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1. A Population Genomics Analysis of the Native Irish Galway Sheep Breed

Author

Gillian P. McHugo, Sam Browett, Imtiaz A. S. Randhawa, Dawn J. Howard, Michael P. Mullen, Ian W. Richardson, Stephen D. E. Park, David A. Magee, Erik Scraggs, Michael J. Dover, Carolina N. Correia, James P. Hanrahan, and David E. MacHugh

Subjects
at-risk breed, conservation genomics, genetic diversity, inbreeding, livestock, selection signature, Genetics, QH426-470
Abstract

The Galway sheep population is the only native Irish sheep breed and this livestock genetic resource is currently categorised as ‘at-risk’. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recent genetic history of the breed. These analyses support the hypothesis that British Leicester sheep were used in the formation of the Galway. When compared to conventional and endangered breeds, the Galway breed was intermediate in effective population size, genomic inbreeding and runs of homozygosity. This indicates that, although the Galway breed is declining, it is still relatively genetically diverse and that conservation and management plans informed by genomic information may aid its recovery. The Galway breed also exhibited distinct genomic signatures of artificial or natural selection when compared to other breeds, which highlighted candidate genes that may be involved in production and health traits.

Published
2019
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2. Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed

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, and David E. MacHugh

Subjects
0301 basic medicine, lcsh:QH426-470, population genomics, Population, biology.animal_breed, Kerry cattle, selection signature, inbreeding, Biology, Population genomics, 03 medical and health sciences, Effective population size, single nucleotide polymorphism, Genetics, education, Genetics (clinical), Original Research, 2. Zero hunger, Genetic diversity, education.field_of_study, business.industry, 0402 animal and dairy science, 04 agricultural and veterinary sciences, genetic diversity, 040201 dairy & animal science, Breed, lcsh:Genetics, endangered breed, 030104 developmental biology, Evolutionary biology, Shorthorn, cattle, conservation genomics, Molecular Medicine, Livestock, business
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 (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.

Published
2017

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