Abstract:To reveal the genetic mechanism underlying hypoxia adaptation, it is important to identify the molecular markers and candidate genes associated with hypoxia adaptation traits. Genome-wide association studies (GWSA) are frequently used in the genetic dissection of both quantitative traits and qualitative traits, while a large number of molecular markers and samples are needed. In this study, the GWSA of the hypoxia adaptation traits of common carp (Cyprinus carpio) was conducted. A total of 1243 samples were collected for the hypoxia stress experiment, and individuals with extreme traits in the hypoxia experiment were selected as the preliminary screening samples. The Carp 250 K single nucleotide polymorphism (SNP) array was used for genotyping, generating genotypes of 199 577 SNPs for 91 samples. After quality control with a genotyping call rate of over 95% and a sample call rate of 90%, a total of 87 222 SNPs and 90 samples were obtained for the association analysis. A principal component analysis (PCA) showed no population stratification in the samples from both the sensitive and tolerant groups. Taking the PCA results as a covariance, a logistic regression was used for the association test with a threshold of the false discovery rate value of 0.05. Four associated SNPs for hypoxia adaptation traits (carp229220, carp195901, carp001519, and carp063890) were identified, and 23 genes were found in the neighboring regions of the four SNPs, including TNF receptor-associated factor 4 (traf4), fatty aldehyde dehydrogenase (aldh3a2), peroxiredoxin 5 (prdx5), estrogen-related receptor gamma (esrrg), guanine nucleotide-binding protein subunit gamma-3 (eng3), G-protein coupled receptor 12 (gpr12), general transcription factor 3C polypeptide 4 (gtf3c4), transcription factor SOX-30 (sox30), and transcription elongation (tcerg1l). Additionally, seven SNPs passed the suggestive line, which could be validated in future research with larger samples. Putative genomic regions related to hypoxia adaptation for domesticated common carp were obtained in this study, which shed new light on the fine mapping and identification of causative genes and the underlying mechanisms of hypoxia adaptation.
