1. Duane Norman Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD duane.norman@ars.usda.gov NDHIA Board – 2009 (1) Update on AIPL research since April 2009 What’s new!

2. Norman NDHIA Board – 2009 (2) Genomic news from the bovine g-nome Norman NDHIA Board – 2009 (2)

3. Norman NDHIA Board – 2009 (3) Calling genotypes l Genotypes called by Tad Sonstegard, BFGL, through April 2009 l AIPL staff trained to run GenomeStudio l Cluster files shared with 4 commercial labs to allow call harmonization l Labs began providing genotypes in June News from the bovine g-nome

4. Norman NDHIA Board – 2009 (4) Commercial labs l GeneSeek (Lincoln, NE) l Genetics & IVF Institute (Fairfax, VA) l Genetic Visions (Middleton, WI) l DNA LandMarks (Saint-Jean-sur-Richelieu, QC, Canada) News from the bovine g-nome

5. Norman NDHIA Board – 2009 (5) Managing sample ID l Web query established for nominations w Indicates pedigree status w Designates nominator w Provides sample status, including rejection reasons l Query used by labs to convert sample ID to registration number and detect ID entry errors News from the bovine g-nome

6. Norman NDHIA Board – 2009 (6) Genotype database l 50,972 SNP called l Calling redone to provide additional genotypes l Many corrections required to make sample ID match l Genotypes from Illumina, University of Missouri, University of Alberta, and Switzerland also included News from the bovine g-nome

7. Norman NDHIA Board – 2009 (7) SNP selection l Call rate of >90% l Not a duplicate l Parent-progeny conflicts of <2% l Minor allele frequency of >1% l Heterozygosity within 20% of expected l For bulls, X heterozygosity of <5% News from the bovine g-nome

8. Norman NDHIA Board – 2009 (8) Evaluation preparation l Pedigree file created w Checked for missing ancestors w Pedigree requested for missing ancestors l Canadian evaluations obtained for cows l Type evaluations obtained for Holsteins News from the bovine g-nome

9. Norman NDHIA Board – 2009 (9) Genomic evaluations l Evaluations official w Holstein and Jerseys (January 2009) w Brown Swiss (August 2009) l June 2009 trait changes w Net merit calculated as sum of traits rather than as an individual trait w Holstein feet & legs and rear teat placement added l Current Interbull evaluation added at final selection-index step triannually News from the bovine g-nome

10. Norman NDHIA Board – 2009 (10) Reliability calculation l Inversion and discounting w Gain in daughter equivalents times 0.6 l Simple approximation w Could be adjusted for breed or number of close relatives w Used in April 2009 to beat deadline News from the bovine g-nome

11. Norman NDHIA Board – 2009 (11) Interbull plans l Convert genomic PTAs (August 2009) w Young bulls from France, Netherlands, and New Zealand w EU requires reliability of ≥50% for marketing l Combine using G-MACE (2010) w Proven bulls next year (2010) w Domestic and genomic evaluations computed 1–2 weeks earlier to meet Interbull deadlines w Currently genomics and MACE at same time News from the bovine g-nome

12. Norman NDHIA Board – 2009 (12) Evaluation options l National w Include cows as predictors? w Include polygenic effect in model? l International w Conversion formulas for young bulls w G-MACE to exchange genomic breeding values w Direct multicountry genomic evaluation News from the bovine g-nome

13. Norman NDHIA Board – 2009 (13) Culling statistics Norman NDHIA Board – 2009 (13)

14. Norman NDHIA Board – 2009 (14) Culling status report l New annual AIPL Research Report by Norman, Wright, and Lombard available at AIPL web site (September 2009) l Based on destination (4) and termination (11) codes provided by DRPCs l Separate summaries by parity and breed w 6 breeds w 2 crossbred groups − Heterosis of >90% (crossbred, CB) − Heterosis of 50 to 90% (backcross, BC)

15. Norman NDHIA Board – 2009 (15) Destination codes Frequency*, % CodeAYBSGUHOJEMSRWCBBC Stayed in herd706863677168 7472 Sold for dairy766377445 Sold for slaughter192124 1722 1820 Died468654655 *Lactations completed between 1-1-07 and 12-31-08

16. Norman NDHIA Board – 2009 (16) Termination codes Frequency*, % CodeAYBSGUHOJEMSRWCBBC Stayed in herd Normal696763667167687371 Abortion<1 111 11 Sold Locomotion1111<1 111 Low yield233433333 Reproduction566536634 Mastitis233433444 Other88111079867 *Lactations completed between 1-1-07 and 12-31-08

17. Norman NDHIA Board – 2009 (17) Left herd but not sold for dairy Frequency*, % Termination codeAYBSGUHOJEMSRWCBBC Sold Locomotion453421443 Low yield11129151412101415 Reproduction222118161423221516 Mastitis10 111213 1716 Other352935333236292829 Died192324212516212221 *Lactations completed between 1-1-07 and 12-31-08

18. Norman NDHIA Board – 2009 (18) Norman NDHIA Board – 2009 (18) AM-PM factors

19. Norman NDHIA Board – 2009 (19) Cooperative research l Purdue University (Mike Schutz) l Objectives w Derive factors to estimate daily yields from 1 record for 2X milking and 1 or 2 records for 3X milking w Compare factors derived by several methods for their accuracy in predicting true daily yield or somatic cell score (SCS) AM-PM factors

20. Norman NDHIA Board – 2009 (20) Progress to date l Adjustment factors developed for Holstein and Jersey milk yield from 2X and 3X milkings l Preliminary Holstein and Jersey 2X AM-PM factors developed for fat, protein, and SCS AM-PM factors

21. Norman NDHIA Board – 2009 (21) Plans l Verification of 2X AM-PM factors for fat and protein l Development and verification of 3X factors for fat and protein l Determination of whether effect of milking interval on somatic cell count is consistent enough to allow adjustment l All breeds combined for final estimation of adjustment factors AM-PM factors

22. Norman NDHIA Board – 2009 (22) Norman NDHIA Board – 2009 (22) Genetic resistance to Johne’s disease

23. Norman NDHIA Board – 2009 (23) Cooperative studies l Characteristics of milk ELISA scores and factors affecting scores w Antel BioSystems (Byrem, Norman) l Estimation of genetic parameters and transmitting ability for milk ELISA scores w University of Minnesota (Attala... Cole) Johne’s disease

24. Norman NDHIA Board – 2009 (24) Milk ELISA characteristics l Average score of 0.04 (±0.18) for 196,412 tests from 696 herds in 16 States from 2002 through 2008 w 3.2 and 6.1% positives based on cutoffs of 0.40 and 0.10 l Same average and SD for 42,778 scores from 25 more comprehensively tested herds in Michigan and Wisconsin w 3.0 and 5.6% positives Johne’s disease

25. Norman NDHIA Board – 2009 (25) Milk ELISA (cont.) l Cows with multiple tests within parity (10%) w 95% negative for last test if 1st test negative w 52% positive for last test if 1st test positive l Cows with multiple tests across parities (27%) w 91% negative for last test if 1st test negative w 51% positive for last test if 1st test positive Johne’s disease

26. Norman NDHIA Board – 2009 (26) Milk ELISA (cont.) l Unusually high percentage (44%) of untested cows removed from herd by end of current lactation likely indicates selection of which cows to test for Johne’s l Tested cows removed from herd w 15% of positive cows w 12% of negative cows l Further analysis needed to optimize usefulness of DHI records in evaluation of milk testing for Johne's Johne’s disease

27. Norman NDHIA Board – 2009 (27) Factors affecting scores l Cow distribution by parity l Score distribution by days from calving to test l Birth and test seasons (four 3-mo seasons starting in January) normally distributed l Score distribution by year Parity123 44 Cows (%)45261514 Test stage (d) 1–6061–120121–180181–240241–300301–360  361 Scores (%)129811231820 Year2002200320042005200620072008* Scores (%)481214202516 *partial year Johne’s disease

28. Norman NDHIA Board – 2009 (28) Score factors (cont.) l Scores generally increased with year, parity, and test stage l Birth and test seasons nonsignificant l Low heritability (4%) l Moderate repeatability (26%) Johne’s disease

29. Norman NDHIA Board – 2009 (29) Correlations 185 Holstein AI sires with  50 daughters l PTA correlation with breeding value for ELISA score w Milk (0.08) w Fat (–0.06) w Protein (0.03) l Selection based on SCS, productive life, DPR, and net merit could improve resistance to Johne’s w SCS (-0.01) w Productive life (–0.19) w DPR (–0.15) w Net merit (–0.16) Johne’s disease