Across- and Within-breed Imputation across Several Genotyping Densities in Dairy and Beef Cattle
نویسندگان
چکیده
Illumina high density genotypes (777,962 SNPs) were available on 3,122 dairy and beef bulls. Animals were partitioned into either a calibration or validation dataset to test the accuracy of imputation. All animals, irrespective of breed, born after 2005 (n=698) were assumed to represent the validation bulls. The high density genotypes were masked in the validation animals to represent a low density (n=6,501) or medium density (n=47,770) genotyping platform. The accuracy of within breed imputation (i.e., correlation between actual and imputed genotype) from medium density to high density (0.987) was superior to that from low-density to high density (0.938) with the difference diminishing as the proportion of back-pedigree genotyped on the highdensity platform increased. Using multiple breeds in the calibration dataset for imputation did not improve the accuracy of imputation.
منابع مشابه
Design of a Bovine Low-Density SNP Array Optimized for Imputation
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 loc...
متن کاملEvaluation of developed low-density genotype panels for imputation to higher density in independent dairy and beef cattle populations.
The objective of this study was to develop, using alternative algorithms, low-density SNP genotyping panels (384 to 12,000 SNP), which can be accurately imputed to higher-density panels across independent cattle populations. Single nucleotide polymorphisms were selected based on genomic characteristics (i.e., linkage disequilibrium [LD], minor allele frequency [MAF], and genomic distance) in a ...
متن کاملProducer uptake: how might genomic information get translated into industry outcomes
The Bovine Respiratory Disease Complex Coordinated Agricultural Project (BRD CAP) is a 5-year USDA-funded Coordinated Agricultural Project to develop genetic markers associated with bovine respiratory disease (BRD) to identify cattle that are less susceptible to BRD. Ultimately the aim of this project is to integrate predictive markers for BRD susceptibility into genetic tests and national catt...
متن کاملAn interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds
This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 ...
متن کاملCongress of Genetics Applied to Livestock Production Genomic Selection in Sheep Breeding Programs
Implementation of genomic selection in sheep breeding provides a number of challenges, compared to dairy cattle, because of the higher genetic diversity between and within sheep breeds, the cost of maintaining reference populations and the limited ability of individual breeders to invest in genotyping. Within this study, we compare theoretical and realized genomic prediction accuracies for trai...
متن کامل