鲤低氧适应性状的全基因组关联分析

Genome-Wide Association Analysis of Hypoxia Adaptation Traits in Common Carp (Cyprinus carpio)

中文关键词: 鲤  低氧适应  单核苷酸多态性分型芯片  全基因组关联分析

英文关键词: Common carp Cyprinus carpio  Hypoxia adaptation  SNP array  Genome-wide association study

中文摘要:

      低氧适应是水产养殖物种的重要性状，筛选用于改良低氧适应性状的分子标记及候选基因有助于鱼类耐低氧品种选育。在数量性状和质量性状的遗传研究中，全基因组关联分析(GWAS)广泛应用于性状相关标记和基因的发掘。本研究对鲤(Cyprinus carpio)养殖群体开展了低氧胁迫实验，选取了低氧敏感和低氧耐受的极端性状个体作为研究对象，应用鲤鱼250K高通量分型芯片进行单核苷酸多态性(single nucleotide polymorphism, SNP)位点分型，经过数据质控后获得90个样本的87 222个多态性位点的分型结果。通过GWAS，筛选到4个低氧适应性状关联的位点：carp229220、carp195901、carp001519和carp063890，在关联位点附近注释到traf4等23个可能与低氧适应性状关联的候选基因；此外，还筛选到7个潜在关联的SNP位点。本研究初步获得了鲤低氧适应性状相关联的基因组区间，为后续效应基因精细定位奠定了基础。

英文摘要:

      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.