International Journal of Marine Science, 2025, Vol.15, No.5, 233-244 http://www.aquapublisher.com/index.php/ijms 238 Secondly, SV can change the regulatory elements and chromatin structure of genes. Some insertion mutations will introduce new promoter or enhancer elements to activate originally silent gene expression; inversion and translocation will change the relative position of genes and regulatory elements, which may cause genes that were originally regulated to be deregulated or obtain new regulation. Studies have shown that changes in the position of cis regulatory elements caused by SV can change the three-dimensional chromatin topology between regulatory elements and target genes, thereby affecting gene transcription. In oysters, there are examples that structural variation leads to differences in gene expression: for example, a repeat sequence deletion in a heat shock gene promoter region was detected in a high-temperature-resistant oyster strain, which caused the gene to be expressed less frequently but was upregulated more significantly during heat stress, which is considered an adaptive regulatory variant (Jiao et al., 2021). 5.2 Correlation with adaptation mechanisms of environmental stress Oyster populations in nature are under the test of various environmental stresses such as salinity, high and low temperatures, and low oxygen. Structural variation, as an important form of genetic variation, is often associated with adaptive traits under these stress conditions. In terms of high salt stress, oysters need to maintain the balance of osmotic pressure in and out of cells, and structural variations in some gene amplification have been proven to be beneficial to this function. Recent studies have found that solute carrier transporter (SLC) gene family has significantly expanded in oyster species living in low-salt estuary environments (Li et al., 2021). The expanded SLC gene helps enhance transmembrane transport of ion and organic osmotics, thereby improving the ability of oysters to regulate cell osmotic pressure at different salinity. In the Jinjiang oyster population in China, some copy number variations in the SLCgene vary in frequency between populations in high-salt and low-salt environments, suggesting that these SVs are selected by the environment and are involved in salinity adaptation (Zhang et al., 2022). In terms of hypoxia stress, benthic shellfish such as oysters often encounter an oxygen-deficient environment during low tides in the intertidal zone. Although structural variations in oyster hypoxia adaptation are rare, some have been found in fish and other studies: For example, a snailfish is fixed inverted chromosomes during freshwater settlement, including multiple genes related to hypoxia tolerance. In terms of temperature stress, structural variation is particularly closely related to the heat resistance of oysters. Large-scale amplification of the heat shock protein gene is one of the important molecular basis for oysters to withstand high temperature. In addition, genetic analysis of temperature adaptation in oyster populations showed that there were selected sites of structural variation among different populations. 5.3 Coupling of genomic structural variation and phenotypic diversity Genome structural variation is one of the important genetic basis for oyster phenotype diversity. There are significant variations in oysters in morphology, physiology and stress resistance, such as shell shape, color, high temperature and low salt resistance, etc., and there are often obvious differences between different populations and strains. Behind these phenotypic differences, the role of structural variation is often implicit. Gene dose changes directly caused by structural variation can lead to continuous phenotypic differences. For example, shell shape and growth traits are controlled by multiple genes. Studies have analyzed oyster breeding populations, which show that some gene regions related to growth have enriched copy number variations, and individuals with higher copy number have larger shell shapes (Jiao et al., 2021). Secondly, regulatory changes caused by structural variation can produce an on/off phenotypic transformation. Also in oysters, certain resistant phenotypes were also observed to be inherited in the form of presence/absence variants: some families either had a repeat amplification of a group of disease-resistant related genes, showing high resistance, or were completely lacking, showing susceptibility. In oyster breeding, the introduction of SV detection is expected to improve the accuracy of genetic assessment of yield and stress-resistant traits (Sun and Mai, 2025).
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