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.
Highlights
10,000 years ago, humans first domesticated wild aurochs (Bos primigenius)—the progenitor of modern cattle—in the Fertile Crescent region of Southwest Asia (Larson and Fuller, 2014; Larson et al, 2014; MacHugh et al, 2017)
The first population sample consisted of peripheral blood and semen straw genomic DNA collected and purified from 36 male and female Kerry cattle in 1991/92, which are a subset of the Kerry cattle population sample (n = 40) we have previously described and used for microsatellite-based population genetics analyses (MacHugh et al, 1997, 1998)
Nasal swab DNA samples were collected from a total of 75 male and female Kerry cattle and owners were consulted to ensure that a representative sample of animals was obtained
Summary
10,000 years ago, humans first domesticated wild aurochs (Bos primigenius)—the progenitor of modern cattle—in the Fertile Crescent region of Southwest Asia (Larson and Fuller, 2014; Larson et al, 2014; MacHugh et al, 2017). Analyses of medium- and high-density SNP genotypes generated using genome sequence data from an extinct British B. primigenius subfossil have shown that Kerry cattle retain a significant genomic signature of admixture from wild aurochs (Park et al, 2015; Upadhyay et al, 2017) This observation highlights the genetic distinctiveness of the Kerry population and has major implications for conservation and management of the breed. These analyses encompassed phylogenetic network reconstruction, evaluation of genetic structure and inbreeding, modelling of historical effective population sizes and functional analyses of artificial and natural selection across the Kerry genome
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