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Front. Genet. | doi: 10.3389/fgene.2018.00051

Genomic characterisation of the indigenous Irish Kerry cattle breed

  • 1School of Environment and Life Sciences, University of Salford, United Kingdom
  • 2UCD School of Agriculture and Food Science, University College Dublin, Ireland
  • 3IdentiGEN, Ltd., Ireland
  • 4UCD School of Agriculture and Food Science, University College Dublin, Ireland
  • 5Irish Cattle Breeding Federation, Ireland
  • 6Sydney School of Veterinary Science, University of Sydney, Australia
  • 7UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland

Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH¬) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.

Keywords: Cattle, conservation genomics, Endangered breed, Inbreeding, genetic diversity, Population Genomics, selection signature, Single nucleotide polymorphism, SNP array

Received: 03 Sep 2017; Accepted: 02 Feb 2018.

Edited by:

Ino Curik, Faculty of Agriculture, University of Zagreb, Croatia

Reviewed by:

Paolo Ajmone Marsan, Università Cattolica del Sacro Cuore, Italy
Gábor Mészáros, University of Natural Resources and Life Sciences, Vienna, Austria  

Copyright: © 2018 Browett, Mc Hugo, Richardson, Magee, Park, Fahey, Kearney, Correia, Randhawa and Machugh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. David E. Machugh, University College Dublin, UCD School of Agriculture and Food Science, Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD Veterinary Sciences Centre, University College Dublin, Belfield, Dublin, D04 V1W8, Dublin, Ireland, david.machugh@ucd.ie