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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

Dementieva, Natalia V., Shcherbakov, Yuri S., Stanishevskaya, Olga I., Vakhrameev, Anatoly B., Larkina, Tatiana A., Dysin, Artem P., Nikolaeva, Olga A., Ryabova, Anna E., Azovtseva, Anastasiia I., Mitrofanova, Olga V., and others. (2024) Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds. Journal of Zhejiang University-SCIENCE B, 25 (4). pp. 324-340. ISSN 1673-1581. E-ISSN 1862-1783. (doi:10.1631/jzus.B2300443) (KAR id:105572)

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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.

Item Type: Article
DOI/Identification number: 10.1631/jzus.B2300443
Uncontrolled keywords: Chicken genome diversity; Single nucleotide polymorphism (SNP) analysis; Gene pool; Global ancestry; Phylogeny; Demographic history
Subjects: Q Science > QH Natural history > QH426 Genetics
Q Science > QH Natural history > QH75 Conservation (Biology)
S Agriculture > SF Animal culture
Divisions: Divisions > Division of Natural Sciences > Centre for Interdisciplinary Studies of Reproduction
Divisions > Division of Natural Sciences > Biosciences
Signature Themes: Food Systems, Natural Resources and Environment
Depositing User: Mike Romanov
Date Deposited: 08 Apr 2024 09:22 UTC
Last Modified: 28 May 2024 16:53 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/105572 (The current URI for this page, for reference purposes)

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