International Journal of Aquaculture, 2025, Vol.15, No.4, 197-207 http://www.aquapublisher.com/index.php/ija 205 Kelly's study found that the degree of DNA methylation differentiation among different geographical populations of oysters in eastern even exceeds genetic differentiation, which means that the epigenetic drift caused by the environment may confer different phenotypic characteristics on the population, making it better adapt to local conditions (Johnson and Kelly, 2020). The research shows that epigenetic variation in disease-resistant oyster populations explains about 25% of disease-resistant phenotypic variations, while pure genetic variation explains only 14%. This suggests that epigenetics contributes more to this rapid adaptation (occurring within just over a decade) (Gawra et al., 2023). However, whether epigenetic adaptation can exist stably for a long time is also a question worth discussing. Without support for genetic variation, apparent markers may gradually recover after environmental stress is relieved, and adaptability may also subside. 7 Epigenetic Research Methods and Technological Progress 7.1 High-throughput sequencing and multi-omics integrated analysis technology With the development of sequencing technology, methods for studying the epigenetics of oysters are becoming increasingly abundant. Whole genome methylation sequencing (WGBS) is widely used to map methylation maps of oysters, and can detect the distribution of 5mC in the genome with a single base resolution. Comparing the methylation differences of oysters with different growth performances by WGBS, key sites that affect growth can be localized. In the case of resource and cost limitations, simplifying representative genomic methylation sequencing (RRBS, MeDIP-Seq, etc.) is also an optional solution, focusing on the analysis of methylated hotspot regions such as CpG islands. In recent years, some studies have tried ChIP-Seq in pearl shells and successfully obtained the distribution of piRNA target sites bound by PIWI protein, providing reference for the subsequent expansion to oysters (Dellong et al., 2024). Another important direction is multiomics integration analysis, that is, obtaining methylation group, transcriptome, and even proteomic and metabolomic data of the same sample at the same time, and correlating different levels of information through bioinformatics to comprehensively analyze the epigenetic regulatory mechanism. This combination allows them to screen out candidates for epiregulatory key genes. 7.2 Epigenome editing and functional verification strategies Epigenetic research is moving from correlation analysis to causal function verification. In order to verify the effect of an apparent marker on the phenotype, it is necessary to be able to modify the marker in a targeted manner. Currently, a cutting-edge technology is to use the modified CRISPR/Cas9 system to achieve epigenome editing, fusing dCas9 that does not cleave DNA with DNA methyltransferase (DNMT) or demethylase (TET), and directed recruitment of RNA to the target gene promoter, thereby manually adding or removing methylation modifications at this site (Morita et al., 2024; Qian and Liu, 2024). Similarly, DNA methyltransferase DNMT or demethylase TET can be knocked down or knocked out to evaluate the effect of changes in global methylation levels on oyster growth and survival. In addition, pharmacological methods are also important means. DNA demethylating agent 5-azacytidine (5-Aza) has been used to test the epigenetic function of oysters: After low dose treatment of pearl oyster larvae, it was found that its DNA methylation level decreased and induced an increase in the expression of some immune-related genes. This suggests that drug treatment can verify the relationship between methylation and traits. 7.3 Shellfish epigenetic database and bioinformatics tools With the accumulation of research data, establishing a professional shellfish epigenetic database will greatly promote the development of this field. Currently, some public databases have included epigenetic data on oysters. The NCBI gene expression database (GEO) contains methylation sequencing data of different tissues of oysters and transcriptome data for stress treatment, which can be reanalysed based on this. The Chinese National Gene Bank also integrates the genomic and epitomical data of oysters to facilitate the retrieval of epigenetic status of specific genes under different conditions (Li et al., 2024). In order to promote data sharing, a resource platform with the nature of the "Aquatic Epigenetics Alliance" is being built internationally to summarize the apparent data and analysis results of fish and shellfish under various conditions. I believe that in the near future, an epigenetic information library specifically targeting oysters and other bivalves will appear, including their genomic
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