Mitochondria are essential organelles that generate cellular energy through oxidative phosphorylation, and mitochondrial DNA copy number (mtDNA-CN) is widely used as an indicator of mitochondrial function and biogenesis. In this study, we developed a high-throughput sequencing-based pipeline to estimate mtDNA-CN in muscle tissues of golden pompano ( Trachinotus ovatus ). The mtDNA-CN showed a normal distribution in the sequenced population, with no significant difference observed between males and females. Then, the mtDNA-CN was defined as a quantitative phenotype, and a genome-wide association study (GWAS) was conducted to identify SNPs and candidate genes involved in mtDNA-CN variation. The results revealed that a total of 105 SNPs were associated with mtDNA-CN traits, and 98 candidate genes were functionally annotated. Results from GO enrichment analysis revealed entries linked to transmembrane transport, including xenobiotic transmembrane transporter activity, ADP transmembrane transporter activity, and ATP transmembrane transporter activity. Genes from the solute carrier (SLC) family were found to be significantly associated, among which SLC25A25 was highlighted. Haplotype analysis identified 13 SNPs within SLC25A25 , with notable differences in mtDNA-CN across various haplotypes. A nonsynonymous mutation (373, Gly > Ser) was detected in this gene. Subcellular localization analysis confirmed that SLC25A25 was localized in the cytoplasm. Functional validation using siRNA-mediated knockdown demonstrated that the suppression of SLC25A25 expression significantly reduced mtDNA-CN by 36.6% and 44.5% after 24 and 48 h, respectively. Meanwhile, the knockdown group showed a significant decrease in ATP production level ( P < 0.05), along with reduced mitochondrial morphology and damaged mitochondrial ultrastructure. Our findings reveal SLC25A25 as a critical regulator of mtDNA-CN and function in fish muscle, providing novel perspectives on the genetic basis of mitochondrial homeostasis in teleosts.
Liang et al. (2026) studied this question.