1. Paul VanRaden, 1 Katie Olson, 2 Dan Null, 1 Mehdi Sargolzaei, 3 Marco Winters, 4 and Jan-Thijs van Kaam 5 1 Animal Improvement Programs Laboratory, ARS, USDA, Beltsville, MD, USA 2 National Association of Animal Breeders, Columbia, MO, USA 3 CGIL, University of Guelph, ON, Canada 4 DairyCo, Agric. & Hort. Development Board, Kenilworth, Warwickshire, UK 5 Associazone Nazionale Allevatori Frisona Italiana, Cremona, Italy 2012 Reliability Increases from Combining 50,000- and 777,000-Marker Genotypes from 4 Countries

2. Interbull annual meeting, May 2012, Cork, Ireland (2)Paul VanRaden 2012  Effect of foreign bulls on U.S. reliability (REL) Model foreign as single-trait (ST) or multitrait (MT) Addition of CAN, GBR, and ITA Holsteins (HOL) Addition of CHE, DEU, and AUT Brown Swiss (BSW)  Compare high-density (HD) with 50K predictions 1,510 HD genotypes for HOL bulls ST USA, CAN, GBR, ITA Topics

3. Interbull annual meeting, May 2012, Cork, Ireland (3)Paul VanRaden 2012  Foreign genomic information could outweigh domestic data (GxE or GxG) Low genetic correlations because of environment (traits are really different between countries) Poor ties between domestic and foreign animals (genetic distance)  Genetic correlation Average correlation for all foreign bulls (MT) Assume MACE EBV are correlated by 1.0 (ST) Multitrait Model Multitrait Model

4. Interbull annual meeting, May 2012, Cork, Ireland (4)Paul VanRaden 2012 Foreign Holstein Reference Bulls 3,593 (28% of total bulls) had no U.S. daughters in 2008 CAN 1,321 bulls ITA 1,677 bulls GBR 247 bulls

5. Interbull annual meeting, May 2012, Cork, Ireland (5)Paul VanRaden 2012 Animals genotyped BSWHOL MaleFemaleMaleFemale May 2012 data2,12597159,705122,528 Reference population1,68237418,50822,800 Foreign reference8707,974 August 2008 data Reference population1,47317110,7185,124 Foreign reference7323,593 U.S. validation bulls1153,404 Reference Genotypes Reference Genotypes

6. Interbull annual meeting, May 2012, Cork, Ireland (6)Paul VanRaden 2012 REL – REL PA (HOL) Trait Foreign excludedSTMT Average (9 traits)21.924.624.5 Milk26.628.728.6 Fat29.031.331.1 Protein20.222.522.3 Productive life19.521.822.2 SCS23.727.2 Daughter pregnancy rate17.521.321.2 Final score22.224.024.1 Stature29.434.033.9 Sire calving ease8.810.49.7

7. Interbull annual meeting, May 2012, Cork, Ireland (7)Paul VanRaden 2012 Foreign Brown Swiss Reference More arriving soon from InterGenomics DEU 318 bulls AUT 52 bulls CHE 403 bulls

8. Interbull annual meeting, May 2012, Cork, Ireland (8)Paul VanRaden 2012 REL – REL PA (BSW) Trait Foreign excluded STMT Average (9 traits)8.511.713.1 Milk15.620.920.6 Fat10.311.412.5 Protein13.516.216.6 Productive life4.96.57.5 SCS5.04.26.6 Daughter pregnancy rate9.86.87.3 Final score2.79.315.7 Stature12.821.524.2 Sire calving ease1.98.76.6

9. Interbull annual meeting, May 2012, Cork, Ireland (9)Paul VanRaden 2012  1,510 HOL Illumina BovineHD 460 ITA bulls 305 USA bulls and 172 USA cows 284 GBR bulls 93 CAN bulls 196 bulls from other countries  Earlier studies of 342 or 1,078 HD HD Genotypes

10. Interbull annual meeting, May 2012, Cork, Ireland (10)Paul VanRaden 2012 HD REL Gains (HOL) Trait REL 50K  REL PA REL HD  REL 50K HD nonlinear  HD linear Average (28 traits)31.50.40.8 Milk28.7  0.31.2 Fat31.30.21.8 Protein22.5  0.50.3 Productive life21.81.61.3 SCS27.20.50.4 Daughter pregnancy rate21.30.70.4 Final score24.0  0.20.1 Stature34.01.80.7 Sire calving ease10.4  2.31.9

11. Interbull annual meeting, May 2012, Cork, Ireland (11)Paul VanRaden 2012  Average REL gain of HD compared with 50K across 28 traits  0.5% decrease using 342 HD 0.5% increase using 1,074 HD 0.4% increase using 1,510 HD  Imputation accuracy tested using simulated chromosome and same population structure as actual Preliminary HD Studies

12. Interbull annual meeting, May 2012, Cork, Ireland (12)Paul VanRaden 2012 Markers Animals Findhap all FImpute All2-step 1 330,0001,11299.8999.96 41,25072,53299.099.3 5,1301,00094.694.796.1 2,55038,44190.591.193.7 0202 3,29593.595.196.7 Imputation Accuracy (% correct) 1 Imputing lower densities to 41,250 and then imputing to 330,000 in a second step instead of all together 2 Dams imputed from  4 progeny

13. Interbull annual meeting, May 2012, Cork, Ireland (13)Paul VanRaden 2012 Conclusions  REL improved with foreign bulls and ST methods 2.6% for HOL and 3.2% for BSW Actual gains larger – Multicountry bulls counted as domestic – More recent HOL bulls are foreign MT added 1.4% REL only for BSW  HD only 0.4% higher REL than 50K Imputation accurate with  1,000 HD FImpute more accurate than findhap

14. Interbull annual meeting, May 2012, Cork, Ireland (14)Paul VanRaden 2012  Genotype exchanges coordinated by Marj Faust, Brian Van Doormaal, Gordon Doak, and Dan Gilbert  Genotypes provided by Cooperative Dairy DNA Repository (USA) Canadian Dairy Network (CAN) Italian Ministry of Agriculture (MIPAAF) Innovagen project (DM 10750-7303-2011) and ANAFI (ITA) Defra and Ruminant Genetic Impr. Network (GBR) Swiss Brown Cattle Breeders’ Federation (CHE) Bavarian State Research Center for Agriculture (DEU) Acknowledgments

15. Interbull annual meeting, May 2012, Cork, Ireland (15)Paul VanRaden 2012  HD bulls to genotype selected by Kent Weigel (University of Wisconsin) Ezequiel Nicolazzi (Parco Tecnologico Padano, Italy)  HD genotypes edited and assembled by USDA’s Animal Improvement Programs Laboratory (AIPL) and Bovine Functional Genomics Laboratory (BFGL ) George Wiggans (AIPL) Lillian Bacheller (AIPL) Mel Tooker (AIPL) Tabatha Cooper (AIPL) Acknowledgments (continued) Tad Sonstegard (BFGL) Erin Connor (BFGL) Alicia Beavers (BFGL)