Cold storage delays peach fruit softening via m⁶A reader PpYTHDFE1 liquid-liquid phase separation-mediated...

N⁶-methyladenosine (m⁶A), the most prevalent epitranscriptomic modification in plant mRNAs, functions as a critical regulatory layer governing environmental response. Refrigeration reduces transcripts of cell wall enzymes to delay softening, however whether m⁶A participated in this progress remains unclear. Here, we identified a cold-inducible m⁶A reader PpYTHDFE1 as a regulator that stabilizes peach (Prunus persica L.) fruit firmness. Epitranscriptomic analysis revealed that firmness maintenance correlates with reduced levels of m⁶A-modified transcripts such as expansin PpEXP3, whose overexpressing accelerates fruit softening. Both in vitro RNA-EMSA and in vivo RIP-qPCR assays demonstrate that PpYTHDFE1 recognizes m⁶A-modified PpEXP3 transcripts. Transcription inhibition assays further confirm that PpYTHDFE1 accelerates the degradation of PpEXP3 through RNA-protein interaction rather than transcriptional modulation. Mechanistically, PpYTHDFE1 participates in liquid-liquid phase separation as evidenced by fluorescence recovery after photobleaching (FRAP) assays, facilitating PpEXP3 degradation. Furthermore, overexpression of PpYTHDFE1 decreases PpEXP3 mRNA levels, while silencing PpYTHDFE1 leads to PpEXP3 transcript accumulation. A significantly negative correlation was observed between PpYTHDFE1 transcripts and firmness during fruit cold storage. Fruit firmness is increased by 44% in peach and 45% in tomato upon PpYTHDFE1 overexpressing. Our findings provide molecular insights into RNA modification-based strategies to reduce postharvest losses and develop cold-resilient horticultural crops.