PyMYB106‐PyLAC12 Modulates Callus Browning Through Phenylpropanoid‐Flavonoid Metabolism in Pinus yunnanensis

ABSTRACT Callus browning is the main obstacle in the process of in vitro culture of woody plants, which is more serious in conifers. Here, multi‐omics integration and transgenic approaches are employed to dissect the regulatory network of callus browning in Pinus yunnanensis . Browning callus showed marked reductions in total phenolics, flavonoids, and flavanols, with a concurrent increase in total quinone content. Non‐browning callus maintained low endogenous hormone homeostasis while sustaining elevated salicylic acid (SA) and 6‐benzylaminopurine (6‐BA) levels to enhance reactive oxygen species scavenging capacity. Weighted gene co‐expression network analysis (WGCNA) and two‐way orthogonal partial least squares (O2PLS) identified PyLAC12 as the central driver of browning. Overexpression of PyLAC12 substantially reduced phenolic acid and flavonoid contents and exacerbated browning, whereas PyLAC12 knockout produced the opposite effect. The upstream transcription factor PyMYB106 was further identified to directly bind the CAACCA motif and positively regulate PyLAC12 . Collectively, this study elucidates the molecular mechanism by which the PyMYB106‐PyLAC12 module drives callus browning through reprogramming flavonoid‐phenylpropanoid metabolic network.