Genetic insights into hypoxia tolerance in silver sillago (Sillago sihama) through QTL mapping and SNP association analysis

Oxygen is vital for the survival, growth, development, and reproduction of organisms. This study investigates the genetic basis of hypoxia tolerance in the silver sillago (Sillago sihama), a species highly valued in aquaculture despite its traditional susceptibility to low oxygen environments. By employing quantitative trait locus (QTL) mapping and single nucleotide polymorphism (SNP) association studies, the study enhances our comprehension of the genetic factors involved in hypoxia tolerance. Six QTLs associated with hypoxia tolerance have been identified, spanning five distinct linkage groups. Enrichment analyses highlighted important biological processes and pathways, particularly those related to potassium ion transport and cytochrome P450-mediated drug metabolism, which play a critical role in responding to hypoxia stress. Seven candidate genes have been identified as relevant to hypoxia tolerance: cyp20a1, mgst3b, kcnh2, cluh, adk, xdh, and slc19a2. Notably, the SNP association analysis has identified 13 SNPs within the mgst3b gene, with five SNPs (g.583 T > C, g.611 A > G, g.629 T > A, g.633 T > A, g.937 A > G) showing a significant association with hypoxia tolerance. This study sheds light on the molecular mechanisms underlying hypoxia tolerance and suggests potential genetic markers that could be used to enhance S. sihama's ability to withstand hypoxic conditions through selective breeding, providing valuable insights for the improvement of sustainable aquaculture practices. •Six QTLs linked to hypoxia tolerance were pinpointed over five linkage groups.•Identification of seven genes possibly contributing to hypoxia resilience.•Discovery of five significant hypoxia-associated SNPs in the mgst3b gene.