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 ORCID:

Natalia V. DEMENTIEVA

https://orcid.org/0000-0003-0210-9344

Darren K. GRIFFIN

https://orcid.org/0000-0001-7595-3226

Michael N. ROMANOV

https://orcid.org/0000-0003-3584-4644

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Journal of Zhejiang University SCIENCE B 2024 Vol.25 No.4 P.324-340

http://doi.org/10.1631/jzus.B2300443


Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds


Author(s):  Natalia V. DEMENTIEVA, Yuri S. SHCHERBAKOV, Olga I. STANISHEVSKAYA, Anatoly B. VAKHRAMEEV, Tatiana A. LARKINA, Artem P. DYSIN, Olga A. NIKOLAEVA, Anna E. RYABOVA, Anastasiia I. AZOVTSEVA, Olga V. MITROFANOVA, Grigoriy K. PEGLIVANYAN, Natalia R. REINBACH, Darren K. GRIFFIN, Michael N. ROMANOV

Affiliation(s):  Russian Research Institute of Farm Animal Genetics and Breeding ? Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia; more

Corresponding email(s):   dementevan@mail.ru, Griffin@kent.ac.uk, m.romanov@kent.ac.uk

Key Words:  Chicken genome diversity, Single nucleotide polymorphism (SNP) analysis, Gene pool, Global ancestry, Phylogeny, Demographic history


Natalia V. DEMENTIEVA, Yuri S. SHCHERBAKOV, Olga I. STANISHEVSKAYA, Anatoly B. VAKHRAMEEV, Tatiana A. LARKINA, Artem P. DYSIN, Olga A. NIKOLAEVA, Anna E. RYABOVA, Anastasiia I. AZOVTSEVA, Olga V. MITROFANOVA, Grigoriy K. PEGLIVANYAN, Natalia R. REINBACH, Darren K. GRIFFIN, Michael N. ROMANOV. Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds[J]. Journal of Zhejiang University Science B, 2024, 25(4): 324-340.

@article{title="Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds",
author="Natalia V. DEMENTIEVA, Yuri S. SHCHERBAKOV, Olga I. STANISHEVSKAYA, Anatoly B. VAKHRAMEEV, Tatiana A. LARKINA, Artem P. DYSIN, Olga A. NIKOLAEVA, Anna E. RYABOVA, Anastasiia I. AZOVTSEVA, Olga V. MITROFANOVA, Grigoriy K. PEGLIVANYAN, Natalia R. REINBACH, Darren K. GRIFFIN, Michael N. ROMANOV",
journal="Journal of Zhejiang University Science B",
volume="25",
number="4",
pages="324-340",
year="2024",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.B2300443"
}

%0 Journal Article
%T Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds
%A Natalia V. DEMENTIEVA
%A Yuri S. SHCHERBAKOV
%A Olga I. STANISHEVSKAYA
%A Anatoly B. VAKHRAMEEV
%A Tatiana A. LARKINA
%A Artem P. DYSIN
%A Olga A. NIKOLAEVA
%A Anna E. RYABOVA
%A Anastasiia I. AZOVTSEVA
%A Olga V. MITROFANOVA
%A Grigoriy K. PEGLIVANYAN
%A Natalia R. REINBACH
%A Darren K. GRIFFIN
%A Michael N. ROMANOV
%J Journal of Zhejiang University SCIENCE B
%V 25
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%P 324-340
%@ 1673-1581
%D 2024
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B2300443

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T1 - Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds
A1 - Natalia V. DEMENTIEVA
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A1 - Olga I. STANISHEVSKAYA
A1 - Anatoly B. VAKHRAMEEV
A1 - Tatiana A. LARKINA
A1 - Artem P. DYSIN
A1 - Olga A. NIKOLAEVA
A1 - Anna E. RYABOVA
A1 - Anastasiia I. AZOVTSEVA
A1 - Olga V. MITROFANOVA
A1 - Grigoriy K. PEGLIVANYAN
A1 - Natalia R. REINBACH
A1 - Darren K. GRIFFIN
A1 - Michael N. ROMANOV
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%@ 1673-1581
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PB - Zhejiang University Press & Springer
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DOI - 10.1631/jzus.B2300443


Abstract: 
The worldwide chicken gene pool encompasses a remarkable, but shrinking, number of divergently selected breeds of diverse origin. This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture, genetic variability, and detailed structure among 49 populations. These populations represent a significant sample of the world’s chicken breeds from Europe (Russia, Czech Republic, France, Spain, UK, etc.), Asia (China), North America (USA), and Oceania (Australia). Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism (SNP) chip, a bioinformatic analysis was carried out. This included the calculation of heterozygosity/homozygosity statistics, inbreeding coefficients, and effective population size. It also included assessment of linkage disequilibrium and construction of phylogenetic trees. Using multidimensional scaling, principal component analysis, and ADMIXTURE-assisted global ancestry analysis, we explored the genetic structure of populations and subpopulations in each breed. An overall 49-population phylogeny analysis was also performed, and a refined evolutionary model of chicken breed formation was proposed, which included egg, meat, dual-purpose types, and ambiguous breeds. Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding. In general, whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.

大规模全基因组SNP分析揭示了鸡品种的全球祖先、种群发展和种群历史的复杂(和多样)的遗传图谱

Natalia V. DEMENTIEVA1, Yuri S. SHCHERBAKOV1, Olga I. STANISHEVSKAYA1, Anatoly B. VAKHRAMEEV1,Tatiana A. LARKINA1, Artem P. DYSIN1, Olga A. NIKOLAEVA1, Anna E. RYABOVA1, Anastasiia I. AZOVTSEVA1,Olga V. MITROFANOVA1, Grigoriy K. PEGLIVANYAN1, Natalia R. REINBACH1, Darren K. GRIFFIN2,Michael N. ROMANOV2,3
1Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
2School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
3L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Oblast, 142132, Russia
摘要:全球范围内的鸡品种基因库中涵盖了数量庞大且多样化起源的多种品系,不过这个数量正逐渐减少。本研究采用了大规模的全基因组分析,探究了49个种群的复杂分子结构、遗传变异性以及详细结构组成。这些种群来自于欧洲(如俄罗斯、捷克共和国、法国、西班牙、英国等)、亚洲(如中国)、北美(如美国)和大洋洲(如澳大利亚),代表了世界各地的鸡品种。我们使用Illumina 60K单核苷酸多态性(SNP)芯片对品种进行了基因型分析,然后进行了生物信息学分析。这一分析包括了杂合子/纯合子统计、近交系数和有效种群大小的计算,以及连锁不平衡的评估和系统发生树的构建。通过多维缩放、主成分分析和ADMIXTURE辅助全球祖先分析,我们探索了每个品种种群和亚群的遗传结构。此外,还进行了总体的49个种群的系统发生分析,并提出了一种精细化的鸡品种形成演化模型,其中包括蛋、肉、兼用型和混合的品种。利用现代基因组方法对家禽养殖中的遗传资源进行如此大规模的调查,不仅对于普遍了解家鸡遗传学的角度具有重要意义,而且对于进一步发展家禽育种中的基因组技术和方法也是至关重要的。总而言之,对来自全球基因库的有发展潜力的鸡品种进行全基因组SNP基因分型,将促进现代基因组学在家禽育种中的进一步发展。

关键词:鸡基因组多样性;单核苷酸多态性分析(SNP);基因库;全球原始祖先;种群发展史;种群大小历史

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

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