DNA Methylation and Subgenome Dominance Reveal the Role of Lipid Metabolism in Jinhu Grouper Heterosis

文献类型： 外文期刊

第一作者： Liu, Yang

作者： Liu, Yang;Wang, Linna;Li, Zhentong;Li, Linlin;Chen, Shuai;Duan, Pengfei;Wang, Xinyi;Qiu, Yishu;Ding, Xiaoyu;Su, Jinzhi;Deng, Yuan;Tian, Yongsheng;Liu, Yang;Wang, Linna;Li, Zhentong;Li, Linlin;Tian, Yongsheng;Liu, Yang;Wang, Linna;Li, Zhentong;Li, Linlin;Tian, Yongsheng

作者机构：

关键词： Jinhu grouper (Epinephelus fuscoguttatus female x E. tukula male); methylome; transcriptome; allele-specific expression (ASE); growth heterosis; lipid metabolism

期刊名称：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES （ 影响因子：4.9； 五年影响因子：5.7 ）

ISSN： 1661-6596

年卷期： 2024 年 25 卷 17 期

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收录情况： SCI

摘要： Heterosis of growth traits in economic fish has benefited the production of aquaculture for many years, yet its genetic and molecular basis has remained obscure. Nowadays, a new germplasm of hybrid Jinhu grouper (Epinephelus fuscoguttatus female x E. tukula male), abbreviated as EFT, exhibiting paternal-biased growth heterosis, has provided an excellent model for investigating the potential regulatory mechanisms of heterosis. We integrated transcriptome and methylome to unravel the changes of gene expression, epigenetic modification, and subgenome dominance in EFT compared with maternal E. fuscoguttatus. Integration analyses showed that the heterotic hybrids showed lower genomic DNA methylation levels than the purebred parent, and the up-regulated genes were mostly DNA hypomethylation. Furthermore, allele-specific expression (ASE) detected paternal subgenome dominance-regulated paternal-biased heterosis, and paternal bias differentially expressed genes (DEGs) were wholly up-regulated in the muscle. Multi-omics results highlighted the role of lipid metabolism, particularly "Fatty acid synthesis", "EPA biosynthesis", and "Signaling lipids", in EFT heterosis formation. Coherently, our studies have proved that the eicosapentaenoic acid (EPA) of EFT was greater than that of maternal E. fuscoguttatus (8.46% vs. 7.46%). Finally, we constructed a potential regulatory network for control of the heterosis formation in EFT. Among them, fasn, pparg, dgat1, igf1, pomca, fgf8a, and fgfr4 were identified as key genes. Our results provide new and valuable clues for understanding paternal-biased growth heterosis in EFT, taking a significant step towards the molecular basis of heterosis.

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