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Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks

Nature Genetics volume 49, pages 470475 (2017) | Download Citation


The yak is remarkable for its adaptation to high altitude and occupies a central place in the economies of the mountainous regions of Asia. At lower elevations, it is common to hybridize yaks with cattle to combine the yak's hardiness with the productivity of cattle. Hybrid males are sterile, however, preventing the establishment of stable hybrid populations, but not a limited introgression after backcrossing several generations of female hybrids to male yaks. Here we inferred bovine haplotypes in the genomes of 76 Mongolian yaks using high-density SNP genotyping and whole-genome sequencing. These yaks inherited 1.3% of their genome from bovine ancestors after nearly continuous admixture over at least the last 1,500 years. The introgressed regions are enriched in genes involved in nervous system development and function, and particularly in glutamate metabolism and neurotransmission. We also identified a novel mutation associated with a polled (hornless) phenotype originating from Mongolian Turano cattle. Our results suggest that introgressive hybridization contributed to the improvement of yak management and breeding.

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A.C. acknowledges P. Boudinot and D. Boichard for interesting discussions about the major histocompatibility complex and the recombination rate in cattle, respectively; M. Boussaha, Y. Djari and C. Klopp for introducing him to the use of SAMtools and Pindel software; and M.-C. Deloche, C. Escouflaire and A. Michenet for their punctual assistance. The authors acknowledge the Zoologischer Garten Berlin, Tierpark Cottbus and Tierpark Hellabrunn Munich (Germany), as well as the Jardin des Plantes de Paris (France) and all the breeders in Europe and Asia for generously providing samples and phenotypes. Apis-Gène is acknowledged for funding the AKELOS research project. LAFUGA is funded by the LMU excellence program.

Author information


  1. Chair of Animal Genetics and Husbandry, Ludwig Maximilians University Munich, Munich, Germany.

    • Ivica Medugorac
    •  & Sophie Rothammer
  2. Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Munich, Germany.

    • Alexander Graf
    • , Helmut Blum
    •  & Stefan Krebs
  3. GABI, INRA, AgroParisTech, Université Paris–Saclay, Jouy-en-Josas, France.

    • Cécile Grohs
    •  & Aurélien Capitan
  4. Mongolian Jak Society, Sum, Ulan Bator, Mongolia.

    • Yondon Zagdsuren
  5. Center of Biotechnology and Molecular Diagnostics of the L.K. Ernst Institute of Animal Husbandry, Moscow region, Russian Federation.

    • Elena Gladyr
    •  & Natalia Zinovieva
  6. INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage GeT-PlaGe Genomic Facility, Castanet-Tolosan, France.

    • Johanna Barbieri
  7. Université de Toulouse, INPT, ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France.

    • Johanna Barbieri
  8. Tierzuchtforschung e.V. München, Grub, Germany.

    • Doris Seichter
    •  & Ingolf Russ
  9. AgriGenomics, Illumina, San Diego, California, USA.

    • André Eggen
  10. Genetics Institute, Faculty of Life Sciences, University College London, London, UK.

    • Garrett Hellenthal
  11. Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria.

    • Gottfried Brem
  12. ALLICE, Paris, France.

    • Aurélien Capitan


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A.C. and I.M. conceived and coordinated the study. A.C., I.M. and S.K. designed the study. I.M. mapped the POLLED locus and performed introgression analysis using SNP chip genotyping data, simulation analyses and neighbor-joining phylogenetic analyses. A.C. performed variant calling, annotation and screening for candidate mutations, analysis of sequence conservation, annotation of the gene content of the introgressed intervals and gene set enrichment analyses. S.K., A.G. and I.M. performed introgression analysis based on WGS data, determination of ancestral alleles, genome and capture sequencing, and R graphics. C.G., S.R. and A.C. performed PCR for Sanger sequencing and for genotyping by PCR and electrophoresis or PCR and Sanger sequencing. J.B. performed WGS. D.S. and I.R. performed SNP chip genotyping and WGS. Y.Z., E.G., N.Z. and G.B. provided samples and phenotypes. H.B. provided sequencing and bioinformatics facilities. A.E. provided Illumina BovineHD SNP chip genotyping data. G.H. provided software and expertise in admixture analysis. A.C., I.M., S.K. and A.G. contributed to writing the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Ivica Medugorac or Aurélien Capitan.

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