State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.
Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China.
Int J Mol Sci. 2024 Sep 9;25(17):9740. doi: 10.3390/ijms25179740.
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 ( ♀ × ♂), 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 . 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 (8.46% vs. 7.46%). Finally, we constructed a potential regulatory network for control of the heterosis formation in EFT. Among them, , , , , , , and 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.
杂种生长优势在经济鱼类中已经造福水产养殖多年，但它的遗传和分子基础仍然不清楚。如今，一种新的杂交金花鱼（♀×♂）种质，简称 EFT，表现出父本偏生长杂种优势，为研究杂种优势的潜在调控机制提供了一个极好的模型。我们综合了转录组和甲基组，以揭示 EFT 与母本相比基因表达、表观遗传修饰和亚基因组优势的变化。整合分析表明，杂种优势杂交鱼的基因组 DNA 甲基化水平低于纯合亲本，上调基因主要是 DNA 去甲基化。此外，等位基因特异性表达（ASE）检测到父本亚基因组优势调控的父本偏生长杂种优势，肌肉中父本偏表达差异基因（DEG）完全上调。多组学结果突出了脂质代谢的作用，特别是“脂肪酸合成”、“EPA 生物合成”和“信号脂质”，在 EFT 杂种优势形成中的作用。一致地，我们的研究证明了 EFT 的二十碳五烯酸（EPA）大于母本（8.46%比 7.46%）。最后，我们构建了一个控制 EFT 杂种优势形成的潜在调控网络。其中， 、 、 、 、 、 、 和 被鉴定为关键基因。我们的结果为理解 EFT 中父本偏生长杂种优势提供了新的有价值的线索，朝着杂种优势的分子基础迈出了重要的一步。
