Abstract
SummaryPlant 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 nonembryogenic 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 in CHH methylation from NEC to EC was 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 facilitate the higher plant regeneration ability and optimize maternal genetic cultivar.
Highlights
Somatic embryogenesis is a cell differentiation process and is involved in de-differentiation and re-differentiation through reconstruction of somatic cells to generate embryogenic cells (EC) (Yang and Zhang, 2010)
The hypocotyls of maternal inbred Y668 cotton plantlets were used as explants for Agrobacterium-mediated genetic transformation with GFP as a reporter gene
The hypocotyls from seeds of R0 plants were used for tissue culture and somatic embryogenesis to generate the R1 generation
Summary
Somatic embryogenesis is a cell differentiation process and is involved in de-differentiation and re-differentiation through reconstruction of somatic cells to generate embryogenic cells (EC) (Yang and Zhang, 2010). The mechanisms of gene regulation during the tissue culture and somatic embryogenesis process have been investigated in several crops, such as soybean, potato, and cotton (Sharma et al, 2008; Thibaud-Nissen et al, 2003; Yang et al, 2012). This somatic embryogenesis process will encounter epigenetic variation, such as non-coding RNAs, DNA methylation, and histone modification, with effects on gene expression (De-la-Pena et al, 2015)
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