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Development and validation of a medium-density chip array for bovine.

N. Deeb




Development and validation of a medium-density chip array for bovine.
N. Deeb*1, C. Neis2, S. Firgens2. 1STgenetics Navasota, TX, 2Genetic Visions Middleton, WI.

Genomic testing has revolutionized animal breeding in almost all agricultural species. Dairy, for the last 12 years, has benefited from cost-effective high-throughput genotyping to improve selection accuracy and reduce generation interval. Here we report on the development of a new 65k Affymetrix Axiom bovine array. For continuity and accuracy of imputation, SNPs on the array have been extracted from existing variants heavily used in the US national dairy genomic evaluation. The recently published Bovine genome assembly (ARS-UCD1.2) was used when selecting the markers along with available information on major effects and known defects to enhance the content and improve the design. The array design featured about 69k SNP markers that converted into 63,836 working assays and several private SNPs. Of the carefully selected set of 60k markers recommended by The Council on Dairy Cattle Breeding (CDCB), about 55k were carried over onto the new chip to ensure high compatibility. Markers covered all autosomes, X and Y chromosomes, and were evenly spaced across the genome with average median gap of 32k bp among autosomes. All 200 ISAG markers were included in the design, and several essential markers used by CDCB to improve on the data quality control such as sex-specific markers, breed-specific markers and markers used for parental verification. Moreover, we included markers to cover all known causal mutations and targeted specific haplotype regions with previously identified associations with deleterious mutations. For validation, we genotyped 768 animals which were previously genotyped using other commercially available SNP chips and compared SNP calls and clustering quality. Finally, we developed priors for all markers on the array to provide the genotype calling algorithm information to assist with genotype calling in situations where genotype clusters are lowly represented.

Keywords: genomics, chip, bovine.