AIPL Update John Cole Paul Van Raden George

AIPL Update John Cole, Paul Van. Raden, George Wiggans, and Melvin Kuhn Animal Improvement Programs Laboratory USDA Agricultural Research Service, Beltsville, MD, USA Paul. Van. Raden@ars. usda. gov 2008 2007

Genotyped animals (October 2008) Breed Bulls Holstein 12, 275 Jersey 1, 205 Brown Swiss 365 Cows 2, 445 369 3 Predictors 7, 821 1, 428 359 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (2) AIPL

Experimental Design Holstein, Jersey, and Brown Swiss breeds Predictor: Bulls born <1999 Cows with data Predictee: Bulls born >1999 HO JE BS 3, 576 743 202 225 1, 759 425 118 Data from 2003 used to predict independent data from 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (3) AIPL

Reliability Gain 1 by Breed Yield traits and NM$ Trait Net merit Milk Fat Protein Fat % Protein % 1 Gain HO 23 23 33 22 43 34 JE 9 11 15 4 41 29 BS 3 0 5 1 10 5 above parent average reliability ~35% 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (4) AIPL

Reliability Gain by Breed Health and type traits Trait Productive life Somatic cell score Dtr pregnancy rate Final score Udder depth Foot angle Stature HO 18 21 16 18 35 14 26 JE 12 1 5 6 13 10 9 BS 2 16 3 3 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (5) AIPL

New Genetic Terms Actual vs. expected genetic similarity • • Genomic relationships and inbreeding Genomic future inbreeding (GFI) vs. EFI Daughter merit vs. son merit Haplotyping and imputation • • • Which allele is from sire vs. dam? Which alleles are linked together? Can missing genotypes be predicted? 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (6) AIPL

Genomic vs. Pedigree Inbreeding Bull O Man Ramos Shottle Planet Earnit Nifty Pedigree F 4. 5 2. 3 5. 6 6. 7 6. 2 3. 1 Genomic F 15. 8 11. 5 11. 9 18. 8 12. 8 11. 7 Correlation =. 68 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (7) AIPL

Genomic vs. Expected Future Inbreeding Bull Blackstar Elevation Chief Emory RC Matt Juror EFI 7. 9 7. 6 7. 1 7. 0 GFI 7. 9 7. 4 6. 8 6. 9 6. 7 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (8) AIPL

Net Merit by Chromosome Planet - high Net Merit bull 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (9) AIPL

Schedule Calculate SNP effects with each of 3 annual traditional evaluations Calculate genomic evaluations once or more between traditional evaluations, monthly? • Recalculate SNP effects if significant number of predictor animals added • Use existing SNP effects if only young animals added 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (10) AIPL

Official release in 2009 Information from genomic evaluations propagated to evaluations of descendents without genotypes NAAB to manage bull-owner notification and sharing among AI organizations Public release of genomic evaluations • Cows soon after calculated • Bulls when enrolled with NAAB or Canadian AI organization • Shared by agreement with owner 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (11) AIPL

Low cost genotyping research Develop a genetic test that is cheap enough to enable use on most animals Provide parentage verification/discovery Provide a genetic estimate useful for first stage screening 384 SNP proposed for first test High throughput procedures being developed 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (12) AIPL

Reliability of evaluations Reliability from inverse of a matrix with order the number of genotyped animals Approximation necessary as number of genotyped animals increases Daughter equivalents discounted by 0. 6 to represent better the reliability of 2003 data in predicting bulls first evaluated in 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (13) AIPL

Plans to increase accuracy Genotype more predictor bulls Reach 1, 500 Brown Swiss, possibly through foreign collaboration Increase genotyped Jerseys from both domestic animals and possible foreign collaboration Investigate across-breed analysis so Holstein data can improve accuracy for Jerseys and Brown Swiss 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (14) AIPL

Haplotyping may increase accuracy Even a SNP very close to a QTL may have a different allele frequency Haplotype allele may have higher correlation with the QTL May assist in imputation of genotypes of missing SNP and perhaps whole animals 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (15) AIPL

International implications All major dairy countries are investigating genomic selection Interbull meeting in January on integration of genomic evaluations Studs must balance competitive benefit from treating genotypes as proprietary with benefits from sharing 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (16) AIPL

Interbull Genomics contribution to accuracy should be reported • Avoid double counting when submitted by multiple countries • Could be processed similar to parent contribution Change in 10 -herd requirement needed to allow marketing bulls with only genomic information in countries without genomic evaluations 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (17) AIPL

Query example 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (18) AIPL

Dystocia Complex Markers on BTA 18 had the largest effects for several traits: • • • Dystocia: Sire and daughter calving ease Conformation: rump width, stature, strength, and body depth Efficiency: longevity and net merit Large calves contribute to shorter PL and decreased NM$ 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (19) AIPL

2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (20) AIPL

Markers on BTA 18 with large effects 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (21) AIPL

SIGLEC proteins Human Siglec-9 highly expressed in the placenta (Foussias, 2000). Human Siglec-6 may be involved in initiation of parturition (Brinkman. Van der Linden et al. , 2007). Siglec-6 binds and sequesters leptin (Brinkman-Van der Linden et al. , 2007). 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (22) AIPL

Proposed mode of action Leptin-deficient mice delay parturition (Mounzih et al. , 1998). Homozygotes may express high levels of Siglec-6, resulting in leptin deficiency and delayed parturition. ss 86324977 may result in increased calf size associated with longer gestation lengths. 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (23) AIPL

Interbull fertility traits Heifer conception as a rate (heifer conception rate). Ability to recycle after calving (days to first breeding). Cow conception as a rate (cow conception rate) and interval (first breeding to conception). Calving to conception (days open). 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (24) AIPL

Status of fertility traits Traits 1 and 3 (heifer and cow conception rates) submitted to Sept. 2008 test run. Work on Trait 2 (days to first breeding) is underway. Trait 4 (ability to conceive as an interval) is now required. We already report Trait 5 (DPR). 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (25) AIPL

Heifer and cow conception rate Heifer conception rate (HCR) is the percentage of inseminated heifers that become pregnant at each service. Cow conception rate (CCR) is defined as the percentage of inseminated cows that become pregnant at each service. 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (26) AIPL

Conception rate variance components 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (27) AIPL

Correlations among fertility PTA Correlations among PTA for bulls with at least 100 CR daughters. 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (28) AIPL

Distribution of Heifer CR PTA 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (29) AIPL

Distribution of Cow CR PTA 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (30) AIPL

Top bulls – Heifer CR 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (31) AIPL

Bottom bulls – Heifer CR 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (32) AIPL

Top bulls – Cow CR 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (33) AIPL

Bottom bulls – Cow CR 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (34) AIPL

Acknowledgments Genomics work supported by NRI Grants 2006 -35205 -16888 and 200635205 -16701 and by NAAB. Much of the work on heifer and cow CR was carried out by Dr. Melvin Kuhn while he was at AIPL. 2008 NAAB Dairy Sire Evaluation Committee, October 27 2008 (35) AIPL