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Title: Characteristics and use of the Illumina BovineLD BeadChip

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

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: 3/5/2012
Publication Date: 6/28/2012
Citation: Wiggans, G.R., Van Raden, P.M., Cooper, T.A., Van Tassell, C.P., Sonstegard, T.S., Simpson, B. 2012. Characteristics and use of the Illumina BovineLD BeadChip. Journal of Dairy Science. 95(Suppl. 2):447(abstr. 450). 2012.

Interpretive Summary:

Technical Abstract: Genotypic information from the 6,909-SNP Illumina BovineLD (LD) Genotyping BeadChip, which replaced the Illumina GoldenGate Bovine3K (3K) Genotyping BeadChip, have been included in US genomic evaluations since November 2011. Of 73 LD single nucleotide polymorphisms (SNP) not used in genomic evaluation, 35 were from the Illumina BovineSNP50 (SNP50) Genotyping BeadChip, and 38 (13 mitochondrial, 9 Y-chromosome, and 16 X-chromosome SNP to improve genome coverage) were from the Illumina BovineHD (HD) Genotyping BeadChip. As of February 2012, the USDA national genotype database for dairy cattle included LD genotypes for 19,515 animals (550 males). Call rate for LD SNP used in genomic evaluation was 99.4%. The 9 Y SNP were highly effective in sex validation (call rate of 98% for males and 0.5% for females). Rate of parent-progeny conflicts on a SNP basis was similar to that for SNP50 SNP. Imputation accuracy averaged 98.9% for Holsteins, 98.3% for Jerseys, and 97.9% for Brown Swiss for LD genotypes compared with 95.9, 94.6, and 93.9% for 3K genotypes. To calculate reliability of genomic evaluations, the fraction of correctly imputed SNP was estimated as a function of the number of low-density SNP that were not missing and the number of animals with SNP50 genotypes. Reliabilities for LD genotypes were about 5 percentage points higher than for 3K genotypes. Using the add-on capability of the LD chip, the GeneSeek Genomic Profiler (GGP) for Dairy Cattle BeadChip was developed with about 9,000 SNP. The additional SNP were for proprietary single-gene tests, detection of haplotypes that affect fertility, imputation of microsatellite alleles to facilitate parentage validation, and improved imputation by including more 3K SNP. The GeneSeek Genomic Profiler 80K (GGP-80) also was developed with around 80,000 SNP. The added SNP were SNP50 and HD SNP with the largest effects on primarily the net merit genomic-economic index. Consideration also was given to spacing as well as maintaining around 30,000 SNP50 SNP for imputation accuracy. The GGP and GGP-80 genotypes are expected to further improve accuracy of imputation and genomic evaluation because of the additional SNP.