Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheepReportar como inadecuado




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Genetics Selection Evolution

, 47:90

First Online: 24 November 2015Received: 16 December 2014Accepted: 02 November 2015

Abstract

BackgroundKnowledge 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 Ne, heterozygosity, fixation index FST 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.

MethodsIn this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD measured by r and D′, 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.

ResultsCompared 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 Ne 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 FST = 0.063 but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection.

ConclusionsThis 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 materialThe 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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Autor: Hawlader Abdullah Al-Mamun - Samuel A Clark - Paul Kwan - Cedric Gondro

Fuente: https://link.springer.com/



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