Lignin deposition in stone cells is a critical factor that limits pear fruit quality, affecting their market value. Calcium ions (Ca 2+) play an essential role in lignin biosynthesis during fruit stone cell production. However, the genetic mechanisms underlying the Ca 2+ regulated lignin synthesis in stone cell formation are not fully understood. In this study, we identified an NAC transcription factor (TF) PuNAC21, which is repressed by CaCl₂ treatment. PuNAC21 bound directly to the lignin biosynthesis gene peroxidase 42-like (PuPRX42-like) promoter, Ca2+ reduced pear fruit stone cell production dependent on PuNAC21 positively regulating PuPRX42-like expression. Furthermore, PuNAC21 directly regulated the expression of PuDof2.5, a TF involved in lignin biosynthesis by binding to PuPRX42-like and caffeoyl-CoA-O-methyltransferase 1(PuCCoAOMT1) promoters. Moreover, PuNAC21 interacted with PuDof2.5 to form a transcriptional regulatory module, lowering the transcription of PuPRX42-like and PuCCoAOMT1 after Ca2+ treatment, which contributed to decrease pear stone cells production. Our results revealed Ca2+-induced PuNAC21–PuDof2.5–PuPRX42-like/PuCCoAOMT1 regulatory module inhibited lignin biosynthesis, giving important insights into reducing the stone cell content in pears via molecular breeding.

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