1	Selection of single nucleotide polymorphisms and genotype quality for genomic prediction of genetic merit in dairy cattle
2	Bovine SNP50 BeadChip
3	Laboratories & animals genotyped Bovine Functional Genomics Laboratory, 8,236 ARS, USDA (Beltsville, MD) GeneSeek (Lincoln, NE) 2,288 University of Alberta (Edmonton, AB) 1,325 University of Missouri (Columbia, MO) 914 Genetics & IVF Institute (Fairfax, VA) 703 Illumina (San Diego, CA) 116
4	Genotypes by breed & sex
5	SNP filtering & counts SNP available 58,336 (including those not supported by Illumina) Insufficient average number of beads 1,389 Unscorable 4,360 Monomorphic in Holsteins 5,734 Minor allele frequency (MAF) of <5% 6,145 Percentage heterozygous different from 282 expected or other scoring issues Highly correlated 2,010 Used for genomic prediction 38,416
6	Bull distribution for unscorable SNP
7	SNP distribution for bulls with unscorable SNP
8	Identical twins & clones Missing SNP Changes GLC Triton-ETN 19 10 GLC Triad-ETN 348 364 GLC Trey-ETN 14 5 Comestar Laureat 13 2 Comestar Loyalty 16 5 Bermath Monroe 160 156 Bermath Morgan 83 76 Granduc Blizzard 13 10 Granduc Spartan 36 33 Granduc Performance 8 4 Granduc Performer 988 984 U-of-Minn W Fatal Twyla 2,272 2,223 U-of-Minn W Fatal Tabina 116 65
9	Genotyping for same bulls 2 laboratories; 46 bulls; 38,416 SNP SNP unscorable only once Mean of 792 SNP Range of 20 to 2,244 SNP SNP conflict (<0.003%) Mean of 0.9 SNP Range of 0 to 7 SNP
10	Highly correlated SNP 4,286 bulls; 40,426 SNP Compare each SNP with all others with MAF within 2% Count all 9 combinations of 0, 1, and 2 for 2 SNP Assumed highly correlated if only combinations with >21 SNP are 00, 11, and 22 or 20, 11, and 02
11	Highly correlated SNP (cont.) 2,444 pairs detected and categorized into 1,696 groups SNP in group Groups Group sizes 2 1,450 for highly 3 198 correlated 4 30 SNP 5 10 6 6 7 1 10 1
12	Highly correlated SNP (cont.) Distance between autosomal SNP 65,531 mean base pairs between consecutive SNP 19,826 base pairs between 1,199 consecutive highly correlated SNP 423,033 base pairs between 469 SNP in group where ³1 SNP in group is not consecutive
13	Minor allele frequency distribution
14	Heterozygosity differences SNP different from expected heterozygosity by >7%
15	Sex determination 605 SNP on X chromosome and not on Y (not in pseudo-autosomal region) Bulls should not be heterozygous Cows (n = 255) Mean of 229.6 heterozygous SNP Range of 133 to 277 heterozygous SNP
16	Parentage verification & discovery Compare parent and progeny SNP if both homozygous If >200 conflicts found, check every other genotype for one with <30 conflicts May be parent, progeny, duplicate, clone, or identical twin
17	Estimating missing SNP − imputing Base population gene frequencies estimated with best linear unbiased prediction Estimates provided for all genotyped animals and ancestors If SNP genotype missing, estimate used if within 0.2 of 0, 1, or 2 6,268 genotyped animals 0.9 % missing 45% filled
18	Summary High-density Illumina BovineSNP50 BeadChip available >38,000 SNP available for Holsteins Genotypes consistent across laboratories Few parent-progeny genotyping errors found If parentage error found, correct parent often can be determined
19	Summary (cont.) SNP on X-chromosome support sex validation Call rate is high and may be improved Detection of highly correlated SNP revealed probable errors in map locations
20	Financial support National Research Initiative grants, USDA Natl. Assoc. of Animal Breeders (NAAB, Columbia, MO) ABS Global (DeForest, WI) Accelerated Genetics (Baraboo, WI) Alta (Balzac, AB) Genex (Shawano, WI) New Generation Genetics (Fort Atkinson, WI) Select Sires (Plain City, OH) Semex Alliance (Guelph, ON) Taurus-Service (Mehoopany, PA) Agricultural Research Service, USDA