Summary
Plant regeneration via somatic embryogenesis is time‐consuming and highly genotype‐dependent. The plant somatic
embryogenesis process provokes many epigenetics changes including DNA
methylation and histone modification. Recently, an elite cotton Jin668, with an
extremely high regeneration ability, was developed from its maternal inbred
Y668 cultivar using a Successive Regeneration Acclimation (SRA) strategy. To
reveal the underlying mechanism of SRA, we carried out a genome‐wide single‐base resolution methylation
analysis for non‐embryogenic
calluses (NECs), ECs, somatic embryos (SEs) during the somatic embryogenesis
procedure and the leaves of regenerated offspring plants. Jin668 (R4)
regenerated plants were CHH hypomethylated compared with the R0 regenerated
plants of SRA process. The increase of CHH methylation from NEC to EC were
demonstrated to be associated with the RNA‐dependent DNA methylation (RdDM) and the H3K9me2‐dependent pathway. Intriguingly,
the hypomethylated CHH differentially methylated regions (DMRs) of promoter
activated some hormone‐related and WUSCHEL‐related homeobox genes during the somatic embryogenesis process.
Inhibiting DNA methylation using zebularine treatment in NEC increased the
number of embryos. Our multi‐omics data provide new insights into the dynamics of DNA methylation
during the plant tissue culture and regenerated offspring plants. This study
also reveals that induced hypomethylation (SRA) may faciliate the higher plant
regeneration ability and optimize maternal genetic cultivar.