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

Xiangyu Yang ¹Yafei Mao ²Xuan-Kai Wang ³Dong-Ni Ma ⁴Zhen Xu ⁵Neng Gong ⁵Barbara Henning ⁶Xu Zhang ⁴Guang He ³Yong-Yong Shi ⁷Evan E.Eichler ⁸Zhi-Qiang Li ⁷Eiki Takahashi ⁹Wei-Dong Li¹⁰

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作者信息

1. Bio-X Institutes,Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders(Ministry of Education),Shanghai Jiao Tong University,Shanghai 200240,China;Institute of Psychology and Behavioral Science,Shanghai Jiao Tong University,Shanghai 200030,China;WLA Laboratories,World Laureates Association,Shanghai 201203,China
2. Bio-X Institutes,Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders(Ministry of Education),Shanghai Jiao Tong University,Shanghai 200240,China;Department of Genome Sciences,University of Washington School of Medicine,Seattle WA 98195,USA
3. Bio-X Institutes,Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders(Ministry of Education),Shanghai Jiao Tong University,Shanghai 200240,China
4. Bio-X Institutes,Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders(Ministry of Education),Shanghai Jiao Tong University,Shanghai 200240,China;WLA Laboratories,World Laureates Association,Shanghai 201203,China
5. Institute of Neuroscience,Key Laboratory of Primate Neurobiology,CAS Center for Excellence in Brain Science and Intelligence Technology,Chinese Academy of Sciences,Shanghai 200031,China
6. Department of Genome Sciences,University of Washington School of Medicine,Seattle WA 98195,USA
7. Bio-X Institutes,Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders(Ministry of Education),Shanghai Jiao Tong University,Shanghai 200240,China;Affiliated Hospital of Qingdao University & Biomedical Sciences Institute of Qingdao University,Qingdao Branch of SJTU Bio-X Institutes,Qingdao University,Qingdao,Shandong 266003,China
8. Department of Genome Sciences,University of Washington School of Medicine,Seattle WA 98195,USA;Howard Hughes Medical Institute,University of Washington,Seattle WA 98195,USA
9. Bio-X Institutes,Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders(Ministry of Education),Shanghai Jiao Tong University,Shanghai 200240,China;Department of Biomedicine,Graduate School of Medical Sciences,Kyushu University,Fukuoka 812-8582,Japan
10. Bio-X Institutes,Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders(Ministry of Education),Shanghai Jiao Tong University,Shanghai 200240,China;Institute of Psychology and Behavioral Science,Shanghai Jiao Tong University,Shanghai 200030,China;WLA Laboratories,World Laureates Association,Shanghai 201203,China;Center for Brain Health and Brain Technology,Global Institute of Future Technology,Shanghai Jiao Tong University,Shanghai 200240,China
折叠

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.

Key words

Common marmoset(Callithrix jacchus)/Population genetics/Whole-genome sequencing/Genetic chimerism/Epilepsy/Risk locus

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基金项目

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)

Shanghai Education Commission Research and Innovation Program(2019-01-07-00-02-E00037)

a National Institutes of Health(NIH)grant(5R01HG002385)

出版年

2023

动物学研究

中国科学院昆明动物研究所中国动物学会

动物学研究

CSTPCDCSCD

影响因子：0.582

ISSN：0254-5853

参考文献量65

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