Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed

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...

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Published in:	Frontiers in genetics Vol. 9; p. 51
Main Authors:	Browett, Sam, McHugo, Gillian, Richardson, Ian W., Magee, David A., Park, Stephen D. E., Fahey, Alan G., Kearney, John F., Correia, Carolina N., Randhawa, Imtiaz A. S., MacHugh, David E.
Format:	Journal Article
Language:	English
Published:	Switzerland Frontiers Media S.A 19.02.2018
Subjects:	cattle conservation genomics endangered breed genetic diversity Genetics inbreeding population genomics genetic diversity conservation genomics single nucleotide polymorphism population genomics selection signature cattle inbreeding endangered breed
ISSN:	1664-8021, 1664-8021
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Abstract	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 ( ) revealed a demographic trend of diminishing over time and that recent estimated values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity ( ) 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.
AbstractList	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 ( ) revealed a demographic trend of diminishing over time and that recent estimated values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity ( ) 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. 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. 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.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.
Author	MacHugh, David E. Park, Stephen D. E. Fahey, Alan G. Kearney, John F. Correia, Carolina N. Randhawa, Imtiaz A. S. McHugo, Gillian Richardson, Ian W. Magee, David A. Browett, Sam
AuthorAffiliation	1 Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford , Salford , United Kingdom 6 UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin , Ireland 2 Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland 3 IdentiGEN Ltd. , Dublin , Ireland 4 Irish Cattle Breeding Federation , Bandon , Ireland 5 Sydney School of Veterinary Science, The University of Sydney , Camden, NSW , Australia
AuthorAffiliation_xml	– name: 4 Irish Cattle Breeding Federation , Bandon , Ireland – name: 3 IdentiGEN Ltd. , Dublin , Ireland – name: 1 Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford , Salford , United Kingdom – name: 2 Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland – name: 5 Sydney School of Veterinary Science, The University of Sydney , Camden, NSW , Australia – name: 6 UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin , Ireland
Author_xml	– sequence: 1 givenname: Sam surname: Browett fullname: Browett, Sam – sequence: 2 givenname: Gillian surname: McHugo fullname: McHugo, Gillian – sequence: 3 givenname: Ian W. surname: Richardson fullname: Richardson, Ian W. – sequence: 4 givenname: David A. surname: Magee fullname: Magee, David A. – sequence: 5 givenname: Stephen D. E. surname: Park fullname: Park, Stephen D. E. – sequence: 6 givenname: Alan G. surname: Fahey fullname: Fahey, Alan G. – sequence: 7 givenname: John F. surname: Kearney fullname: Kearney, John F. – sequence: 8 givenname: Carolina N. surname: Correia fullname: Correia, Carolina N. – sequence: 9 givenname: Imtiaz A. S. surname: Randhawa fullname: Randhawa, Imtiaz A. S. – sequence: 10 givenname: David E. surname: MacHugh fullname: MacHugh, David E.
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Copyright	Copyright © 2018 Browett, McHugo, Richardson, Magee, Park, Fahey, Kearney, Correia, Randhawa and MacHugh. 2018 Browett, McHugo, Richardson, Magee, Park, Fahey, Kearney, Correia, Randhawa and MacHugh
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Keywords	genetic diversity conservation genomics single nucleotide polymorphism population genomics selection signature cattle inbreeding endangered breed
Language	English
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Reviewed by: Gábor Mészáros, University of Natural Resources and Life Sciences, Vienna, Austria; Paolo Ajmone Marsan, Università Cattolica del Sacro Cuore, Italy Edited by: Ino Curik, Faculty of Agriculture, University of Zagreb, Croatia This article was submitted to Livestock Genomics, a section of the journal Frontiers in Genetics
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Snippet	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...
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SubjectTerms	cattle conservation genomics endangered breed genetic diversity Genetics inbreeding population genomics
Title	Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed
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