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Development of Low Density Genotype Panels for Dairy and Beef Cattle
The objective of this study was to develop, using three algorithms, lower density genotyping panels with varying number of single nucleotide plymorphisms; SNPs, which can be accurately imputed to higher density panels. The panels were developed based on genomic architecture in a population of 1,267 Holstein-Friesian animals genotyped on the Illumina Bovine50 beadchip (54,001 SNPs). The panels were validated separately in 1) a population of 750 Holstein-Friesian animals (1,249 animals in the reference population) and 2) a population of 265 Limousin and Charolais cattle (1,865 animals in the reference population). Irrespective of the validation population, the accuracy of imputation improved at a diminishing rate as the number of SNPs included in the lower density genotype panel increased. In the dairy population the correlation between the imputed and actual genotypes (both sire and dam genotyped) for a 3,000 SNP panel was 0.98.
Keywords:
Imputation
Single nucleotide polymorphism
Genomic selection
