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...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fgene.2018.00051/full |
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| author | Sam Browett Gillian McHugo Ian W. Richardson David A. Magee Stephen D. E. Park Alan G. Fahey John F. Kearney Carolina N. Correia Imtiaz A. S. Randhawa David E. MacHugh David E. MacHugh |
| author_facet | Sam Browett Gillian McHugo Ian W. Richardson David A. Magee Stephen D. E. Park Alan G. Fahey John F. Kearney Carolina N. Correia Imtiaz A. S. Randhawa David E. MacHugh David E. MacHugh |
| author_sort | Sam Browett |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T07:59:00Z |
| format | Article |
| id | doaj.art-59ecc05053dc415eba14db4361db30f0 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-13T07:59:00Z |
| publishDate | 2018-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-59ecc05053dc415eba14db4361db30f02022-12-22T02:55:19ZengFrontiers Media S.A.Frontiers in Genetics1664-80212018-02-01910.3389/fgene.2018.00051308410Genomic Characterisation of the Indigenous Irish Kerry Cattle BreedSam Browett0Gillian McHugo1Ian W. Richardson2David A. Magee3Stephen D. E. Park4Alan G. Fahey5John F. Kearney6Carolina N. Correia7Imtiaz A. S. Randhawa8David E. MacHugh9David E. MacHugh10Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, United KingdomAnimal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, IrelandIdentiGEN Ltd., Dublin, IrelandAnimal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, IrelandIdentiGEN Ltd., Dublin, IrelandAnimal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, IrelandIrish Cattle Breeding Federation, Bandon, IrelandAnimal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, IrelandSydney School of Veterinary Science, The University of Sydney, Camden, NSW, AustraliaAnimal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, IrelandUCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, IrelandKerry 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.http://journal.frontiersin.org/article/10.3389/fgene.2018.00051/fullcattleconservation genomicsendangered breedinbreedinggenetic diversitypopulation genomics |
| spellingShingle | Sam Browett Gillian McHugo Ian W. Richardson David A. Magee Stephen D. E. Park Alan G. Fahey John F. Kearney Carolina N. Correia Imtiaz A. S. Randhawa David E. MacHugh David E. MacHugh Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed Frontiers in Genetics cattle conservation genomics endangered breed inbreeding genetic diversity population genomics |
| title | Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed |
| title_full | Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed |
| title_fullStr | Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed |
| title_full_unstemmed | Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed |
| title_short | Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed |
| title_sort | genomic characterisation of the indigenous irish kerry cattle breed |
| topic | cattle conservation genomics endangered breed inbreeding genetic diversity population genomics |
| url | http://journal.frontiersin.org/article/10.3389/fgene.2018.00051/full |
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