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Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement

文献类型： 外文期刊

作者： Song, Bobo 1 ; Yu, Jinshan 1 ; Li, Xiaolong 3 ; Li, Jiaming 1 ; Fan, Jing 4 ; Liu, Hainan 5 ; Wei, Weilin 1 ; Zhang, Lingchao 1 ; Gu, Kaidi 6 ; Liu, Dongliang 1 ; Zhao, Kejiao 1 ; Wu, Jun 1 ;

作者机构： 1.Nanjing Agr Univ, Coll Hort, State Key Lab Crop Genet & Germplasm Enhancement, Nanjing 210095, Jiangsu, Peoples R China

2.Zhongshan Biol Breeding Lab, Nanjing 210014, Jiangsu, Peoples R China

3.Zhejiang A&F Univ, Coll Hort Sci, Key Lab Qual & Safety Control Subtrop Fruit & Vege, Minist Agr & Rural Affairs, Hangzhou 311300, Zhejiang, Peoples R China

4.Hubei Acad Agr Sci, Inst Fruit & Tea, Wuhan 430072, Peoples R China

5.Henan Univ Sci & Technol, Coll Hort & Plant Protect, Luoyang 471023, Peoples R China

6.Shandong Agr Univ, Coll Hort Sci & Engn, Tai An 271018, Shandong, Peoples R China

关键词： DNA methylation; Domestication and improvement; Pear; Early ripening

期刊名称：GENOME BIOLOGY （ 影响因子：12.3； 五年影响因子：17.4 ）

ISSN： 1474-760X

年卷期： 2024 年 25 卷 1 期

页码：

收录情况： SCI

摘要： Background DNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown.Results Here, we investigate the variation in DNA methylation during pear domestication and improvement using whole-genome bisulfite sequencing in 41 pear accessions. Contrary to the significant decrease during rice domestication, we detect a global increase in DNA methylation during pear domestication and improvement. We find this specific increase in pear is significantly correlated with the downregulation of Demeter-like1 (DML1, encoding DNA demethylase) due to human selection. We identify a total of 5591 differentially methylated regions (DMRs). Methylation in the CG and CHG contexts undergoes co-evolution during pear domestication and improvement. DMRs have higher genetic diversity than selection sweep regions, especially in the introns. Approximately 97% of DMRs are not associated with any SNPs, and these DMRs are associated with starch and sucrose metabolism and phenylpropanoid biosynthesis. We also perform correlation analysis between DNA methylation and gene expression. We find genes close to the hypermethylated DMRs that are significantly associated with fruit ripening. We further verify the function of a hyper-DMR-associated gene, CAMTA2, and demonstrate that overexpression of CAMTA2 in tomato and pear callus inhibits fruit ripening.Conclusions Our study describes a specific pattern of DNA methylation in the domestication and improvement of a perennial pear tree and suggests that increased DNA methylation plays an essential role in the early ripening of pear fruits.

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