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Title: Technical note: Characteristics and use of the Illumina BovineLD and GeneSeek Genomic Profiler low-density bead chips for genomic evaluation

Author
item Wiggans, George
item Cooper, Tabatha
item Van Tassell, Curtis - Curt
item Sonstegard, Tad
item SIMPSON, E - Geneseek Inc, A Neogen Company

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/30/2012
Publication Date: 2/1/2013
Citation: Wiggans, G.R., Cooper, T.A., Van Tassell, C.P., Sonstegard, T.S., Simpson, E.B. 2013. Technical note: Characteristics and use of the Illumina BovineLD and GeneSeek Genomic Profiler low-density bead chips for genomic evaluation. Journal of Dairy Science. 96(2):1258-1263.

Interpretive Summary: Some dairy producers have been unable to obtain genetic evaluations based on genomic information for their cattle because of the expense of genotyping with the Illumina BovineSNP50 genotyping chip, which is the industry standard. The GeneSeek Genomic Profiler (GGP) genotyping chip with fewer genetic markers and lower cost became available commercially in February 2012. It was created using the add-on capability of the Illumina BovineLD chip, a low-density chip that replaced the Bovine3K chip in October 2011. This study documents the characteristics and use of the new GGP chip. The GGP chip contains 6,909 BovineLD SNPs as well as additional SNPs to improve imputation accuracy and provide single-gene tests. Both BovineLD and GGP chips have received widespread use, but the GGP chip has been used to a greater extent than the BovineLD chip for bulls because it provides single-gene tests. The GGP chip slightly improves accuracy of imputation to BovineSNP50 genotypes compared with the BovineLD chip. For September 2012 U.S. genomic evaluations, 82,510 BovineLD and GGP genotypes were included. Accuracy of evaluations using BovineLD and GGP genotypes were 3 percentage points higher than for Bovine3K genotypes. BovineLD and GGP genotypes resulted in genomic evaluations of only slightly lower accuracy than those from BovineSNP50 genotypes at approximately half the genotyping cost, which is a benefit to dairy producers.

Technical Abstract: The GeneSeek Genomic Profiler (GGP) BeadChip, which became available commercially in February 2012, is based on the Illumina BovineLD Genotyping BeadChip with 1,745 additional single nucleotide polymorphisms (SNPs) for genomic evaluation and SNPs for proprietary single-gene tests. The BovineLD chip with 6,909 SNPs, which replaced the Illumina GoldenGate Bovine3K Genotyping BeadChip, has been available since October 2011. The GGP chip’s additional SNPs for genomic evaluation were selected to improve imputation by filling SNP gaps on chromosomes and including more Bovine3K SNPs and to impute microsatellite alleles to facilitate parentage validation. The SNPs for single-gene tests were included to minimize the number of separate tests required for those genes, particularly for bulls. The September 2012 U.S. national genomic evaluation included genotypes from BovineLD and GGP chips for 82,510 animals. For those data, BovineLD and GGP performance was similar. The call rate for SNPs on these chips that were used in genomic evaluation was 99.6%. The 9 Y SNPs in common for the BovineLD and GGP chips were highly effective in sex validation (call rate of 99% for males and 0.01% for females). For both chips, rate of parent-progeny conflicts on a SNP basis (<0.005%) was similar to that for SNPs on the Illumina BovineSNP50 Genotyping BeadChip. Imputation accuracy averaged 99.4% for Holsteins. Imputation accuracy was slightly higher for the GGP chip compared with the BovineLD chip because of its additional SNP. Reliability for genomic evaluations using BovineLD and GGP genotypes were 3 percentage points higher than for Bovine3K genotypes. BovineLD and GGP genotypes resulted in genomic evaluations of only slightly lower accuracy than those from BovineSNP50 genotypes at approximately half the genotyping cost. The GGP chip demonstrates the value of the add-on capability of the BovineLD chip.