1. H. D. Norman Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350 duane.norman@ars.usda.gov 2011 DRMS annual meeting & NDHIA board meeting (1) AIPL Research Update

2. Norman DRMS annual meeting & NDHIA board meeting (2) 2011 Topic 1 Effect of bulk-tank SCC standard in DHI and Federal Milk Orders

3. Norman DRMS annual meeting & NDHIA board meeting (3) 2011 DHI noncompliance by herd size – NMPF 3 of 5 consecutive BTSCC tests exceeding a limit of 750,000 cells/mL 600,000 cells/mL 500,000 cells/mL 400,000 cells/mL

4. Norman DRMS annual meeting & NDHIA board meeting (4) 2011 DHI noncompliance by herd size – NDHIA 4 consecutive 3-mo geometric mean BTSCC exceeding a limit of 750,000 cells/mL 600,000 cells/mL 500,000 cells/mL 400,000 cells/mL

5. Norman DRMS annual meeting & NDHIA board meeting (5) 2011 DHI noncompliance by herd size – NMC 3-mo geometric mean BTSCC exceeding limit plus next BTSCC test exceeding a limit of 750,000 cells/mL 550,000 cells/mL

6. Norman DRMS annual meeting & NDHIA board meeting (6) 2011 FMO noncompliance by milk sold – NMPF 3 of 5 consecutive BTSCC tests exceeding a limit of 750,000 cells/mL 600,000 cells/mL 500,000 cells/mL 400,000 cells/mL

7. Norman DRMS annual meeting & NDHIA board meeting (7) 2011 FMO noncompliance by milk sold – NDHIA 4 consecutive 3-mo geometric mean BTSCC exceeding a limit of 750,000 cells/mL 600,000 cells/mL 500,000 cells/mL 400,000 cells/mL

8. Norman DRMS annual meeting & NDHIA board meeting (8) 2011 FMO noncompliance by milk sold – NMC 3-mo geometric mean BTSCC exceeding limit plus next BTSCC test exceeding a limit of 750,000 cells/mL 550,000 cells/mL

9. Norman DRMS annual meeting & NDHIA board meeting (9) 2011 Topic 2 Genotyping

10. Norman DRMS annual meeting & NDHIA board meeting (10) 2011 New genotypes 0 1,000 2,000 3,000 4,000 5,000 6,000 9-1010-1011-1012-101-112-113-114-115-116-117-11 50K and HD – 77,553 total Totals as of July 2011 3K – 42,512 total

11. Norman DRMS annual meeting & NDHIA board meeting (11) 2011 Sex distribution – August 2010 Males 61% Females 39% All genotypes

12. Norman DRMS annual meeting & NDHIA board meeting (12) 2011 Sex distribution – July 2011 Males 42% All genotypes Females 58%

13. Norman DRMS annual meeting & NDHIA board meeting (13) 2011 3K sample characteristics l 93% of 3K genotypes are from females l 3K sample types include − Hair (79%) − Blood (10%) − Nasal (10%) − Semen (1%)

14. Norman DRMS annual meeting & NDHIA board meeting (14) 2011 Low-density chip (BovineLD – 6,909 SNPs) l Data first available in October 2011 l Evaluations coming in November 2011 l Expected to replace 3K chip because of greater genotyping accuracy w 98.9% for Holsteins (versus 95.9% for 3K) w 98.2% for Jerseys (versus 94.6% for 3K) w 97.9% for Brown Swiss (versus 93.9% for 3K) l Repeatabilities also higher with LD genotypes

15. Norman DRMS annual meeting & NDHIA board meeting (15) 2011 Improving pedigree accuracy l As genotypes are received, maternal grandsires (MGS) are checked, and those unlikely are reported l When MGS is unlikely, other males are examined, and the most likely alternatives are provided

16. Norman DRMS annual meeting & NDHIA board meeting (16) 2011 Topic 3 Discovery of haplotypes with recessive effects impacting fertility

17. Norman DRMS annual meeting & NDHIA board meeting (17) 2011 Dominant-recessive example l Black versus red coat color in Holsteins l Assume frequency is 90% (.90) for black allele B l Then, homozygous black (BB) frequency is expected to be 81% (.90 ×.90) l Homozygous red (bb) frequency is expected to be 1% (.10 ×.10) l Heterozygous black (Bb) frequency is expected to be 18% (2 ×.90 ×.10); i.e., red carriers

18. Norman DRMS annual meeting & NDHIA board meeting (18) 2011 Similar inheritance l 5 haplotypes with recessive effects impacting fertility discovered w Additive effects small and already in evaluations w Most (or all) populations already carry these l At least 19 countries have “health” laws that exclude carriers of defects w Irony: Only countries that test are banned w Thus, import restrictions make little sense

19. Norman DRMS annual meeting & NDHIA board meeting (19) 2011 Recessive defect discovery l Check for homozygous haplotypes w 7 – 90 expected, but 0 observed w 5 of top 11 haplotypes confirmed as lethal w 936 – 52,449 carrier sire  carrier MGS fertility records w 3.0 – 3.7% lower conception rates l Confirmed brachyspina same way

20. Norman DRMS annual meeting & NDHIA board meeting (20) 2011 Haplotypes impacting fertility Nam e BTA chromo -some Location, Mbases Carrier frequency, %Earliest known ancestors HH1 562–68 4.5Pawnee Farm Arlinda Chief HH2 193–98 4.6Willowholme Mark Anthony HH3 892–97 4.7Glendell Arlinda Chief, Gray View Skyliner JH11511–1623.4Observer Chocolate Soldier BH1 742–4714.0West Lawn Stretch Improver

21. Norman DRMS annual meeting & NDHIA board meeting (21) 2011 Effect on fertility l Determine fertility differences between matings that could have produced a recessive versus those that could not have l 3 types of bulls: tested carriers, tested noncarriers, and not tested l 9 types of sire × MGS matings (3 × 3) l Subtract fertility effects for animals with carrier sire and carrier MGS from those for animals with noncarrier sires

22. Norman DRMS annual meeting & NDHIA board meeting (22) 2011 Haplo- type Additive effect, CR Sire x MGS interaction NR60 NR100 NR140CR280 CVM0.121.0 1.21.6 2.4 BY0.462.0 2.32.4 2.7 HH10.351.0 1.41.8 2.8 HH20.362.5 4.24.0 4.4 HH30.362.7 3.13.0 2.9 JH12.223.7 3.6 BH10.982.8 4.03.2 Additive and nonadditive decreases* *Nonreturn rates or full gestation conception

23. Norman DRMS annual meeting & NDHIA board meeting (23) 2011 Haplo- type Conception rate BullService sireHeiferCow BYRamosN/A+0.1+5.2 HH1Lucius+3.1+2.5 HH2Colby+2.2+5.2+5.4 HH3O-Man+0.6+2.1+3.5 JH1Country – 0.5+2.7+3.2 BH1Payoff+1.5 +3.4 Carrier bulls with high fertility

24. Norman DRMS annual meeting & NDHIA board meeting (24) 2011 Conclusions l Recessive defects found in 3 breeds (HH1, HH2, HH3, JH1, BH1) w Officially reported in August w Most embryo losses at <60 days l Breeders should select for fertility (not against individual defects) and mate carriers to noncarriers l Research underway to fine map the recessives

25. Norman DRMS annual meeting & NDHIA board meeting (25) 2011 Acknowledgment Paul VanRaden (AIPL) discovered the haplotypes that affect fertility with the assistance of: Dan Null (AIPL) Katie Olson (NAAB), and Jana Hutchison (AIPL)