文章摘要
鲤低氧适应性状的全基因组关联分析
Genome-wide Association Analysis of Hypoxia Adaptation Trait of Common Carp
投稿时间:2020-12-18  修订日期:2021-01-25
DOI:
中文关键词:   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  Hypoxia adaptation  SNP Array  Genome-wide association study
基金项目:国家重点研发计划(2018YFD0900102)和中央级公益性基本科研业务费(2020TD24,2015C007)共同资助 [This work was funded by the National Key Research and Development Program (2018YFD0900102), the Special Scientific Research Funds for Central Non-profit Institutes, Chinese Academy of Fishery Sciences (2020TD24,2015C007)]
作者单位E-mail
吴碧银 上海海洋大学
中国水产科学研究院 
wuby1619@126.com 
许建 中国水产科学研究院  
曹顶臣 中国水产科学研究院黑龙江水产研究所  
徐鹏 厦门大学  
张瀚元 中国水产科学研究院  
朱优秀 上海海洋大学
中国水产科学研究院 
 
江炎亮 中国水产科学研究院
 
 
赵紫霞 中国水产科学研究院 zhaozx@cafs.ac.cn 
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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对鱼类耐低氧品种选育具有借鉴意义。在数量性状和质量性状的遗传研究中,全基因组关联分析广泛应用于性状相关标记和基因的发掘。本研究对鲤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87222个多态性位点的分型结果。通过GWAS分析筛选到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,此外还筛选到了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 molecular markers and candidate genes associated with hypoxia adaptation trait. Genome-wide association studies were frequently used in genetic dissection of both quantitative traits and qualitative traits, while large number of molecular makers and samples were needed. In this study, the genome-wide association analysis of the hypoxia adaptation trait was conducted on common carp. Totally 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 250K Single Nucleotide Polymorphism (SNP) Array was used for genotyping, generating genotypes of 199577 SNPs for 91 samples. After quality control with genotyping call rate over 95% and sample call rate of 90%, a total of 87222 SNPs and 90 samples were obtained for association analysis. Principal Component Analysis was conducted and showed no population stratification in the samples from both sensitive group and tolerant group. Taken the PCA results as a covariance, logistic regression was used for association test with a threshold of FDR value of 0.05. Four associated SNPs for hypoxia adaptation trait (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), peroxiredosin 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 would possibly 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 into the fine mapping and identification of causative genes and the underlying mechanism.
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