Jiang Lihua, Guo Yongqi, Li Tianyu, Song Weihua, Chen Shun, Liu Yifan, Zheng Jialang
National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, No. 1 Haida South Road, Dinghai District, Zhoushan, 316022, Zhejiang Province, China.
Mol Biol Rep. 2024 Dec 31;52(1):93. doi: 10.1007/s11033-024-10154-y.
Larimichthys crocea is an important aquaculture species along the southeastern coast of China, with diverse environment and farming practices since artificial breeding, these different aquatic habitats are subject to significant variations in environmental factors that may involve modulation of gene expression through epigenetic mechanisms to enable species to survive and reproduce.
This study aimed to identify methylation variation sites (SMVs) in different sequence contexts (CG, CHG, and CHH) within populations of L. crocea in different habitats. All SMV sites were subjected to linear regression with environmental factors to identify candidate genes involved environmental stress. The results indicate a significant correlation between SMV sites and various environmental factors. For the wild populations in Jinmen and Zhanjiang, the primary environmental pressures for adapting are temperature and salinity. In contrast, for the domesticated populations in Zhoushan and farmed population in Xiangshan, the main environmental pressures are nitrate and dissolved oxygen. Furthermore, genes related to temperature adaptation in different aquatic environments were identified, including nr3c2, igf1, hsp70, trpm3, and fgf1. The gene rasa3 was found to be associated with pH adaptation, while genes such as atp6ap1lb, slc15a4, and gpr39 were linked to salinity, ammonia nitrogen, and dissolved oxygen. Research on the association between single methylation variation sites (SMVs) and environmental factors in aquatic organisms is scarce.
These results suggest that selection pressures can influence a significant proportion of methylation sites in this species, indirectly implying that epigenetic variation is not solely attributed to patterns of genetic variation, but is also closely linked to environmental differences. These results highlight the complex interactions between epigenetic regulation and environmental influences. Hence, this study provides preliminary evidence for a new perspective on the role of methylation patterns in L. crocea in environmental adaptation.
大黄鱼是中国东南沿海重要的水产养殖品种，自人工繁育以来，其生存环境多样，养殖方式各异，这些不同的水生栖息地的环境因素存在显著差异，可能通过表观遗传机制调节基因表达，以使物种能够生存和繁殖。
本研究旨在鉴定不同栖息地大黄鱼群体中不同序列背景（CG、CHG和CHH）下的甲基化变异位点（SMV）。所有SMV位点均与环境因素进行线性回归，以鉴定涉及环境应激的候选基因。结果表明，SMV位点与各种环境因素之间存在显著相关性。对于金门和湛江的野生群体，适应的主要环境压力是温度和盐度。相比之下，对于舟山的养殖群体和象山的养殖群体，主要环境压力是硝酸盐和溶解氧。此外，还鉴定了与不同水生环境温度适应相关的基因，包括nr3c2、igf1、hsp70、trpm3和fgf1。发现基因rasa3与pH适应相关，而atp6ap1lb、slc15a4和gpr39等基因与盐度、氨氮和溶解氧相关。关于水生生物中单个甲基化变异位点（SMV）与环境因素之间关联的研究较少。
这些结果表明，选择压力可影响该物种中相当一部分甲基化位点，间接表明表观遗传变异不仅归因于遗传变异模式，还与环境差异密切相关。这些结果突出了表观遗传调控与环境影响之间的复杂相互作用。因此，本研究为大黄鱼甲基化模式在环境适应中的作用提供了一个新视角的初步证据。
