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Title: Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep
Contributor(s): Al-Mamun, Hawlader Abdullah (author); Clark, Sam A  (author)orcid ; Kwan, Paul H  (author); Gondro, Cedric  (author)orcid 
Publication Date: 2015
Open Access: Yes
DOI: 10.1186/s12711-015-0169-6Open Access Link
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Abstract: '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 r² and D¹), Ne, heterozygosity, FST 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 Nₑthan 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.
Publication Type: Journal Article
Grant Details: ARC/DP130100542
Source of Publication: Genetics Selection Evolution, v.47, p. 1-14
Publisher: BioMed Central Ltd
Place of Publication: United Kingdom
ISSN: 1297-9686
Field of Research (FOR): 070201 Animal Breeding
080301 Bioinformatics Software
060405 Gene Expression (incl. Microarray and other genome-wide approaches)
Socio-Economic Objective (SEO): 890201 Application Software Packages (excl. Computer Games)
830310 Sheep - Meat
830311 Sheep - Wool
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
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