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The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity

Heredity (2018) | Download Citation

Abstract

Traditional Dutch chicken breeds are marginalised breeds of ornamental and cultural-historical importance. In the last decades, miniaturising of existing breeds (so called neo-bantam) has become popular and resulted in alternatives to original large breeds. However, while backcrossing is increasing the neo-bantams homozygosity, genetic exchange between breeders may increase their genetic diversity. We use the 60 K SNP array to characterise the genetic diversity, demographic history, and level of inbreeding of Dutch heritage breeds, and particularly of neo-bantams. Commercial white layers are used to contrast the impact of management strategy on genetic diversity and demography. A high proportion of alleles was found to be shared between large fowls and neo-bantams, suggesting gene flow during neo-bantams development. Population admixture analysis supports these findings, in addition to revealing introgression from neo-bantams of the same breed and of phenotypically similar breeds. The prevalence of long runs of homozygosity (ROH) confirms the importance of recent inbreeding. A high diversity in management, carried out in small breeding units explains the high heterogeneity in diversity and ROH profile displayed by traditional breeds compared to commercial lines. Population bottlenecks may explain the long ROHs in large fowls, while repetitive backcrossing for phenotype selection may account for them in neo-bantams. Our results highlight the importance of using markers to inform breeding programmes on potentially harmful homozygosity to prevent loss of genetic diversity. We conclude that bantamisation has generated unique and identifiable genetic diversity. However, this diversity can only be preserved in the near future through structured breeding programmes.

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Acknowledgements

We would like to acknowledge the owners and breed associations of the chicken populations used in this study for their help and cooperation during sampling. We would also like to thank the Centre for Genetic Resources for providing some of the samples used in this study. The research leading to some of these results has been conducted as part of the IMAGE project, which received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Grant Agreement No. 677353.

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Affiliations

  1. Animal Breeding and Genetics Group, Wageningen University & Research, Wageningen, The Netherlands

    • Chiara Bortoluzzi
    • , Richard P. M. A. Crooijmans
    • , Mirte Bosse
    • , Martien A. M. Groenen
    •  & Hendrik-Jan Megens
  2. Centre for Genetic Resources (CGN), Wageningen University & Research, Wageningen, The Netherlands

    • Sipke Joost Hiemstra

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The authors declare that they have no conflict of interest.

Corresponding author

Correspondence to Chiara Bortoluzzi.

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DOI

https://doi.org/10.1038/s41437-018-0072-3