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Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep

BACKGROUND: Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (N(e)), heterozygosity, fi...

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Autores principales: Al-Mamun, Hawlader Abdullah, A Clark, Samuel, Kwan, Paul, Gondro, Cedric
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4659207/
https://www.ncbi.nlm.nih.gov/pubmed/26602211
http://dx.doi.org/10.1186/s12711-015-0169-6
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author Al-Mamun, Hawlader Abdullah
A Clark, Samuel
Kwan, Paul
Gondro, Cedric
author_facet Al-Mamun, Hawlader Abdullah
A Clark, Samuel
Kwan, Paul
Gondro, Cedric
author_sort Al-Mamun, Hawlader Abdullah
collection PubMed
description BACKGROUND: Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (N(e)), heterozygosity, fixation index (F(ST)) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates. METHODS: In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r(2) and D′), N(e), heterozygosity, F(ST) and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP). RESULTS: Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller N(e) than MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest F(ST) = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection. CONCLUSIONS: This study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This knowledge will also be useful to design reference populations for genomic prediction of breeding values in sheep. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12711-015-0169-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-46592072015-11-26 Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep Al-Mamun, Hawlader Abdullah A Clark, Samuel Kwan, Paul Gondro, Cedric Genet Sel Evol Research Article BACKGROUND: Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (N(e)), heterozygosity, fixation index (F(ST)) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates. METHODS: In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r(2) and D′), N(e), heterozygosity, F(ST) and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP). RESULTS: Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller N(e) than MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest F(ST) = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection. CONCLUSIONS: This study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This knowledge will also be useful to design reference populations for genomic prediction of breeding values in sheep. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12711-015-0169-6) contains supplementary material, which is available to authorized users. BioMed Central 2015-11-24 /pmc/articles/PMC4659207/ /pubmed/26602211 http://dx.doi.org/10.1186/s12711-015-0169-6 Text en © Al-Mamun et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Al-Mamun, Hawlader Abdullah
A Clark, Samuel
Kwan, Paul
Gondro, Cedric
Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep
title Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep
title_full Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep
title_fullStr Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep
title_full_unstemmed Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep
title_short Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep
title_sort genome-wide linkage disequilibrium and genetic diversity in five populations of australian domestic sheep
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4659207/
https://www.ncbi.nlm.nih.gov/pubmed/26602211
http://dx.doi.org/10.1186/s12711-015-0169-6
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