Gene body demethylation increases expression and is associated with self-pruning during grape genome duplication

Luming Zou; Wenwen Liu; Zhan Zhang; Everard J Edwards; Elias Kirabi Gathunga; Peige Fan; Wei Duan; Shaohua Li; Zhenchang Liang

doi:10.1038/s41438-020-0303-7

Gene body demethylation increases expression and is associated with self-pruning during grape genome duplication

Hortic Res. 2020 Jun 1;7(1):84. doi: 10.1038/s41438-020-0303-7. eCollection 2020.

Authors

Luming Zou^#^{1

2}, Wenwen Liu^#^{1

2}, Zhan Zhang^{1

2

3}, Everard J Edwards⁴, Elias Kirabi Gathunga^{1

2}, Peige Fan¹, Wei Duan¹, Shaohua Li^{1

2}, Zhenchang Liang^{1

5}

Affiliations

¹ Beijing Key Laboratory of Grape Science and Enology and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 PR China.
² University of the Chinese Academy of Sciences, Beijing, 100049 PR China.
³ College of Life Science, Shanxi Normal University, Shanxi, 041004 PR China.
⁴ CSIRO Agriculture & Food, Locked Bag 2, Glen Osmond, SA 5064 Australia.
⁵ Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 PR China.

^# Contributed equally.

Abstract

A colchicine-induced autotetraploid grapevine exhibiting potentially valuable agronomic traits for grape production and breeding, including self-pruning, was identified. This study investigated DNA methylation variation and its role in gene expression during self-pruning in the autotetraploid grapevine. We used RNA-Seq to estimate differentially expressed genes between diploid and autotetraploid grapevine shoot tips. The genes showing increases in the autotetraploid were mainly related to stress response pathways, whereas those showing decreases in the autotetraploid were related to biological metabolism and biosynthesis. Whole-genome bisulfite sequencing was performed to produce single-base methylomes for the diploid and autotetraploid grapevines. Comparison between the methylomes revealed that they were conserved in CG and CHG contexts. In the autotetraploid grapevine, hypodifferentially methylated regions (DMRs) and hyper-DMRs in the gene body increased or decreased gene expression, respectively. Our results indicated that a hypo-DMR in the ACO1 gene body increased its expression and might promote self-pruning. This study reports that hypo-DMRs in the gene body increase gene expression in plants and reveals the mechanism underlying the changes in the modifications affecting gene expression during genome duplication. Overall, our results provide valuable information for understanding the relationships between DNA methylation, gene expression, and autotetraploid breeding in grape.

Keywords: DNA methylation.