Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations
James A. Ward,
Gillian P. McHugo,
Michael J. Dover,
Thomas J. Hall,
Said Ismael Ng'ang'a,
Tad S. Sonstegard,
Daniel G. Bradley,
Laurent A.F. Frantz,
Michael Salter-Townshend,
David E. MacHugh
Affiliations
James A. Ward
Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
Gillian P. McHugo
Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
Michael J. Dover
Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
Thomas J. Hall
Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
Said Ismael Ng'ang'a
Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, 80539 Munich, Germany; School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
Tad S. Sonstegard
Acceligen, 3388 Mike Collins Drive, Eagan, MN 55121, USA
Daniel G. Bradley
Smurfit Institute of Genetics, Trinity College Dublin, D04 V1W8 Dublin, Ireland
Laurent A.F. Frantz
Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, 80539 Munich, Germany; School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
Michael Salter-Townshend
UCD School of Mathematics and Statistics, University College Dublin, D04 V1W8 Dublin, Ireland
David E. MacHugh
Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; Corresponding author
Summary: The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions, human-mediated selection preferences, and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which diverged 150–500 thousand years ago. Despite extensive admixture, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu biparental and male uniparental nuclear ancestry. This has been interpreted as the result of human-mediated dispersal ultimately stemming from zebu bulls imported from South Asia during the last three millennia. Here, we assess whether ancestry at mitochondrially targeted nuclear genes in African admixed cattle is impacted by mitonuclear functional interactions. Using high-density SNP data, we find evidence for mitonuclear coevolution across hybrid African cattle populations with a significant increase of taurine ancestry at mitochondrially targeted nuclear genes. Our results, therefore, support the hypothesis of incompatibility between the taurine mitochondrial genome and the zebu nuclear genome.
