International Journal of Molecular Zoology, 2025, Vol.15, No.2, 48-57 http://animalscipublisher.com/index.php/ijmz 52 oxygen sensing pathway genes (such as the HIF axis), oxygen transport and stress defense genes (such as hemoglobin, heat shock protein, etc.). These changes at the gene level enable catfish populations to optimize survival and reproduction in different oxygen-containing environments, and record the imprint of natural selection from the changes in gene frequency (Kang et al., 2017; Babin et al., 2024). RAD-seq analysis of high-altitude and low-altitude catfish populations in the Nujiang River Basin in China found that there were significant allele frequency differences between high-altitude tributary populations and low-altitude main stream populations at several gene loci. These differential loci are enriched in functional categories such as multicellular organism development and cell metabolism, showing traces of selection related to adaptation to hypoxic environments. Further comparison of these candidate genes with a list of 1 351 known hypoxia-related genes revealed that several of them (such as SENP3, BMPR2, DNAJB5, etc.) are key genes involved in hypoxia response and oxygen balance regulation (Kang et al., 2017). 4.2 Epigenetic regulatory mechanism The epigenetic mechanism provides catfish with another flexible means of adapting to hypoxia, enabling them to make reversible gene expression adjustments during their individual life course according to changes in environmental oxygen levels, and may pass on the beneficial effects of these adjustments to offspring, thereby fixing them in the population (Abdelnour et al., 2024; Johnston et al., 2025). Studies have found that some epigenetic enzymes themselves are sensitive to oxygen concentrations. For example, TET dioxygenases responsible for removing DNA methylation and JmjC domain proteins that mediate histone demethylation both require molecular oxygen as a cofactor. In anoxic environments, the activity of these enzymes decreases, which may lead to a decrease in 5-hydroxymethylcytosine (5hmC) in the promoter region of genes or an increase in the level of histone hypermethylation, thereby affecting the expression of related genes (Johnston et al., 2025). For species such as catfish that live in seasonally hypoxic waters for a long time, their genomes may accumulate adaptive epigenetic characteristics. For example, hypoxia-tolerant fish may respond quickly to energy crises by reducing DNA methylation in the promoters of key metabolic genes and increasing their expression in hypoxia. 4.3 Evolutionary dynamics of gene-environment interactions Gene-environment interactions play a central role in the evolution of catfish hypoxia tolerance: environmental hypoxia shapes the direction of gene selection, and the presence of genetic variation determines how quickly and to what extent fish can adapt to new oxygen-containing conditions. This feedback mechanism ensures that catfish populations can continuously optimize their tolerance strategies as the environment changes, achieving a dynamic match between gene frequency and habitat (Mandic and Regan, 2018; Yu et al., 2021). For example, artificial hybrids of African catfish and closely related species were found to have stronger environmental tolerance, including improved tolerance to hypoxia. Hybridization recombines genes from different ecological backgrounds, which may produce some genotypes that are more adaptable to extreme environments than purebreds, thus providing raw materials for breeding and adaptive evolution (Nguinkal et al., 2024). 5 Experimental Research and Functional Validation Progress 5.1 Transcriptomics and metabolomics combined analysis reveals hypoxia stress response pathways Omics technology is advancing the study of catfish hypoxia adaptation to the system level, not only verifying the important position of previous candidate genes such as HIF and sugar metabolism enzymes, but also discovering new participants such as immune and signaling pathways. These studies are of great significance in guiding genetic breeding and molecular improvement of hypoxia-tolerant varieties (Yang et al., 2018; Mu et al., 2020). Taking channel catfish as an example, Yang et al. (2018) conducted transcriptome analysis on the swim bladder tissue of adult and juvenile fish under hypoxia and normoxic conditions, and identified 155 genes in adult fish and 2 127 genes in juvenile fish whose expression was significantly changed under hypoxia. Pathway enrichment analysis showed that these differentially expressed genes were significantly enriched in the HIF signaling pathway and the MAPK, PI3K/Akt/mTOR, Ras, and VEGF cascade pathways. Metabolomics can measure changes in metabolite concentrations in fish, providing direct evidence for analyzing energy metabolism reconstruction under
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