The effect of rare alleles on estimated genomic relationships from whole genome sequence dataReport as inadecuate

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BMC Genetics

, 16:24

First Online: 12 March 2015Received: 05 December 2014Accepted: 24 February 2015DOI: 10.1186-s12863-015-0185-0

Cite this article as: Eynard, S.E., Windig, J.J., Leroy, G. et al. BMC Genet 2015 16: 24. doi:10.1186-s12863-015-0185-0


BackgroundRelationships between individuals and inbreeding coefficients are commonly used for breeding decisions, but may be affected by the type of data used for their estimation. The proportion of variants with low Minor Allele Frequency MAF is larger in whole genome sequence WGS data compared to Single Nucleotide Polymorphism SNP chips. Therefore, WGS data provide true relationships between individuals and may influence breeding decisions and prioritisation for conservation of genetic diversity in livestock. This study identifies differences between relationships and inbreeding coefficients estimated using pedigree, SNP or WGS data for 118 Holstein bulls from the 1000 Bull genomes project. To determine the impact of rare alleles on the estimates we compared three scenarios of MAF restrictions: variants with a MAF higher than 5%, variants with a MAF higher than 1% and variants with a MAF between 1% and 5%.

ResultsWe observed significant differences between estimated relationships and, although less significantly, inbreeding coefficients from pedigree, SNP or WGS data, and between MAF restriction scenarios. Computed correlations between pedigree and genomic relationships, within groups with similar relationships, ranged from negative to moderate for both estimated relationships and inbreeding coefficients, but were high between estimates from SNP and WGS 0.49 to 0.99. Estimated relationships from genomic information exhibited higher variation than from pedigree. Inbreeding coefficients analysis showed that more complete pedigree records lead to higher correlation between inbreeding coefficients from pedigree and genomic data. Finally, estimates and correlations between additive genetic A and genomic G relationship matrices were lower, and variances of the relationships were larger when accounting for allele frequencies than without accounting for allele frequencies.

ConclusionsUsing pedigree data or genomic information, and including or excluding variants with a MAF below 5% showed significant differences in relationship and inbreeding coefficient estimates. Estimated relationships and inbreeding coefficients are the basis for selection decisions. Therefore, it can be expected that using WGS instead of SNP can affect selection decision. Inclusion of rare variants will give access to the variation they carry, which is of interest for conservation of genetic diversity.

KeywordsWhole genome sequence Additive genetic relationship Rare variants Minor allele frequency Inbreeding AbbreviationsMAFMinor allele frequency

SNPSingle nucleotide polymorphism

WGSWhole genome sequence

AAdditive relationship matrix

GGenomic relationship matrix

IBDIdentity by descent

IBSIdentity by state

Electronic supplementary materialThe online version of this article doi:10.1186-s12863-015-0185-0 contains supplementary material, which is available to authorized users.

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Author: Sonia E Eynard - Jack J Windig - Grégoire Leroy - Rianne van Binsbergen - Mario PL Calus


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