G.R. Wiggans 1, T. A. Cooper 1 *, K.M. Olson 2 and P.M. VanRaden 1 1 Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville,

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G.R. Wiggans 1, T. A. Cooper 1 *, K.M. Olson 2 and P.M. VanRaden 1 1 Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2 National Association of Animal Breeders, Columbia, MO ADSA · ASAS Joint Annual Meeting July 2011 (1) 2011 Use of the Illumina Bovine3K BEAD chip in dairy genomic evaluation

ADSA · ASAS Joint Annual Meeting July 2011 (2) 2011 Introduction l To increase the adoption of genomic testing, a low density test was developed. l Genomic evaluations using genotypes from the Illumina Bovine3K BEAD chip became available in September l Official genomic evaluations based on 3K genotypes were released in December l Approximately 3,700 new 3K genotypes are submitted monthly for evaluation.

ADSA · ASAS Joint Annual Meeting July 2011 (3) 2011 Number of New Genotypes /1010/1011/1012/1001/1102/1103/1104/1105/1106/1107/11 50K and HD 3K 42,512 77,553 Totals as of July 2011

ADSA · ASAS Joint Annual Meeting July 2011 (4) 2011 Sex Distribution August 2010 Females Males 39% 61% All genotypes

ADSA · ASAS Joint Annual Meeting July 2011 (5) 2011 Sex Distribution July 2011 Females 58% Males 42% All genotypes

ADSA · ASAS Joint Annual Meeting July 2011 (6) K Sample Characteristics l 93% of 3K genotypes are from females l 3K Sample types include: − Hair (79%) − Blood (10%) − Nasal (10%) − Semen (1%)

ADSA · ASAS Joint Annual Meeting July 2011 (7) 2011 l For animal w Pedigree incorrect w Genotype unreliable (3K) l For SNP w SNP unreliable w Clustering needs adjustment Parent Progeny Parent-Progeny conflicts

ADSA · ASAS Joint Annual Meeting July 2011 (8) 2011 Parent Progeny Conflicts 50K Conflicts (%) Number of Genotypes

ADSA · ASAS Joint Annual Meeting July 2011 (9) Number of Genotypes Conflicts (%) Detecting Unreliable 3K Genotypes Accept Unreliable Genotype (Reject)

ADSA · ASAS Joint Annual Meeting July 2011 (10) 2011 Maternal Grandsire (SNP) Maternal Grandsire 2 nd Most related male >5 yrs The difference between the true maternal grandsire and the 2 nd most related male ranged from 0.0% to 15.5%. Percent Conflicts Number of Genotypes

ADSA · ASAS Joint Annual Meeting July 2011 (11) 2011 Maternal Grandsire (haplotype) l New method for maternal grandsire validation and discovery by haplotype subtraction l Remove the contribution of the confirmed genomic sire by subtracting his known haplotypes (group of SNP, generally inherited together) from the progeny. l Count the remaining haplotype (contribution from the dam) matches between the animal and MGS in question l Count is low = Error; Count is High = Ancestor is detected

ADSA · ASAS Joint Annual Meeting July 2011 (12) 2011 Maternal Grandsire (haplotype) l To test, 71 Brown Swiss animals had MGS blanked on their pedigree. l 62 out of 71 (87%) were able to be recovered correctly. l Why could we not find them all? − The difference between the true MGS and the 2 nd animal was too small − Different relative had fewer conflicts

ADSA · ASAS Joint Annual Meeting July 2011 (13) 2011 Integration into Evaluation l 3K genotypes are imputed from 2,614 SNP to 42,503 SNP used in evaluation of 50K genotypes. l Reliability is discounted to recognize errors associated with imputation. l The average 3K genomic evaluation reliability is 5 points lower than 50K evaluations.

ADSA · ASAS Joint Annual Meeting July 2011 (14) 2011 Imputation & Pedigree l The average imputed call rate for 3K genotypes is 95.2% and ranges from 71.0% % l Animals that have a low imputed call rate are those who have unknown pedigree or no genotyped relatives l Proportion with 1+ genotyped parents w 50K – 94.5% w 3K – 84.2%

ADSA · ASAS Joint Annual Meeting July 2011 (15) 2011 Conclusions l The 3K chip has been successful in extending genotyping to a larger portion of the cow population. l The evaluation system has been modified to accommodate the characteristics of a low density chip. l Improvements in imputation will increase accuracy. l New BovineLD chip (6K)

ADSA · ASAS Joint Annual Meeting July 2011 (16) 2011 Thank You!