2015 John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD Genomic improvement programs for US dairy cattle

CRV, Arnhem, The Netherlands, 14 April 2015 (2) Cole U.S. DHI dairy statistics (2011) l 9.1 million U.S. cows l ~75% bred AI l 47% milk recorded through Dairy Herd Information (DHI) w 4.4 million cows − 86% Holstein − 8% crossbred − 5% Jersey − <1% Ayrshire, Brown Swiss, Guernsey, Milking Shorthorn, Red & White w 20,000 herds w 220 cows/herd w 10,300 kg/cow

CRV, Arnhem, The Netherlands, 14 April 2015 (3) Cole Genomic data flow DNA samples genotypes genomic evaluations nominations, pedigree data genotype quality reports genomic evaluations DNA samples genotypes DNA samples Dairy Herd Improvement (DHI) producer Council on Dairy Cattle Breeding (CDCB) DNA laboratory AI organization, breed association AI organization, breed association

CRV, Arnhem, The Netherlands, 14 April 2015 (4) Cole Genotypes are abundant

CRV, Arnhem, The Netherlands, 14 April 2015 (5) Cole Sources of DNA for genotyping SourceSamples (no.)Samples (%) Blood 10,7274 Hair113,45539 Nasal swab2,9541 Semen3,4321 Tissue149,30151 Unknown12,3014

CRV, Arnhem, The Netherlands, 14 April 2015 (6) Cole SNP count for different chips ChipSNP (no.)ChipSNP (no.) 50K54,001GP219,809 50K v254,609ZLD11,410 3K2,900ZMD56,955 HD777,962ELD9,072 Affy648,875LD26,912 LD6,909GP326,151 GGP8,762ZL217,557 GHD77,068ZM260,914

CRV, Arnhem, The Netherlands, 14 April 2015 (7) Cole 2014 genotypes by chip SNP density Chip SNP densityFemaleMale All animals Low 239,07129,631268,702 Medium9,09814,20223,300 High All248,309 43,861292,170

CRV, Arnhem, The Netherlands, 14 April 2015 (8) Cole 2014 genotypes by breed and sex BreedFemaleMale All animals Female: male Ayrshire 1, ,69488:12 Brown Swiss9448,6419,58510:90 Guernsey1, ,11084:16 Holstein212,76530,883243,64887:13 Jersey31,3233,79335,11689:11 Milking Shorthorn21367:33 Normande0100:100 Crossbred :0 All248,30943,861292,17085:15

CRV, Arnhem, The Netherlands, 14 April 2015 (9) Cole Genotypes by age (last 12 months) 

CRV, Arnhem, The Netherlands, 14 April 2015 (10) Cole Growth in bull predictor population BreedJan mo gain Ayrshire Brown Swiss6, Holstein26,7592,174 Jersey4,448245

CRV, Arnhem, The Netherlands, 14 April 2015 (11) Cole Growth in US predictor population BullsCows 1,2 BreedJan mo gainJan mo gain Ayrshire Brown Swiss6, , Holstein26,7592,174109,71451,950 Jersey4, ,01210,601 1 Predictor cows must have domestic records. 2 Counts include 3k genotypes, which are not included in the predictor population.

CRV, Arnhem, The Netherlands, 14 April 2015 (12) Cole TraitBias* Reliability (%) Reliability gain (% points) Milk (kg)− Fat (kg)− Protein (kg)− Fat (%) Protein (%) Productive life (mo)− Somatic cell score Daughter pregnancy rate (%) Sire calving ease Daughter calving ease− Sire stillbirth rate Daughter stillbirth rate Holstein prediction accuracy *2013 deregressed value – 2009 genomic evaluation

CRV, Arnhem, The Netherlands, 14 April 2015 (13) Cole Reliability gains Reliability (%)Ayrshire Brown SwissJerseyHolstein Genomic Parent average2830 Gain Reference bulls 6805,767 4,207 24,547 Animals genotyped 1,7889,01659,923469,960 Exchange partners CanadaCanada, Interbull Canada, Denmark Canada, Italy, UK Source: VanRaden, Advancing Dairy Cattle Genetics: Genomics and Beyond presentation, Feb. 2014

CRV, Arnhem, The Netherlands, 14 April 2015 (14) Cole Parent ages of marketed Holstein bulls

CRV, Arnhem, The Netherlands, 14 April 2015 (15) Cole Active AI bulls that were genomic bulls

CRV, Arnhem, The Netherlands, 14 April 2015 (16) Cole Marketed Holstein bulls Year entered AI Traditional progeny- tested Genomic marketed All bulls 20081, , , , , , , , , , , ,453

CRV, Arnhem, The Netherlands, 14 April 2015 (17) Cole Genetic merit of marketed Holstein bulls Average gain: $19.77/year Average gain: $52.00/year Average gain: $85.60/year

CRV, Arnhem, The Netherlands, 14 April 2015 (18) Cole Stability of genomic evaluations l 642 Holstein bulls w Dec NM$ compared with Dec NM$ w First traditional evaluation in Aug w  50 daughters by Dec l Top 100 bulls in 2012 w Average rank change of 9.6 w Maximum drop of 119 w Maximum rise of 56 l All 642 bulls w Correlation of 0.94 between 2012 and 2014 w Regression of 0.92

CRV, Arnhem, The Netherlands, 14 April 2015 (19) Cole % genotyped mates of top young bulls Net Merit (Aug 2013 ) Percentage of mates genotyped Supersire Numero Uno S S I Robust Topaz Garrold Mogul

CRV, Arnhem, The Netherlands, 14 April 2015 (20) Cole Haplotypes affecting fertility l Rapid discovery of new recessive defects w Large numbers of genotyped animals w Affordable DNA sequencing l Determination of haplotype location w Significant number of homozygous animals expected, but none observed w Narrow suspect region with fine mapping w Use sequence data to find causative mutation

CRV, Arnhem, The Netherlands, 14 April 2015 (21) Cole Name BTA chromo- some Location* (Mbp) Carrier frequency (%)Earliest known ancestor HH1563.2*3.8Pawnee Farm Arlinda Chief HH – Willowholme Mark Anthony HH3895.4*5.9Glendell Arlinda Chief, Gray View Skyliner HH411.3*0.7Besne Buck HH – Thornlea Texal Supreme JH *24.2Observer Chocolate Soldier JH – Liberators Basilius BH – West Lawn Stretch Improver BH – Rancho Rustic My Design AH *26.0Selwood Betty’s Commander Haplotypes affecting fertility *Causative mutation known

CRV, Arnhem, The Netherlands, 14 April 2015 (22) Cole Recessive Haplo- type BTA chromo- some Tested animals (no.) Concord- ance (%) New carriers (no.) BrachyspinaHH021??? BLADHHB 1*11, CVMHHC 3*13,226—2,716 DUMPSHHD 1*3, Mule footHHM15* PolledHHP1345—2,050 Red coat color HHR18*4,137—5,927 SDMBHD11* SMABHM24* WeaverBHW Haplotypes tracking known recessives *Causative mutation known

CRV, Arnhem, The Netherlands, 14 April 2015 (23) Cole Weekly evaluations l Released to nominators, breed associations, and dairy records processing centers at 8 am each Tuesday l Calculations restricted to genotypes that first became usable during the previous week l Computing time minimized by not calculating reliability or inbreeding

CRV, Arnhem, The Netherlands, 14 April 2015 (24) Cole SNP used for genomic evaluations l 60,671 SNP used after culling on w MAF w Parent-progeny conflicts w Percentage heterozygous (departure from HWE) l SNP for HH1, BLAD, DUMPS, CVM, polled, red, and mulefoot included w JH1 included for Jerseys l Some SNP eliminated because incorrect location  haplotype non-inheritance

CRV, Arnhem, The Netherlands, 14 April 2015 (25) Cole Some novel phenotypes studied recently ● Claw health (Van der Linde et al., 2010) ● Dairy cattle health (Parker Gaddis et al., 2013) ● Embryonic development (Cochran et al., 2013) ● Immune response (Thompson-Crispi et al., 2013) ● Methane production (de Haas et al., 2011) ● Milk fatty acid composition (Soyeurt et al., 2011) ● Persistency of lactation (Cole et al., 2009) ● Rectal temperature (Dikmen et al., 2013) ● Residual feed intake (Connor et al., 2013)

CRV, Arnhem, The Netherlands, 14 April 2015 (26) Cole Evaluation methods for traits l Animal model (linear) w Yield (milk, fat, protein) w Type (AY, BS, GU, JE) w Productive life w Somatic cell score w Daughter pregnancy rate w Heifer conception rate w Cow conception rate l Sire–maternal grandsire model (threshold) w Service sire calving ease w Daughter calving ease w Service sire stillbirth rate w Daughter stillbirth rate Heritability 8.6% 3.6% 3.0% 6.5% 25 – 40% 7 – 54% 8.5% 12% 4% 1% 1.6%

CRV, Arnhem, The Netherlands, 14 April 2015 (27) Cole Holstein daughter pregnancy rate (%) Phenotypic base = 22.6% Sires Cows  0.1%/yr

CRV, Arnhem, The Netherlands, 14 April 2015 (28) Cole Holstein calving ease (%) Daughte r Service-sire phenotypic base = 7.9% Daughter phenotypic base = 7.5% Service sire 0.18%/yr 0.01%/yr

CRV, Arnhem, The Netherlands, 14 April 2015 (29) Cole What do US dairy farmers want? National workshop in Tempe, AZ in February Producers, industry, academia, and government Farmers want new tools Additional traits (novel phenotypes) Better management tools Foot health and feed efficiency were of greatest interest

CRV, Arnhem, The Netherlands, 14 April 2015 (30) Cole What can farmers do with novel traits? Put them into a selection index Correlated traits are helpful Apply selection for a long time There are no shortcuts Collect phenotypes on many daughters Repeated records of limited value Genomics can increase accuracy

CRV, Arnhem, The Netherlands, 14 April 2015 (31) Cole What can DRPCs do with novel traits? Short-term – Benchmarking tools for herd management Medium-term – Custom indices for herd management Additional types of data will be helpful Long-term – Genetic evaluations Lots of data needed, which will take time

CRV, Arnhem, The Netherlands, 14 April 2015 (32) Cole International challenges National datasets are siloed Recording standards differ between countries ICAR standards help here Farmers are concerned about the security of their data Many populations are small Low accuracies Small markets

CRV, Arnhem, The Netherlands, 14 April 2015 (33) Cole Conclusions l Genomic research is ongoing w Detect causative genetic variants w Find more haplotypes affecting fertility w Improve accuracy through more SNPs, more predictor animals, and more traits l Genetic trend is favorable for some important, low-heritability traits w More traits are desirable w Data availability remains a challenge for new phenotypes

CRV, Arnhem, The Netherlands, 14 April 2015 (34) Cole Questions?