Design of a Bovine Low-Density SNP Array Optimized for Imputation
Top Cited Papers
Open Access
- 28 March 2012
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 7 (3), e34130
- https://doi.org/10.1371/journal.pone.0034130
Abstract
The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs) that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.This publication has 23 references indexed in Scilit:
- Haplotype phasing: existing methods and new developmentsNature Reviews Genetics, 2011
- Imputation of Missing Genotypes From Sparse to High Density Using Long-Range PhasingGenetics, 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
- Dual Origins of Dairy Cattle Farming – Evidence from a Comprehensive Survey of European Y-Chromosomal VariationPLOS ONE, 2011
- Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithmsJournal of Dairy Science, 2010
- A Hidden Markov Model Combining Linkage and Linkage Disequilibrium Information for Haplotype Reconstruction and Quantitative Trait Locus Fine MappingGenetics, 2010
- Development and Characterization of a High Density SNP Genotyping Assay for CattlePLOS ONE, 2009
- Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle BreedsScience, 2009
- A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic PhaseAmerican Journal of Human Genetics, 2006