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Received: 2023-06-21

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Journal of Zhejiang University SCIENCE B

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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


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 – more

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

Key Words:  Chicken genome diversity; SNP analysis; Gene pool; Global ancestry; Phylogeny; Demographic history


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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, 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,in press.Frontiers of Information Technology & Electronic Engineering,in press.https://doi.org/10.1631/jzus.B2300443

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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",
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%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
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A1 - Anastasiia I. AZOVTSEVA
A1 - Olga V. MITROFANOVA
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A1 - Michael N. ROMANOV
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doi="https://doi.org/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, Asia (including three from China), North America, and 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.

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