DNA hypomethylation associated with chilling-induced lignification in postharvest loquat fruit

Abstract Previous studies have identified that chilling affects DNA methylation and lignin biosynthesis in plants. Storing red-fleshed loquat fruit at 0 °C tends to induce lignification and leads to a decrease in the edible and commercial properties of fruit. However, it remains unclear whether and how DNA methylome changes in loquat fruit under chilling stress. In this study, whole-genome bisulfite sequencing (WGBS) was applied to analyze the global DNA methylation levels of postharvest loquat fruit stored at 0 °C. Our results revealed a genome-wide reduction in DNA methylation during 0 °C storage, which was associated with the upregulation of the DNA demethylase gene EjDML1-1 and reduced activity of RNA-directed DNA methylation (RdDM). Notably, lower methylation levels in the promoters of lignin biosynthesis (EjPAL1, EjPAL2, Ej4CL1, Ej4CL11, Ej4CL12, and EjPRX12) and activator genes (EjMYB1, EjERF39, and EjNAC5) corresponded with increased transcript levels of these genes. Furthermore, treatment with the DNA methyltransferase inhibitor 5’-Aza resulted in increased or decreased expression of these genes and enhanced lignin deposition in loquat fruit, indicating the role of DNA demethylation in lignin biosynthesis. Collectively, our findings demonstrate that low temperature stress triggers DNA demethylation, which contributes significantly to chilling-induced lignification in loquat fruit.