**5. Conclusions**

We found that both tissue culture and transgenic processes cause global methylation changes. The tissue culture process generally leads to a reduction in global methylation whereas the transgenic process causes global methylation changes that are dependent on the background. Transgenes could cause the global methylation decrease in WYJ7 and increase in NP. In addition, tissue culture caused abundant hypo-DMRs while the transgenic process caused hyper-DMRs. Epigenetic changes such as large amounts of methylation can influence phenotype during the tissue culture process. This happened in CK, resulting in small-sized plants compared to the wild-type WYJ7, even with no transformed gene. In the transgenic lines, while the phenotype is mainly determined by the nature and function of the transgene, but the global epigenetic modification in transgenic lines occurred and resulting in different patterns of changes in plants of different genetic backgrounds. Our results indicate a potential reason behind the occurrence of transgenic plants with random and undesirable phenotypes.
