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杨翔宇, 毛亚飞, 王宣凯, 马冬霓, 徐桢, 龚能, BarbaraHenning, 张旭, 贺光, 师咏勇, EvanE. Eichler, 李志强, 高桥英机, 李卫东. 2023: 全基因组测序分析揭示亚洲灵长类中心狨猴种群遗传结构及癫痫风险遗传位点. 动物学研究, 44(5): 837-847. DOI: 10.24272/j.issn.2095-8137.2022.514
引用本文: 杨翔宇, 毛亚飞, 王宣凯, 马冬霓, 徐桢, 龚能, BarbaraHenning, 张旭, 贺光, 师咏勇, EvanE. Eichler, 李志强, 高桥英机, 李卫东. 2023: 全基因组测序分析揭示亚洲灵长类中心狨猴种群遗传结构及癫痫风险遗传位点. 动物学研究, 44(5): 837-847. DOI: 10.24272/j.issn.2095-8137.2022.514
Xiangyu Yang, Yafei Mao, Xuan-Kai Wang, Dong-Ni Ma, Zhen Xu, Neng Gong, Barbara Henning, Xu Zhang, Guang He, Yong-Yong Shi, Evan E. Eichler, Zhi-Qiang Li, Eiki Takahashi, Wei-Dong Li. 2023. Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing. Zoological Research, 44(5): 837-847. DOI: 10.24272/j.issn.2095-8137.2022.514
Citation: Xiangyu Yang, Yafei Mao, Xuan-Kai Wang, Dong-Ni Ma, Zhen Xu, Neng Gong, Barbara Henning, Xu Zhang, Guang He, Yong-Yong Shi, Evan E. Eichler, Zhi-Qiang Li, Eiki Takahashi, Wei-Dong Li. 2023. Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing. Zoological Research, 44(5): 837-847. DOI: 10.24272/j.issn.2095-8137.2022.514

全基因组测序分析揭示亚洲灵长类中心狨猴种群遗传结构及癫痫风险遗传位点

Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing

  • 摘要: 普通狨猴(Callithrix jacchus)已成为生物医学研究中常见的非人灵长类研究动物,并于三年前发布了高质量的参考基因组组装。前期研究报道了两个亚洲灵长类中心饲养的部分狨猴中存在癫痫表型。然而,这些灵长类中心的狨猴种群遗传学以及癫痫狨猴相关的遗传变异尚未被阐明。在该研究中,我们利用全基因组测序技术对来自两个癫痫狨猴家系41个样本的遗传关系和癫痫风险变异进行探究。从41个样本中鉴定出了14 558 184个单核苷酸多态性(SNP),并发现血液样本比指尖样本具有更高的基因嵌合水平。基因分析显示这些灵长类中心的狨猴具有四级亲缘关系。此外,SNP和拷贝数变异(CNV)分析表明,WWOXPTPN21基因可能与两个家系中狨猴的癫痫发作有关;并且KCTD18样基因缺失在癫痫狨猴中比对照组狨猴更为常见。综上,该研究提供了来自两个亚洲灵长类中心的狨猴种群基因组数据资源,通过基因分析为制定维持两个亚洲灵长类中心圈养狨猴遗传多样性的合理繁殖策略提供了参考,并且利用对照研究揭示了与狨猴癫痫相关的潜在风险基因和变异。

     

    Abstract: The common marmoset (Callithrix jacchus) has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies. Epileptic marmosets have been independently reported in two Asian primate research centers. Nevertheless, the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated. Here, we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing. We identified 14 558 184 single nucleotide polymorphisms (SNPs) from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples. Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers. In addition, SNP and copy number variation (CNV) analyses suggested that the WW domain-containing oxidoreductase (WWOX) and Tyrosine-protein phosphatase nonreceptor type 21 (PTPN21) genes may be associated with epilepsy in marmosets. Notably, KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets. This study provides valuable population genomic resources for marmosets in two Asian primate centers. Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers, while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.

     

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