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

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

doi:10.1631/jzus.B2300443

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Research Article | Updated：2024-04-07

Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds
Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds
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
Journal of Zhejiang University-SCIENCE B (Biomedicine & Biotechnology) Vol. 25, Issue 4, Pages: 324-340(2024)
Affiliations：

1.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
2.School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
3.L K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Oblast, 142132, Russia
Funds：
DOI：10.1631/jzus.B2300443
CLC：
CSTR：
Published： 15 April 2024 ，

Received： 21 June 2023 ，

Revised： 10 October 2023 ，

Natalia V. DEMENTIEVA,Yuri S. SHCHERBAKOV,Olga I. STANISHEVSKAYA等.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[J].浙江大学学报（英文版）（B辑：生物医学和生物技术）,2024,25(04):324-340.

Natalia V. DEMENTIEVA, Yuri S. SHCHERBAKOV, Olga I. STANISHEVSKAYA, et al. 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 (Biomedicine & Biotechnology) 25(4):324-340(2024)
Natalia V. DEMENTIEVA,Yuri S. SHCHERBAKOV,Olga I. STANISHEVSKAYA等.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[J].浙江大学学报（英文版）（B辑：生物医学和生物技术）,2024,25(04):324-340. DOI： 10.1631/jzus.B2300443.

Natalia V. DEMENTIEVA, Yuri S. SHCHERBAKOV, Olga I. STANISHEVSKAYA, et al. 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 (Biomedicine & Biotechnology) 25(4):324-340(2024) DOI： 10.1631/jzus.B2300443.

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。

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

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.

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

Keywords

Chicken genome diversitySingle nucleotide polymorphism (SNP) analysisGene poolGlobal ancestryPhylogenyDemographic history

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