1. April 2010 (1) Prediction of Breed Composition & Multibreed Genomic Evaluations K. M. Olson and P. M. VanRaden

2. April 2010 (2) Background - Prediction of Breed l 200 Breed specific SNP were used to verify an animal received the correct breed code in the quality control data step l Several animals had fewer breed-specific SNPs and lower genomic relationships and inbreeding l Wanted to investigate a more precise way to look at breed composition

3. April 2010 (3) Materials & Methods – Prediction of Breed l Y- Variable was breed of animal l Used both females and males l 3 different sizes of SNP sets were used for the genomic evaluation w The Full 43,385 SNP set w The proposed 3 K SNP set w The 600 breed specific set − Each breed has ~ 200 – used for the basic check currently not a genomic evaluation

4. April 2010 (4) Materials & Methods – Prediction of Breed l Training data set – animal reliability set to 99% and parent average reliability set to 50% w Proven as of July 2009 w Total of 14,039 animals across all breeds l Validation data set – reliabilities set to 0% w Unproven as of July 2009 w 15,809 animals across all breeds

5. April 2010 (5) Results – Prediction of Breed l All three tests were able to determine a Holstein that was by pedigree 1/8 (12.5%) Jersey w 43 K test predicted her as 85.9% Holstein and 13.3% Jersey w 3 K predicted she was 84.4% Holstein and 15.5% Jersey w 600 SNP set she was 83.0% Holstein and 16.6% Jersey

6. April 2010 (6) Results – Prediction of Breed SNP set/ Breed43 K3 K600 Holstein (N = 14,794) 1.000±0.0081.004±0.0311.002±0.019 Jersey (N = 919) 0.996±0.0280.978±0.0630.989±0.036 Brown Swiss (N = 96) 0.994±0.0210.989±0.0360.992±0.051 Means and standard deviations for given breed of the validation data set

7. April 2010 (7) Conclusions – Prediction of Breed l The 43 K chip was the most accurate at prediction of breed composition l The 3 K chip could identify individuals that had large amounts (> 13%) of foreign DNA

8. April 2010 (8) Obstacles – Prediction of Breed l There is a patent w Located at http://www.patentstorm.us/patents/751112 7/fulltext.html http://www.patentstorm.us/patents/751112 7/fulltext.html l May not be accurate for animals from different populations w foreign animals w older animals

9. April 2010 (9) Background - Multibreed l Multibreed methods are currently used in traditional methods l Only within breed methods are used for genomics evaluations l Previous research has shown little improvement in accuracy from using all breeds with the 50K SNP chip however, little research has been done using multi-trait methodology

10. April 2010 (10) Objectives – Multibreed genomic evaluations l To investigate three different methods of multibreed genomic evaluations using Holsteins, Jerseys, and Brown Swiss genotypes

11. April 2010 (11) Materials & Methods – Multibreed (Animals) l The training data set - animals were proven by Nov. 2004 w Holsteins – 5,331 w Jerseys – 1,361 w Brown Swiss – 506 l The validation data set - animals were unproven as of Nov. 2004 and proven by June 2009 w Holsteins – 2,477 w Jerseys – 410 w Brown Swiss - 182

12. April 2010 (12) Material & Methods – Multibreed (Methods) l Method 1 estimated SNP effects within breed then applied those effects to the other breeds l Method 2 (across-breed) used a common set of SNP effects from the combined breed genotypes and phenotypes l Method 3 (multi-breed) used a correlated SNP effects using a multitrait method ( as explained by VanRaden and Sullivan, 2010)

13. April 2010 (13) Results – P – Values for Protein Yield HolsteinJerseyBrown Swiss Traditional PTA< 0.001 0.061 GPTA< 0.001 0.086 R 2 adj 0.50450.48740.1030 Method 1 HOL GPTA< 0.0010.6680.344 JER GPTA0.873< 0.0010.844 BSW GPTA0.8130.4730.107 PTA< 0.001 0.054 R 2 adj 0.50410.48540.0978

14. April 2010 (14) Results – P-values for protein yield HolsteinJerseyBrown Swiss Method 2 PTA< 0.001 0.088 GPTA< 0.001 0.316 ABGPTA0.0020.2900.007 R 2 adj 0.50630.48760.1337 Method 3 PTA< 0.001 0.080 GPTA0.7420.3240.140 MBGPTA< 0.001 0.060 R 2 adj 0.50600.49160.1127

15. April 2010 (15) Results – P-Values for protein yield HolsteinJerseyBrown Swiss Method 2 PTA<0.001 0.2016 ABGPTA< 0.001 0.0023 R 2 adj 0.4742 0.1336 Method 3 PTA< 0.001 0.055 MBGPTA< 0.001 0.081 R 2 adj 0.50600.49160.1067 The traditional GPTA was not included in these analyses

16. April 2010 (16) Conclusions – Multibreed Genomic Evaluation l Method 1 did not help the estimates for genomic evaluations l Method 2 increased the predictive ability, however the traditional GPTA accounted for more variation than the across-breed GPTA l Method 3 increased the predictive ability and the multi-breed GPTA accounted for more variation than the traditional GPTA

17. April 2010 (17) Implications l The multibreed genomic evaluations do slightly increase the accuracy of the evaluations, but may not warrant the increased computational demands l A higher density SNP chip would most likely increase the gains in accuracy for multibreed genomic evaluations l Multibreed would be needed for genomic selection in crossbred herds w Not much demand for that yet