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Within- and across-breed imputation of high-density genotypes in dairy and beef cattle from medium- and low-density genotypes
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2013-12-05
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Berry, D.P., McClure, M.C. and Mullen, M.P. (2014), Within- and across-breed imputation of high-density genotypes in dairy and beef cattle from medium- and low-density genotypes. J. Anim. Breed. Genet., 131: 165–172. doi:10.1111/jbg.12067
Abstract
The objective of this study was to evaluate, using three different genotype
density panels, the accuracy of imputation from lower- to higher-density
genotypes in dairy and beef cattle. High-density genotypes consisting of
777 962 single-nucleotide polymorphisms (SNP) were available on 3122
animals comprised of 269, 196, 710, 234, 719, 730 and 264 Angus, Belgian
Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental
bulls, respectively. Three different genotype densities were generated:
low density (LD; 6501 autosomal SNPs), medium density (50K; 47 770
autosomal SNPs) and high density (HD; 735 151 autosomal SNPs). Imputation
from lower- to higher-density genotype platforms was undertaken
within and across breeds exploiting population-wide linkage disequilibrium.
The mean allele concordance rate per breed from LD to HD when
undertaken using a single breed or multiple breed reference population
varied from 0.956 to 0.974 and from 0.947 to 0.967, respectively. The
mean allele concordance rate per breed from 50K to HD when undertaken
using a single breed or multiple breed reference population varied from
0.987 to 0.994 and from 0.987 to 0.993, respectively. The accuracy of
imputation was generally greater when the reference population was
solely comprised of the breed to be imputed compared to when the reference
population comprised of multiple breeds, although the impact