Allele-specific DNA methylation and gene expression during shoot organogenesis in tissue culture of hybrid poplar

Abstract

Plant tissue regeneration is critical for genetic transformation and genome editing techniques. During the regeneration process, changes in epigenetic modifications accompany the cell fate transition. However, how allele-specific DNA methylation in two haplotypes contributes to the transcriptional dynamics during regeneration remains elusive. Here we applied an inter-species hybrid poplar (Populus alba × P. glandulosa cv. 84 K) as a system to characterize the DNA methylation landscape during de novo shoot organogenesis at allele level. Both direct and indirect shoot organogenesis showed a reduction in genome-wide DNA methylation. At gene level, non-expressed genes were hypermethylated in comparison with expressed genes. Among the genes exhibiting significant correlations between levels of DNA methylation and gene expression, the expression patterns of 75% of genes were negatively correlated with DNA methylation in the CG context, whereas the correlation patterns in the CHH context were the reverse. The allele-biased DNA methylation was consistent during shoot organogenesis, with fewer than one-thousandth of allele-specific methylation regions shifted. Analysis of allele-specific expression revealed that there were only 1909 genes showing phase-dependent allele-biased expression in the regeneration process, among which the allele pairs with greater differences in transcription factor binding sites at promoter regions exhibited greater differences in allele expression. Our results indicated a relatively independent transcriptional regulation in two subgenomes during shoot organogenesis, which was contributed by cis-acting genomic and epigenomic variations.

Acknowledgements

This work was supported by the STI 2030 Major Projects (grant 2023ZD0405601), National Natural Science Foundation of China (grants 32171826 and 32201595) and the Natural Science Foundation of Jiangsu Province (grant BK20220411).

Author contributions

L.X. and Y.G. designed and supervised this project. Y.F., Y.J., J.H., Z.W., H.L., and Q.W. performed the data analyses and visualization. G.Y. and Y.G. performed the experiments. Y.G. and L.X. wrote the manuscript.

Data availability

The raw sequencing reads have been deposited in the Sequence Read Archive (SRA) database of NCBI under accession number PRJNA1052603 (RNA sequencing data) and PRNA1053515 (bisulfite sequencing data).

Conflict of interest

The authors declare that they have no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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