Volume 44 Issue 5
Sep.  2023
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Article Contents
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. Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing. Zoological Research, 2023, 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. Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing. Zoological Research, 2023, 44(5): 837-847. doi: 10.24272/j.issn.2095-8137.2022.514

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

doi: 10.24272/j.issn.2095-8137.2022.514
The raw genomic sequencing reads can be downloaded from the NCBI (PRJNA807054), China National Center for Bioinformation (PRJCA016608), and Science Data Bank databases (DOI: 10.57760/sciencedb.08059).
Supplementary data to this article can be found online.
E.E.E. is a scientific advisory board (SAB) member of Variant Bio, Inc. All other authors declare no competing interests.
X.Y., Y.M., and W.D.L. designed the experiment. X.Y., Z.X., E.T., N.G., and W.D.L. contributed to sample collection and sample processing. X.Y., Y.M., X.K.W., Z.Q.L., B.H., G.H., and Y.Y.S. contributed to data analysis. D.N.M. and X.Z. contributed to SNP and CNV validation. E.E.E. provided computational resources. X.Y., Y.M., X.K.W., W.D.L., E.T., and Z.Q.L. generated tables and figures and drafted the manuscript. All authors contributed to editing and approved the final version of the manuscript.
Funds:  This work was supported by the National Natural Science Foundation of China (82001372), National Key Research and Development Program of China (2018YFE0126700), Shanghai Jiao Tong University 2030 Initiative (WH510363001-7), Shanghai Municipal Commission of Science and Technology Program (21dz2210100), and Shanghai Education Commission Research and Innovation Program (2019-01-07-00-02-E00037), as well as a National Institutes of Health (NIH) grant (5R01HG002385) to E.E.E.
More Information
  • 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.

  • The raw genomic sequencing reads can be downloaded from the NCBI (PRJNA807054), China National Center for Bioinformation (PRJCA016608), and Science Data Bank databases (DOI: 10.57760/sciencedb.08059).
    Supplementary data to this article can be found online.
    E.E.E. is a scientific advisory board (SAB) member of Variant Bio, Inc. All other authors declare no competing interests.
    X.Y., Y.M., and W.D.L. designed the experiment. X.Y., Z.X., E.T., N.G., and W.D.L. contributed to sample collection and sample processing. X.Y., Y.M., X.K.W., Z.Q.L., B.H., G.H., and Y.Y.S. contributed to data analysis. D.N.M. and X.Z. contributed to SNP and CNV validation. E.E.E. provided computational resources. X.Y., Y.M., X.K.W., W.D.L., E.T., and Z.Q.L. generated tables and figures and drafted the manuscript. All authors contributed to editing and approved the final version of the manuscript.
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