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Targeted Sequencing for Studying Economically Useful Traits and Phylogenetic Diversity of Ancient Sheep

  • ANIMAL GENETICS
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Abstract

Sheep were one of the first animals to be domesticated. The history of sheep domestication and their widespread distribution dates to about ten thousand years ago, during which sheep exhibit both physical changes and modifications at the genetic level. The authors developed a system of 49 oligonucleotide primers for targeted Next Generation Sequencing (NGS) of genetic loci for phylogenetic analysis and identifying economically useful traits. Altogether, NGS libraries were prepared and sequenced on an Illumina MiSeq platform(Illumina) for 48 samples, for 40 of which it was possible to determine phylogenetic lineages: 28 belonged to haplogroup B, 10 to haplogroup A, and one sample each to haplogroups C and D. Study of the genes associated with economically useful traits revealed the samples with nucleotide substitutions in the MC1R gene leading to black coat color: two samples with c.218T>A, one with c.361G>A, and two with both substitutions simultaneously, as well as one sample with the substitution in the GDF8 gene associated with muscle hypertrophy and one with the substitution in the TYRP1 gene associated with brown coat color. The data obtained confirm a high genetic diversity of sheep from ancient southwestern Siberia and the utility of targeted sequencing for the study of ancient DNA samples.

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ACKNOWLEDGMENTS

We are grateful to D.V. Panin and Ya.V. Frolov for the samples from archaeological sites Rublevo-VI and Firsovo-XIV provided for the comparative analysis and to the native English speaker T.R. Hermes for thorough text revision.

Funding

This work was supported by the Russian Science Foundation (project no. 16-18-10033 “Formation and Evolution of Life Support Systems in Nomadic Societies of Altai and Adjacent Territories in the Late Antiquity and Middle Ages: Complex Reconstruction”).

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Authors and Affiliations

  1. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia

    A. A. Kechin, M. A. Dymova & M. L. Filipenko

  2. Department of Molecular Biology and Biotechnology, Novosibirsk State University, 630090, Novosibirsk, Russia

    A. A. Kechin

  3. Department of Clinical Biochemistry, Novosibirsk State University, 630090, Novosibirsk, Russia

    A. A. Kechin & M. L. Filipenko

  4. Department of Archeology, Ethnography, and Museology, Altai State University, 656049, Barnaul, Russia

    A. A. Tishkin, S. P. Grushin & M. L. Filipenko

  5. Department of Political History, National and State Confessional Relations, Altai State University, 656049, Barnaul, Russia

    P. K. Dashkovskiy

Authors
  1. A. A. Kechin
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  2. M. A. Dymova
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  3. A. A. Tishkin
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  4. S. P. Grushin
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  5. P. K. Dashkovskiy
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  6. M. L. Filipenko
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Corresponding author

Correspondence to A. A. Kechin.

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The authors declare that they have no conflict of interest. This article does not contain any studies involving animals or human participants performed by any of the authors.

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Translated by A. Barkhash

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Kechin, A.A., Dymova, M.A., Tishkin, A.A. et al. Targeted Sequencing for Studying Economically Useful Traits and Phylogenetic Diversity of Ancient Sheep. Russ J Genet 55, 1499–1505 (2019). https://doi.org/10.1134/S102279541912007X

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  • DOI: https://doi.org/10.1134/S102279541912007X

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