Hot topic: Performance of bovine high-density genotyping platforms in Holsteins and Jerseys

Abstract

Two high-density single nucleotide polymorphism (SNP) genotyping arrays have recently become available for bovine genomic analyses, the Illumina High-Density Bovine BeadChip Array (777,962 SNP) and the Affymetrix Axiom Genome-Wide BOS 1 Array (648,874 SNP). These products each have unique design and chemistry attributes, and the extent of marker overlap and their potential utility for quantitative trait loci fine mapping, detection of copy number variation, and multibreed genomic selection are of significant interest to the cattle community. This is the first study to compare the performance of these 2 arrays. Deoxyribonucleic acid samples from 16 dairy cattle (10 Holstein, 6 Jersey) were used for the comparison. An independent set of DNA samples taken from 46 Jersey cattle and 18 Holstein cattle were used to ascertain the amount of SNP variation accounted by the 16 experimental samples. Data were analyzed with SVS7 software (Golden Helix Inc., Bozeman, MT) to remove SNP having a call rate less than 90%, and linkage disequilibrium pruning was used to remove linked SNP (r² ≥ 0.9). Maximum, average, and median gaps were calculated for each analysis based on genomic position of SNP on the bovine UMD3.1 genome assembly. All samples were successfully genotyped (≥ 98% SNP genotyped) with both platforms. The average number of genotyped SNP in the Illumina platform was 775,681 and 637,249 for the Affymetrix platform. Based on genomic position, a total of 107,896 SNP were shared between the 2 platforms; however, based on genotype concordance, only 96,031 SNP had complete concordance at these loci. Both Affymetrix BOS 1 and Illumina BovineHD genotyping platforms are well designed and provide high-quality genotypes and similar coverage of informative SNP. Despite fewer total SNP on BOS 1, 19% more SNP remained after linkage disequilibrium pruning, resulting in a smaller gap size (5.2 vs. 6.9 kb) in Holstein and Jersey samples relative to BovineHD. However, only 224,115 Illumina and 241,038 Affymetrix SNP remained following removal of SNP with a minor allele frequency of zero in Holstein and Jersey samples, resulting in an average gap size of 11,887 bp and 11,018 bp, respectively. Combining the 354,348 informative (r² ≥ 0.9), polymorphic (minor allele frequency ≥ 0), unique SNP data from both platforms decreased the average gap size to 7,560 bp. Genome-wide copy number variant analyses were performed using intensity files from both platforms. The BovineHD platform provided an advantage to the copy number variant data compared with the BOS 1 because of the larger number of SNP, higher intensity signals, and lower background effects. The combined use of both platforms significantly improved coverage over either platform alone and decreased the gap size between SNP, providing a valuable tool for fine mapping quantitative trait loci and multibreed animal evaluation.

Association analysis for udder health based on SNP-panel and sequence data in Danish Holsteins

“…Currently, a medium-density (MD) SNP chip with ~54 000 markers is widely used for GWAS in dairy cattle [17–19]. In recent years, two high-density (HD) SNP chips with 777 962 SNPs from Illumina Inc. [20] and 648 874 SNPs from Affymetrix Inc. [21], and whole-genome sequencing (SEQ) data [22] have become available. Higher marker densities mean that markers are in stronger linkage disequilibrium (LD) with QTL that affect the trait of interest.…”

BREEDING AND GENETICS SYMPOSIUM: Networks and pathways to guide genomic selection1–3

“…The high-density arrays (i.e., >600,000 SNP), which are now available for cattle (Rincon et al, 2011), provide genotypes for SNP that are more certain to have high correlations with unknown QTL than the dense 50K assays. Increased marker density alone, however, does not increase marker-QTL correlations.…”

Performance of bovine high density SNPs genotyping array in indigenous Pakistani cattle breeds

“…The linkage disequilibrium method is used to identify linked SNPs to defined genetic variation in genome wide association studies (GWAS) [14]. SNPs linkage or in high linkage disequilibrium (LD) genetic information is same in runs of homozygosity, therefore LD pruning is recommended [17].…”