G.R. WIGGANS,* T.S. SONSTEGARD,* P.M. VANRADEN,* L.K. MATUKUMALLI,*† R.D. SCHNABEL,‡, J.F. TAYLOR, ‡ F.S. SCHENKEL,§ and C. P. VAN TASSELL*
*Agricultural Research Service,
USDA, Beltsville, MD 20705-2350
†George Mason University,
Manassas, VA 20110
‡ University of Missouri, Columbia
65211
§University of Guelph, Ontario N1G-2W1, Canada
2008 J. Dairy Sci. (?)
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Nearly 57,000 single-nucleotide polymorphisms (SNP) on the Illumina BovineSNP50™ chip were investigated to determine their usefulness for genomic prediction. Genotypes were obtained for 12,591 Holstein bulls and cows, and SNP were selected based on 5,503 bulls with genotypes from a larger set of SNP. There were 6,572 SNP that were monomorphic, 3,213 with problems being read, and 3,649 with minor allele frequency of <2%, which were deleted. Number of SNP for each minor allele frequency class (>2%) was fairly uniform (777 to 1,004). For 5 SNP assigned to chromosome 7, no bulls were heterozygous, which indicated that those SNP are actually on the nonpseudoautosomal portion of the X chromosome. Another 178 SNP that were not assigned to a chromosome with many fewer heterozygotes than expected also were assigned to the X chromosome. Existence of Hardy-Weinberg equilibrium was investigated by comparing observed with expected heterozygosity. Eleven SNP had the expected heterozygosity percentage differ from actual by more than 15 and were deleted. For 2,638 SNP, there was a high correlation with the genotype of another SNP (genotypes the same for >99.5% of bulls), and they were deleted. In most cases, these were adjacent SNP or one was unassigned, but 9 were assigned to different chromosomes by the Btau 4.0 sequence assembly. Those edits left 40,874 SNP. A parent-progeny conflict was declared when the genotypes were opposite homozygotes. When the pedigree relationship was correct, the mean number of conflicts was 2.3 and, when incorrect was 2,411. The sire was genotyped for >93% of animals. The maternal grandsire's genotype was checked similarly, but because opposite homozygotes could be valid, up to 16% of cases where both animals were homozygous for different alleles were accepted. Scanning for identical genotypes detected 3 members of a clonal family, 3 sets of split embryos, 5 sets from ET, and 7 identical twins. Genotyping consistency was investigated for 21 bulls genotyped twice with differences primarily from SNP that were not scored for one animal. Concordance for readable SNP was extremely high, (99.96 to 100%). Thousands of SNP that were polymorphic in Holsteins were monomorphic in Jerseys or Brown Swiss, which indicated breed-specific sets of SNP are required or all breeds need to be considered in the selection. The genotypes from the Illumina chip are of high accuracy and provide the basis for genomic evaluations in North American Holsteins.
(Key words: genomic prediction, genotyping, single nucleotide polymorphism)