Population structure and history of the Welsh sheep breeds determined by whole genome genotyping

Sarah E Beynon, Gancho T Slavov, Marta Farré, Bolormaa Sunduimijid, Kate Waddams, Brian Davies, William Haresign, James Kijas, Iona M MacLeod, C Jamie Newbold, Lynfa Davies, Denis M Larkin

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Abstract

BACKGROUND: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project.

RESULTS: Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise F ST between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825.

CONCLUSIONS: Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK.

Original languageEnglish
Article number65
JournalBMC Genetics
Volume16
DOIs
Publication statusPrint publication - 20 Jun 2015
Externally publishedYes

Fingerprint

Sheep
Genome
Population Density
Population
HapMap Project
Genetic Structures
Genome-Wide Association Study
Wales
Linkage Disequilibrium
Genomics
Agriculture
Haplotypes
Breeding
Cluster Analysis
History

Keywords

  • Animals
  • Breeding
  • Cluster Analysis
  • Genetics, Population
  • Genome
  • Genomics
  • Genotyping Techniques
  • Haplotypes
  • Inbreeding
  • Linkage Disequilibrium
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • Sheep/classification

Cite this

Beynon, S. E., Slavov, G. T., Farré, M., Sunduimijid, B., Waddams, K., Davies, B., ... Larkin, D. M. (2015). Population structure and history of the Welsh sheep breeds determined by whole genome genotyping. BMC Genetics, 16, [65]. https://doi.org/10.1186/s12863-015-0216-x
Beynon, Sarah E ; Slavov, Gancho T ; Farré, Marta ; Sunduimijid, Bolormaa ; Waddams, Kate ; Davies, Brian ; Haresign, William ; Kijas, James ; MacLeod, Iona M ; Newbold, C Jamie ; Davies, Lynfa ; Larkin, Denis M. / Population structure and history of the Welsh sheep breeds determined by whole genome genotyping. In: BMC Genetics. 2015 ; Vol. 16.
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abstract = "BACKGROUND: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project.RESULTS: Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise F ST between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825.CONCLUSIONS: Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK.",
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Beynon, SE, Slavov, GT, Farré, M, Sunduimijid, B, Waddams, K, Davies, B, Haresign, W, Kijas, J, MacLeod, IM, Newbold, CJ, Davies, L & Larkin, DM 2015, 'Population structure and history of the Welsh sheep breeds determined by whole genome genotyping', BMC Genetics, vol. 16, 65. https://doi.org/10.1186/s12863-015-0216-x

Population structure and history of the Welsh sheep breeds determined by whole genome genotyping. / Beynon, Sarah E; Slavov, Gancho T; Farré, Marta; Sunduimijid, Bolormaa; Waddams, Kate; Davies, Brian; Haresign, William; Kijas, James; MacLeod, Iona M; Newbold, C Jamie; Davies, Lynfa; Larkin, Denis M.

In: BMC Genetics, Vol. 16, 65, 20.06.2015.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Population structure and history of the Welsh sheep breeds determined by whole genome genotyping

AU - Beynon, Sarah E

AU - Slavov, Gancho T

AU - Farré, Marta

AU - Sunduimijid, Bolormaa

AU - Waddams, Kate

AU - Davies, Brian

AU - Haresign, William

AU - Kijas, James

AU - MacLeod, Iona M

AU - Newbold, C Jamie

AU - Davies, Lynfa

AU - Larkin, Denis M

PY - 2015/6/20

Y1 - 2015/6/20

N2 - BACKGROUND: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project.RESULTS: Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise F ST between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825.CONCLUSIONS: Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK.

AB - BACKGROUND: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project.RESULTS: Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise F ST between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825.CONCLUSIONS: Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK.

KW - Animals

KW - Breeding

KW - Cluster Analysis

KW - Genetics, Population

KW - Genome

KW - Genomics

KW - Genotyping Techniques

KW - Haplotypes

KW - Inbreeding

KW - Linkage Disequilibrium

KW - Phylogeny

KW - Polymorphism, Single Nucleotide

KW - Sheep/classification

U2 - 10.1186/s12863-015-0216-x

DO - 10.1186/s12863-015-0216-x

M3 - Article

C2 - 26091804

VL - 16

JO - BMC Genetics

JF - BMC Genetics

SN - 1471-2156

M1 - 65

ER -