting in yield reductions of 27.96 and 20.37% in 2023 and 2024, respectively. Compared with D, DS3 significantly increased the levels of rhizosphere N- and sugar-related metabolites and enhanced soil microbial diversity, thereby stabilizing soil nitrogen cycling and enriching beneficial taxa (g_Bacillus). Consequently, nitrogen use efficiency increased by 26.21%, leaf superoxide dismutase (SOD) activity increased by 40.31%, and grain yield increased by 22.98 and 20.90% across the two years. Validation experiments further demonstrated that the combined application of Si and N/sugar-related metabolites (Ethanamine, Tagatose, Urea, Sorbose, and Fumaric acid) significantly promoted upland rice growth and soil nutrient accumulation, stimulated the proliferation of strain BT021, strengthened soil N cycling, increased soil N-related enzyme activities, and enhanced plant growth and antioxidant capacity. Structural equation modeling (SEM) revealed that Si directly regulated yield variation under drought through metabolite–microbiome coupling–driven nutrient cycling. Overall, Si fertilization reshapes rhizosphere processes via metabolite–microbe synergy, improves soil N cycling and rhizosphere environmental quality under drought, promotes plant nutrient transport, and stabilizes yield, providing new mechanistic insights and an applicable paradigm for green, stress-resilient yield improvement in upland agriculture.