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.
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。
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Data availability statement
The proprietary SNP genotyping data produced and analyzed in this study were generated using the 60K chicken SNP chip produced by Illumina Inc. for the GWMAS Consortium represented by Cobb-Vantress Inc. (Siloam Springs, AR, USA) and Hendrix Genetics B. V. (Boxmeer, The Netherlands). As such, the datasets generated using this chip are confidential and protected as intellectual property or as trade secrets. As a consequence, the SNP genotyping information used in this study was not made public but rather is kept in a secure database at the RRIFAGB. However, the data can be provided upon reasonable request and can be shared with the third parties upon approval with the GWMAS Consortium. The authors affirm that all data necessary for confirming the conclusions of the article are present within the article, figures, and tables.
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Acknowledgments
This research was supported by the Ministry of Science and Higher Education of the Russian Federation (No. 075-15-2021-1037, Internal No. 15. BRK. 21.0001). We thank the United States Department of Agriculture (USDA) Chicken GWMAS Consortium, Cobb-Vantress Inc., and Hendrix Genetics B.V. for access to the developed 60K chicken SNP chip produced by Illumina Inc. for the GWMAS Consortium. The skilled technical assistance of Olga M. ROMANOVA in preparing Fig. 4 is kindly appreciated.
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Natalia V. DEMENTIEVA: conceptualization, methodology, software application, investigation, writing - original draft, project administration, and funding acquisition. Michael N. ROMANOV: conceptualization, methodology, software application, investigation, writing - original draft, visualization, project administration, and writing - review & editing. Olga A. NIKOLAEVA, Anna E. RYABOVA, and Artem P. DYSIN: validation. Yuri S. SHCHERBAKOV and Tatiana A. LARKINA: formal analysis. Olga I. STANISHEVSKAYA, Olga V. MITROFANOVA, and Anastasiia I. AZOVTSEVA: resources. Anatoly B. VAKHRAMEEV and Grigoriy K. PEGLIVANYAN: data curation. Darren K. GRIFFIN: writing - review & editing and supervision. Natalia R. REINBACH: visualization. All authors have read and approved the content of the manuscript, and therefore, have full access to all the data in the study and take responsibility for the integrity and security of the data.
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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, and Michael N. ROMANOV declare that they have no conflict of interest.
All applicable institutional and/or national guidelines for the care and use of animals were followed. The experiments on chickens were carried out following the ethical approval by the institutional review board of the RRIFAGB, Branch of the L. K. Ernst Federal Research Center for Animal Husbandry (Protocol No. 2020–4 dated 3 March 2020).
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11585_2024_443_MOESM1_ESM.pdf
Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds
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Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds
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Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds
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Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds
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Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds
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Dementieva, N.V., Shcherbakov, Y.S., Stanishevskaya, O.I. 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. Zhejiang Univ. Sci. B 25, 324–340 (2024). https://doi.org/10.1631/jzus.B2300443
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DOI: https://doi.org/10.1631/jzus.B2300443
Key words
- Chicken genome diversity
- Single nucleotide polymorphism (SNP) analysis
- Gene pool
- Global ancestry
- Phylogeny
- Demographic history