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RESEARCH ARTICLE
Contents Vol 50(8)

Effect of SNP origin on analyses of genetic diversity in cattle

Laercio R. Porto Neto A B C and William Barendse A B D
+ Author Affiliations
- Author Affiliations

A Cooperative Research Centre for Beef Genetic Technologies, CJ Hawkins Homestead, University of New England, Armidale, NSW 2351, Australia.

B CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Qld 4067, Australia.

C The University of Queensland, School of Animal Studies, Gatton, Qld 4343, Australia.

D Corresponding author. Email: bill.barendse@csiro.au

Animal Production Science 50(8) 792-800 https://doi.org/10.1071/AN10073
Submitted: 14 May 2010  Accepted: 8 June 2010   Published: 31 August 2010

Abstract

The methods of single nucleotide polymorphism (SNP) identification can lead to ascertainment bias, which will affect population genetic analyses based on those data. In livestock species, the methods of SNP identification through genome sequencing are likely to suffer from this ascertainment bias. In the present study, a subset of data from the Bovine HapMap Project was re-analysed to quantify the effects of ascertainment bias on a range of common analyses and statistics. Data from 189 animals of the zebu breeds Brahman, Nelore and Gir, taurine beef Angus, Limousin and Hereford and taurine dairy Holstein, Jersey and Brown Swiss were analysed. There were 141 SNPs each of Angus, Brahman and Holstein origin, giving a total of 423 SNPs organised in 141 triplets. Each triplet consisted of one SNP of each breed, separated on average by 0.75 Mb within each triplet and where triplets were separated by 14.96 Mb to ensure that each triplet was unaffected by linkage disequilibrium. The minor allele frequency distribution, estimates of the F-statistic, FST, the partitioning of variance and population substructure were relatively unaffected by breed of origin of the SNPs. Estimates of heterozygosity were significantly affected by breed of origin of the SNPs. The clustering of animals of closely related breeds varied in the principal component analyses (PCA). However, in the PCA the effect of breed of origin of 141 SNPs was similar to the effect of using different panels of 141 SNPs of all three breeds, so the differences found in the PCA may not be all due to bias by the origin of the SNPs. Based on these results, analyses that depend on FST, including signatures of selection, gene flow and effective population size are unlikely to be strongly affected by SNP origin. Analyses that partition genetic variance and some analyses of population substructure will also be largely unaffected. However, analyses that are dependent on locus heterozygosity, which can be used for studying population bottlenecks, or those that study selection using extended haplotype homozygosity may be significantly affected by breed of origin of the SNPs.


Acknowledgements

We thank James Kijas for many valuable discussions of genetic diversity in livestock. We thank the Bovine HapMap Consortium for access to the raw genotypes in the BHP. LRPN is supported by an Endeavour International Postgraduate Research Scholarship, a University of Queensland International Student Living Allowance and a Beef CRC scholarship.


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