H. D. Norman Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD DRMS annual meeting & NDHIA board meeting (1) AIPL Research Update Norman DRMS annual meeting & NDHIA board meeting (2) 2011 Topic 1 Effect of bulk-tank SCC standard in DHI and Federal Milk Orders 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 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 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 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 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 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 Norman DRMS annual meeting & NDHIA board meeting (9) 2011 Topic 2 Genotyping Norman DRMS annual meeting & NDHIA board meeting (10) 2011 New genotypes 0 1,000 2,000 3,000 4,000 5,000 6, K and HD 77,553 total Totals as of July K 42,512 total Norman DRMS annual meeting & NDHIA board meeting (11) 2011 Sex distribution August 2010 Males 61% Females 39% All genotypes Norman DRMS annual meeting & NDHIA board meeting (12) 2011 Sex distribution July 2011 Males 42% All genotypes Females 58% Norman DRMS annual meeting & NDHIA board meeting (13) K sample characteristics l 93% of 3K genotypes are from females l 3K sample types include Hair (79%) Blood (10%) Nasal (10%) Semen (1%) 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 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 Norman DRMS annual meeting & NDHIA board meeting (16) 2011 Topic 3 Discovery of haplotypes with recessive effects impacting fertility 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 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 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 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 56268 4.5Pawnee Farm Arlinda Chief HH2 19398 4.6Willowholme Mark Anthony HH3 89297 4.7Glendell Arlinda Chief, Gray View Skyliner JH115111623.4Observer Chocolate Soldier BH1 7424714.0West Lawn Stretch Improver 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 Norman DRMS annual meeting & NDHIA board meeting (22) 2011 Haplo- type Additive effect, CR Sire x MGS interaction NR60 NR100 NR140CR280 CVM BY HH HH HH JH BH Additive and nonadditive decreases* *Nonreturn rates or full gestation conception Norman DRMS annual meeting & NDHIA board meeting (23) 2011 Haplo- type Conception rate BullService sireHeiferCow BYRamosN/A HH1Lucius HH2Colby HH3O-Man JH1Country BH1Payoff Carrier bulls with high fertility 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