High-density marker imputation accuracy in sixteen French cattle breeds
Authors:
- Chris HozéCHChris Hozé
- Marie-Noëlle FouillouxMFMarie-Noëlle Fouilloux
- Eric VenotEVEric Venot
- François GuillaumeFGFrançois Guillaume
- Romain DassonnevilleRDRomain Dassonneville
- Sébastien FritzSFSébastien Fritz
- Vincent DucrocqVDVincent Ducrocq
- Florence PhocasFPFlorence Phocas
- Didier BoichardDBDidier Boichard
- Pascal CroiseauPCPascal Croiseau
Open Access
- 3 September 2013
- journal article
- research article
- Published by Springer Nature in Genetics Selection Evolution
- Vol. 45 (1) , 1-33
Abstract
Genotyping with the medium-density Bovine SNP50 BeadChip® (50K) is now standard in cattle. The high-density BovineHD BeadChip®, which contains 777 609 single nucleotide polymorphisms (SNPs), was developed in 2010. Increasing marker density increases the level of linkage disequilibrium between quantitative trait loci (QTL) and SNPs and the accuracy of QTL localization and genomic selection. However, re-genotyping all animals with the high-density chip is not economically feasible. An alternative strategy is to genotype part of the animals with the high-density chip and to impute high-density genotypes for animals already genotyped with the 50K chip. Thus, it is necessary to investigate the error rate when imputing from the 50K to the high-density chip.Keywords
This publication has 28 references indexed in Scilit:
- A common reference population from four European Holstein populations increases reliability of genomic predictionsGenetics Selection Evolution, 2011
- Accuracy of genotype imputation in sheep breedsAnimal Genetics, 2011
- A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypesGenetics Selection Evolution, 2011
- Genomic evaluations with many more genotypesGenetics Selection Evolution, 2011
- MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypesGenetic Epidemiology, 2010
- A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association StudiesPLOS Genetics, 2009
- Development and Characterization of a High Density SNP Genotyping Assay for CattlePLOS ONE, 2009
- Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype ClusteringThe American Journal of Human Genetics, 2007
- A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic PhaseThe American Journal of Human Genetics, 2006
- Linkage disequilibrium in finite populationsTheoretical and Applied Genetics, 1968