Lignin is a major component of the plant cell wall and has a conserved basic defense function in higher plants, helping the plants cope with pathogen infection. However, the regulatory mechanism of lignin biosynthesis in plants under phytoplasma stress remains unclear. In this study, we reported that peroxidase 51 (ZjPOD51), which is involved in lignin monomer polymerization, was induced by phytoplasma infection and that overexpression of ZjPOD51 in phytoplasma-infected jujube seedlings and Arabidopsis plants significantly increased their defense response against phytoplasma. Yeast one-hybrid (Y1H) and luciferase (LUC) assays showed that ZjPOD51 transcription was directly upregulated by ZjMYB44. Genetic validation demonstrated that ZjMYB44 expression was also induced by phytoplasma infection and contributed to lignin accumulation, which consequently enhanced phytoplasma defense in a ZjPOD51-dependent manner. These results demonstrated that the ZjMYB44-ZjPOD51 module enhanced the jujube defense response against phytoplasma by upregulating lignin biosynthesis. Overall, our study first elucidates how plants regulate lignin to enhance their defense response against phytoplasma and provides clues for jujube resistance breeding.

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