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. 2024 Dec 31;52(1):93.
doi: 10.1007/s11033-024-10154-y.

Environmental influence on single methylation variation sites (SMVs) in the large yellow croaker (Larimichthys crocea): identification and correlation analysis

Lihua Jiang  1 , Yongqi Guo  2 , Tianyu Li  2 , Weihua Song  2 , Shun Chen  2 , Yifan Liu  2 , Jialang Zheng  2
Affiliations

Environmental influence on single methylation variation sites (SMVs) in the large yellow croaker (Larimichthys crocea): identification and correlation analysis

Lihua Jiang et al. Mol Biol Rep. .

Abstract

Background: 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.

Methods and results: 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.

Conclusions: 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.

Keywords: Larimichthys crocea; Environmental stress; Epigenetics; Methylation variation sites.

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Conflict of interest statement

Declarations. Conflict of interest: We declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in, or the review of, the manuscript entitled “Environmental Influence on Single Methylation Variation Sites (SMVs) in the Large Yellow Croaker (Larimichthys crocea): Identification and Correlation Analysis”. Ethical approval: All procedures were conducted in accordance with the Regulations for the Administration of Laboratory Animals (Decree No. 2 of the State Science and Technology Commission of the People’s Republic of China, November 14, 1988), and approved by the Animal Ethics Committee of Zhejiang Ocean University (Zhoushan, China). Informed consent: Not applicable.

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