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 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.

• Publication year

  2018

• Venue

  Frontiers in Genetics

• Publication date

  2018-02-19

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.3389/fgene.2018.00051PMID 29520297PMCID 5827531
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Genomics of a revived breed: Case study of the Belgian campine cattle

  2017cited by this paper
• Taming the Past: Ancient DNA and the Study of Animal Domestication.

  2017cited by this paper
• The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds

  2017cited by this paper
• Estimation of inbreeding depression on female fertility in the Finnish Ayrshire population

  2017cited by this paper
• Identification of molecular markers for oocyte competence in bovine cumulus cells

  2017cited by this paper
• Extranuclear Sirtuins and Metabolic Stress

  2017cited by this paper
• Genome-wide mapping and estimation of inbreeding depression of semen quality traits in a cattle population.

  2017cited by this paper
• Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK

  2016cited by this paper
• Rab35 Functions in Axon Elongation Are Regulated by P53-Related Protein Kinase in a Mechanism That Involves Rab35 Protein Degradation and the Microtubule-Associated Protein 1B

  2016cited by this paper
• Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe.

  2016cited by this paper
• Review: Towards the agroecological management of ruminants, pigs and poultry through the development of sustainable breeding programmes: I-selection goals and criteria.

  2016cited by this paper
• Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

  2016influential reference
• Review: Towards the agroecological management of ruminants, pigs and poultry through the development of sustainable breeding programmes. II. Breeding strategies.

  2016cited by this paper
• Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

  2016cited by this paper
• Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data.

  2016cited by this paper
• Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data

  2016cited by this paper
• Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs

  2016cited by this paper
• Biosynthesis of coenzyme Q in eukaryotes

  2016cited by this paper
• Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds.

  2016cited by this paper
• Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non-random SNP heterozygosity.

  2016cited by this paper
• Domesticated Animal Biobanking: Land of Opportunity

  2016cited by this paper
• Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds.

  2016cited by this paper
• The Second Report on the State of the World's Animal Genetic Resources for Food and Agriculture

  2015cited by this paper
• Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle

  2015cited by this paper
• Multiple sources of bias confound functional enrichment analysis of global -omics data

  2015cited by this paper
• The Relationship between Runs of Homozygosity and Inbreeding in Jersey Cattle under Selection

  2015cited by this paper
• The first aurochs genome reveals the breeding history of British and European cattle

  2015cited by this paper
• The BioMart community portal: an innovative alternative to large, centralized data repositories

  2015cited by this paper
• Origins of cattle on Chirikof Island, Alaska, elucidated from genome-wide SNP genotypes

  2015cited by this paper
• Genome-wide insights into population structure and genetic history of tunisian local cattle using the illumina bovinesnp50 beadchip

  2015cited by this paper
• Population structure and history of the Welsh sheep breeds determined by whole genome genotyping

  2015cited by this paper
• SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data

  2015cited by this paper
• Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries

  2015cited by this paper
• Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

  2015cited by this paper
• Challenges and opportunities in genetic improvement of local livestock breeds

  2015cited by this paper
• Composite Selection Signals for Complex Traits Exemplified Through Bovine Stature Using Multibreed Cohorts of European and African Bos taurus

  2015cited by this paper
• What can livestock breeders learn from conservation genetics and vice versa?

  2015cited by this paper
• The Second Report on the State of the World's Animal Genetic Resources for Food and Agriculture

  2015cited by this paper
• Draxin from neocortical neurons controls the guidance of thalamocortical projections into the neocortex

  2015cited by this paper
• Arctic sea ice and Eurasian climate: A review

  2014cited by this paper
• fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

  2014cited by this paper
• Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep

  2014cited by this paper
• Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle

  2014cited by this paper
• Genetic characterization of a herd of the endangered Danish Jutland cattle.

  2014cited by this paper
• Genetic resources and genomics for adaptation of livestock to climate change

  2014cited by this paper
• Selection for complex traits leaves little or no classic signatures of selection

  2014cited by this paper
• Effects of Arctic Sea Ice Decline on Weather and Climate: A Review

  2014cited by this paper
• Conservation of cattle genetic resources: the role of breeds

  2014cited by this paper
• Current perspectives and the future of domestication studies

  2014cited by this paper
• The Evolution of Animal Domestication

  2014cited by this paper
• Applications of Population Genetics to Animal Breeding, from Wright, Fisher and Lush to Genomic Prediction

  2014cited by this paper
• Runs of homozygosity and distribution of functional variants in the cattle genome

  2014cited by this paper
• Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations.

  2013cited by this paper
• Using genomic tools to maintain diversity and fitness in conservation programmes

  2013cited by this paper
• Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding.

  2013cited by this paper
• Long runs of homozygosity are enriched for deleterious variation.

  2013cited by this paper
• Climate Change Impacts on Global Food Security

  2013cited by this paper
• Climate change and sustainable food production

  2012cited by this paper
• Estimation of historical effective population size using linkage disequilibria with marker data.

  2012cited by this paper
• Runs of homozygosity and population history in cattle

  2012cited by this paper
• Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

  2012cited by this paper
• On the Breeds of Cattle—Historic and Current Classifications

  2011cited by this paper
• Using genome-wide information to minimize the loss of diversity in conservation programmes.

  2011cited by this paper
• Climate change and the characterization, breeding and conservation of animal genetic resources.

  2010cited by this paper
• Dopamine D1, D2 and mu-opioid receptors are co-expressed with adenylyl cyclase 5 and phosphodiesterase 7B mRNAs in striatal rat cells.

  2010cited by this paper
• Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds

  2010cited by this paper
• A whole-genome assembly of the domestic cow, Bos taurus

  2009cited by this paper
• Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

  2009cited by this paper
• The population genetic effects of ancestry and admixture in a subdivided cattle breed.

  2009cited by this paper
• The Genome Response to Artificial Selection: A Case Study in Dairy Cattle

  2009cited by this paper
• The philosophy of scientific experimentation: a review

  2009cited by this paper
• Draxin, a Repulsive Guidance Protein for Spinal Cord and Forebrain Commissures

  2009cited by this paper
• Development and Characterization of a High Density SNP Genotyping Assay for Cattle

  2009influential reference
• Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics

  2009cited by this paper
• Genetic management of small populations: A review

  2009influential reference
• Runs of homozygosity in European populations.

  2008cited by this paper
• A Novel Function of RING Finger Protein 10 in Transcriptional Regulation of the Myelin-Associated Glycoprotein Gene and Myelin Formation in Schwann Cells

  2008cited by this paper
• The state of the world's animal genetic resources for food and agriculture

  2007cited by this paper
• PLINK: a tool set for whole-genome association and population-based linkage analyses.

  2007influential reference
• Population Structure and Eigenanalysis

  2006cited by this paper
• Criteria to assess the degree of endangerment of livestock breeds in Europe

  2004cited by this paper
• Novel multilocus measure of linkage disequilibrium to estimate past effective population size.

  2003cited by this paper
• Genetic Structure of Human Populations

  2002cited by this paper
• Genetic evidence for Near-Eastern origins of European cattle

  2001cited by this paper
• Early medieval cattle remains from a Scandinavian settlement in Dublin: genetic analysis and comparison with extant breeds.

  1999cited by this paper
• The importance of genetic diversity in livestock populations of the future.

  1999cited by this paper
• Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers.

  1998cited by this paper
• Molecular definition of an allelic series of mutations disrupting the myostatin function and causing double-muscling in cattle

  1998cited by this paper
• Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus).

  1997cited by this paper
• Kerry and Dexter Cattle and Other Ancient Irish Breeds: A History

  1990influential reference
• Analysis of breeding structure of the Kerry breed

  1990cited by this paper
• Manuscript: “Pericentrosomal targeting of Rab6 secretory vesicles by Bicaudal-D related protein-1 (BICDR-1) regulates neuritogenesis ” by Schlager et al. SUPPLEMENTAL FIGURE LEGENDS

  year unknowncited by this paper

• Global meta-analysis shows action is needed to halt genetic diversity loss

  2025cites this paper
• Review: Assessing available genetic diversity estimates of rare breeds of livestock

  2025cites this paper
• Bovine Genome Database: new curated collection of selective sweeps in bovine populations across the world

  2025cites this paper
• Genomic profiling of selective sweeps through haplotype differentiation unravelled genes associated with production and reproduction traits in Indian goat breeds

  2024cites this paper
• The use of SNP markers for cattle breed identification

  2024cites this paper
• Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations

  2024cites this paper
• Genomic Insights into the Population History and Adaptive Traits of 1 Latin American Criollo Cattle

  2023cites this paper
• Legacies of domestication, Neolithic diffusion and trade between Indian subcontinent and Island Southeast Asia shape maternal genetic diversity of Andaman cattle

  2022cites this paper
• An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds

  2021cites this paper
• Phylogenetic relationships of Argentinean Creole with other Latin American Creole Cattle as revealed by a medium density Single Nucleotide polymorphism microarray

  2021cites this paper
• Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity

  2021cites this paper
• Assessment of the genetic diversity of Two Czech autochthonous sheep breeds

  2020cites this paper
• Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

  2020cites this paper
• Selection in Australian Thoroughbred horses acts on a locus associated with early two-year old speed

  2020cites this paper
• Genome Wide Assessment of Genetic Variation and Population Distinctiveness of the Pig Family in South Africa

  2020cites this paper
• Evolution and domestication of the Bovini species.

  2020cites this paper
• Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of Coat Color

  2020cites this paper
• Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle

  2020cites this paper
• Genetic characteristics of Korean Jeju Black cattle with high density single nucleotide polymorphisms

  2020cites this paper
• Genetic characteristics and diversity of Korean Jeju Black cattle by whole genome SNP markers

  2020cites this paper
• Identifying Loci Under Positive Selection in Yellow Korean Cattle (Hanwoo)

  2019cites this paper
• Genomic variation across European cattle: contribution of gene flow

  2019cites this paper
• Genomic relatedness and diversity of Swedish native cattle breeds

  2019cites this paper
• Genomic inbreeding trends in the global Thoroughbred horse population driven by influential sire lines and selection for exercise trait-related genes

  2019cites this paper
• A Population Genomics Analysis of the Native Irish Galway Sheep Breed

  2019influential citation
• Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

  2019cites this paper
• Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds

  2019cites this paper
• The effectiveness of feed efficiency and husbandry in mitigating the enteric methane emissions of dairy and beef cattle in temperate farming systems; a rapid synthesis and network meta-analysis

  year unknowncites this paper