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Whole-genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions

View ORCID ProfileMelak Weldenegodguad, Ruslan Popov, View ORCID ProfileKisun Pokharel, Innokentyi Ammosov, Ming Yao, Zoya Ivanova, View ORCID ProfileJuha Kantanen
doi: https://doi.org/10.1101/390369
Melak Weldenegodguad
1Production Systems Department, Natural Resources Institute Finland (Luke), Jokioinen, Finland
2Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
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Ruslan Popov
3Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), Yakutsk, Russia
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Kisun Pokharel
1Production Systems Department, Natural Resources Institute Finland (Luke), Jokioinen, Finland
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Innokentyi Ammosov
4Board of Agricultural Office of Eveno-Bytantaj Region, Batagay-Alyta, Russia
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Ming Yao
5BGI-Shenzhen, Shenzhen, China
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Zoya Ivanova
3Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), Yakutsk, Russia
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Juha Kantanen
1Production Systems Department, Natural Resources Institute Finland (Luke), Jokioinen, Finland
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  • For correspondence: juha.kantanen@luke.fi
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Abstract

Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where cattle farming has been traditionally practiced. In this study, we performed whole-genome resequencing to genetically characterize three rare native breeds Eastern Finncattle, Western Finncattle and Yakutian cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian taurine cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European taurine breeds. This result is in contrast to the results of marker-based cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic taurine cattle may have been higher than that of the European cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on cattle genomes and on the value of the adapted breeds for the conservation of cattle genetic resources.

  • ABBREVIATIONS

    nsSNPs
    :nonsynonymous SNPs;
    GO
    :gene ontology;
    CLR
    :composite likelihood ratio;
    SFS
    :site frequency spectrum;
    PCA
    :principal component analysis;
    PSMC
    :pairwise sequentially Markovian coalescent;
    ∂a∂i
    :diffusion approximation for demographic inference;
    Gb
    :gigabases
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    Posted August 16, 2018.
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    Whole-genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions
    Melak Weldenegodguad, Ruslan Popov, Kisun Pokharel, Innokentyi Ammosov, Ming Yao, Zoya Ivanova, Juha Kantanen
    bioRxiv 390369; doi: https://doi.org/10.1101/390369
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    Whole-genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions
    Melak Weldenegodguad, Ruslan Popov, Kisun Pokharel, Innokentyi Ammosov, Ming Yao, Zoya Ivanova, Juha Kantanen
    bioRxiv 390369; doi: https://doi.org/10.1101/390369

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