Wiggans, 2013China Emerging Markets Program Seminar Dr. George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD (voice) (fax) Current status of genomic evaluation for U.S. dairy cattle

Wiggans, 2013China Emerging Markets Program Seminar Genotypes received (last 12 months) BreedFemaleMale All animals Female: male Ayrshire :40 Brown Swiss ,30754:46 Holstein149,71228,191177,90384:16 Jersey18,6003,05921,65986:14 All169,52832,193201,72184:16

Wiggans, 2013China Emerging Markets Program Seminar 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

Wiggans, 2013China Emerging Markets Program Seminar Evaluation flow l Animal nominated for genomic evaluation by breed association or AI organization l Hair or other DNA source sent to genotyping lab  SourceSamples (no.)Samples (%) Blood 27,04314 Hair116,83359 Nasal swab4,6192 Semen4,1192 Tissue45,01823

Wiggans, 2013China Emerging Markets Program Seminar Evaluation flow (continued) l DNA extracted and placed on chip for 3-day genotyping process l Genotypes sent from genotyping lab to CDCB for accuracy review  

Wiggans, 2013China Emerging Markets Program Seminar Laboratory quality control l Each SNP evaluated for w Call rate w Portion heterozygous w Parent-progeny conflicts l Clustering investigated if SNP exceeds limits l Number of failing SNPs indicates genotype quality l Target of <10 SNPs in each category

Wiggans, 2013China Emerging Markets Program Seminar Before clustering adjustment 86% call rate

Wiggans, 2013China Emerging Markets Program Seminar After clustering adjustment 100% call rate

Wiggans, 2013China Emerging Markets Program Seminar Evaluation flow (continued) l Genotype calls modified as necessary l Genotypes loaded into database l Nominators receive reports of parentage and other conflicts l Pedigree or animal assignments corrected l Genotypes extracted and imputed to 45K     

Wiggans, 2013China Emerging Markets Program Seminar Imputation l Based on splitting genotype into individual chromosomes (maternal and paternal contributions) l Missing SNPs assigned by tracking inheritance from ancestors and descendants l Imputed dams increase predictor population l Genotypes from all chips merged by imputing SNPs not present

Wiggans, 2013China Emerging Markets Program Seminar findhap l Developed by Dr. Paul VanRaden, ARS, USDA l Divides chromosomes into segments l Allows for successively shorter segments (usually 3 runs) w Long segments lock in identical by descent w Shorter segments fill in missing SNPs l Separates genotype into maternal and paternal contribution, haplotypes (phasing) l Builds haplotype library sequenced by frequency

Wiggans, 2013China Emerging Markets Program Seminar Evaluation flow (continued) l SNP effects estimated l Final evaluations calculated l Evaluations released to dairy industry w Download from CDCB FTP site with separate files for each nominator w Monthly release for new animals w All genomic evaluations updated 3 times each year with traditional evaluations   

Wiggans, 2013China Emerging Markets Program Seminar Information sources for evaluations l Traditional evaluations of genotyped bulls and cows used to estimate SNP effects l Combined final evaluation w Sum of SNP effects for an animal’s alleles w Polygenetic effect w Traditional evaluation l Pedigree data used and validated by genotypes

Wiggans, 2013China Emerging Markets Program Seminar Genotypes evaluated

Wiggans, 2013China Emerging Markets Program Seminar Holstein prediction accuracy *2013 deregressed value – 2009 genomic evaluation 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

Wiggans, 2013China Emerging Markets Program Seminar Holstein prediction accuracy *2013 deregressed value – 2009 genomic evaluation TraitBias*Reliability (%) Reliability gain (% points) Final score Stature− Dairy form− Rump angle Rump width− Feed and legs Fore udder attachment − Rear udder height − Udder depth − Udder cleft− Front teat placement − Teat length−

Wiggans, 2013China Emerging Markets Program Seminar Genotypes by animal age (last 12 months)  

Wiggans, 2013China Emerging Markets Program Seminar Parent ages for marketed Holstein bulls Birth year Parent age (mo) Sire

Wiggans, 2013China Emerging Markets Program Seminar Marketed Holstein bulls Year entered AI Traditional progeny- tested Young genotyped All bulls 20081, , , , , , , , ,931

Wiggans, 2013China Emerging Markets Program Seminar Genetic merit of marketed Holstein bulls Average gain: $20.21/year Average gain: $43.76/year Average gain: $77.51/year

Wiggans, 2013China Emerging Markets Program Seminar Genomic prediction of progeny test Select parents, transfer embryos to recipients Calves born and DNA tested Calves born from DNA-selected parents Bull receives progeny test Reduce generation interval from 5 to 2 years

Wiggans, 2013China Emerging Markets Program Seminar Benefit of genomics l Determine value of bull at birth l Increase accuracy of selection l Reduce generation interval l Increase selection intensity l Increase rate of genetic gain

Wiggans, 2013China Emerging Markets Program Seminar Why genomics works for dairy cattle l Extensive historical data available l Well-developed genetic evaluation program l Widespread use of AI sires l Progeny-test programs l High-value animals worth the cost of genotyping l Long generation interval that can be reduced substantially by genomics

Wiggans, 2013China Emerging Markets Program Seminar Current organizational roles l Council on Dairy Cattle Breeding (CDCB) responsible for receiving data, computing, and delivering U.S. genetic evaluations for dairy cattle l Animal Improvement Programs Laboratory (AIPL) responsible for research and development to improve the evaluation system l CDCB and USDA employees co-located in Beltsville

Wiggans, 2013China Emerging Markets Program Seminar Funding l CDCB evaluation calculation and dissemination funded by fee system w Based on animals genotyped w About 80% of revenue from bulls w Higher fees for herds that contribute less information l AIPL research on evaluation methodology funded by U.S. Federal government $

Wiggans, 2013China Emerging Markets Program Seminar Ways to increase accuracy l Automatic addition of traditional evaluations of genotyped bulls when bull is 5 years old l Possible genotyping of 10,000 bulls with semen in repository l Collaboration with other countries l Use of more SNPs from HD chips l Full sequencing (identify causative mutations)

Wiggans, 2013China Emerging Markets Program Seminar Evaluation accuracy by included SNPs *Difference in reliability from 45K in parentheses Reliability(%)* Trait45K Milk69.2 Fat68.4 Protein60.9 Fat percentage93.7 Protein percentage86.3 Net merit51.6 Productive life73.7 Somatic cell score64.9 Daughter pregnancy rate53.4 Service-sirecalving ease45.8 Daughter calving ease44.2 Service-sire stillbirth rate28.2 Daughterstillbirth rate K 69.3(0.1) 68.7(0.3) 60.8(–0.1) 94.4(0.7) 87.1(0.8) 51.7(0.1) 74.0(0.3) 65.8(0.9) 54.1(0.7) 45.7(–0.1) 45.8(1.6) 28.3(0.1) 37.8(0.2) 75K 68.9(–0.3) 68.6(0.2) 60.6(–0.3) 93.9(0.2) 86.3(0.0) 51.6(0.0) 73.1(–0.6) 65.6(0.7) 53.6(0.2) 45.1(–0.7) 44.9(0.7) 28.7(0.5) 37.1(–0.5) 91K 69.2(0.0) 68.4(0.0) 60.8(–0.1) 93.5(–0.2) 86.1(–0.2) 51.3(–0.3) 73.8(0.1) 65.6(0.7) 53.8(0.4) 46.2(0.4) 44.9(0.7) 29.9(1.7) 39.2(1.6)

Wiggans, 2013China Emerging Markets Program Seminar Evaluation accuracy (continued) *Difference in reliability from 45K in parentheses Reliability(%)* Trait45K Finalscore58.8 Stature68.5 Dairyform71.8 Rumpangle70.2 Rumpwidth65.0 Feet andlegs44.0 Foreudder attachment70.4 Rearudder height59.4 Udderdepth75.3 Uddercleft62.1 Frontteat placement69.9 Teatlength K 58.7(–0.1) 69.0(0.5) 72.2(0.4) 70.9(0.7) 65.4(0.4) 45.1(1.1) 70.6(0.2) 59.9(0.5) 76.2(0.9) 62.2(0.1) 70.1(0.2) 67.2(0.5) 75K 58.4(–0.4) 68.8(0.3) 71.9(0.1) 70.7(0.5) 65.0(0.0) 45.1(1.1) 70.0(–0.4) 59.6(0.2) 76.0(0.7) 62.0(–0.1) 70.2(0.3) 66.6(–0.1) 91K 58.7(–0.1) 69.1(0.6) 72.0(0.2) 70.9(0.7) 65.2(0.2) 45.1(1.1) 70.4(0.0) 59.8(0.4) 76.1(0.8) 62.2(0.1) 70.4(0.5) 66.9(0.2) All production, type, and fitnesstraits(0.5)(0.1)(0.4)

Wiggans, 2013China Emerging Markets Program Seminar Key issues for the dairy industry l Inbreeding and genetic diversity (including across breeds) l Sequencing, new genes, and mutations l Novel traits, resource populations (feed efficiency, health, milk properties)

Wiggans, 2013China Emerging Markets Program Seminar Application to more traits l Animal’s genotype good for all traits l Traditional evaluations required for accurate estimates of SNP effects l Traditional evaluations not currently available for heat tolerance or feed efficiency l Research populations could provide data for traits that are expensive to measure l Will resulting evaluations work in target population?

Wiggans, 2013China Emerging Markets Program Seminar What’s already planned l Genomic evaluations for new traits w Health (e.g., resistance to heat stress) w Feed efficiency l Genomic mating programs w Selection of favorable minor alleles w Reduction of genomic inbreeding l Genomic evaluations based on more SNPs (60K) l Adding SNPs for causative genetic variants

Wiggans, 2013China Emerging Markets Program Seminar What’s already planned (continued) l BARD project (Volcani Center, Israel) w A priori granddaughter design (APGD) w Identification of causative variants for economically important traits l International collaboration on sequencing w United States, United Kingdom, Italy, Canada w Bulls selected using APGD

Wiggans, 2013China Emerging Markets Program Seminar Parentage validation and discovery l Parent-progeny conflicts detected w Animal checked against all other genotypes w Reported to breeds and requesters w Correct sire usually detected l Maternal grandsire (MGS) checking w SNP at a time checking w Haplotype checking more accurate l Breeds moving to accept SNPs in place of microsatellites

Wiggans, 2013China Emerging Markets Program Seminar MGS detection — HAP method l Based on common haplotypes l After imputation of all loci, determine maternal contribution by removing paternal haplotype l Count maternal haplotypes in common with MGS l Remove haplotypes from MGS and check remaining against maternal great-grandsire (MGGS)

Wiggans, 2013China Emerging Markets Program Seminar MGS detection — SNP method l Based on SNP conflicts l Check if animal and MGS have opposite homozygotes (duo test) l If sire is genotyped, some heterozygous SNPs can be checked (trio test)

Wiggans, 2013China Emerging Markets Program Seminar MGS detection by breed Ancestors confirmed (%) SNP methodHAP method BreedMGS MGGS Brown Swiss Holstein Jersey9195

Wiggans, 2013China Emerging Markets Program Seminar 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

Wiggans, 2013China Emerging Markets Program Seminar Haplotypes affecting fertility *Causative mutation known Name BTA chromo- some Location* (Mbp) Carrier frequency (%)Earliest known ancestor HH1563.2*4.5Pawnee Farm Arlinda Chief HH2194.9– Willowholme Mark Anthony HH3895.4*4.7 Glendell Arlinda Chief, Gray View Skyliner HH411.3*0.7Besne Buck HH5992.4– Thornlea Texal Supreme JH *23.4Observer Chocolate Soldier BH1742.8– West Lawn Stretch Improver BH – Rancho Rustic My Design AH – Selwood Betty’s Commander

Wiggans, 2013China Emerging Markets Program Seminar Haplotype tracking of known recessives *Causative mutation known RecessiveHaplotype BTA chromo- some Tested animals (no.) Concord- ance (%) New carriers (no.) BLADHHB 1*11, CVMHHC 3*13,226—2,716 DUMPSHHD 1*3, Mule footHHM15* PolledHHP1345—2,050 Red coat colorHHR18*4,137—5,927 SDMBHD11* SMABHM24* WeaverBHW

Wiggans, 2013China Emerging Markets Program Seminar Progression of chips Official 3K evaluations Dec Unofficial 3K evaluations Sep Bovine3K BeadChip (3K) Jul BovineHD BeadChip (777K) Jan Official 50K Brown Swiss evaluations Aug Official 50K Holstein & Jersey evaluations Jan Unofficial 50K evaluations Apr BovineSNP50 BeadChip (50K) Jan Official 12K evaluations Oct Zoetis LD BeadChip (12K) Sep GGP v2 BeadChip (19K) May Official 19K evaluations May Official 77K evaluations Jan GGP HD BeadChip (77K) Dec Official 8K evaluations Mar GeneSeek Genomic Profiler (GGP) BeadChip (8K) Feb Official 7K & 648K evaluations Dec BovineLD BeadChip (7K) Sep Official 777K evaluations Aug Affymetrix BOS 1 Plate Array (648K) Jan

Wiggans, 2013China Emerging Markets Program Seminar International dairy breeding l Genotype alliances w North America (US, Canada, UK, Italy) w Ireland, New Zealand w Netherlands, Australia w Eurogenomics (Denmark/Sweden/Finland, France, Germany, Netherlands/Belgium, Spain, Poland) l Interbull genomic multitrait across-country evaluation (GMACE)

Wiggans, 2013China Emerging Markets Program Seminar GMACE reference populations (August) CountryAnimals (no.) Australia5,314 Denmark/Finland/Sweden23,961 France24,313 Germany25,624 Italy21,041 Netherlands23,047 Poland3,174 Switzerland (Red Holstein)4,194

Wiggans, 2013China Emerging Markets Program Seminar Impact on breeders l Haplotype and gene tests in selection and mating programs l Trend towards a small number of elite breeders that are investing heavily in genomics l About 30% of young males genotyped directly by breeders since April 2013 l Prices for top genomic heifers can be very high (e.g., $265,000 )

Wiggans, 2013China Emerging Markets Program Seminar Impact on dairy producers l General w Reduced generation interval w Increased rate of genetic gain w More inbreeding/homozygosity?

Wiggans, 2013China Emerging Markets Program Seminar Impact on dairy producers (continued) l Sires w Higher average genetic merit of available bulls w More rapid increase in genetic merit for all traits w Larger choice of bulls in terms of traits and semen price w Greater use of young bulls

Wiggans, 2013China Emerging Markets Program Seminar Conclusions l Genomic evaluation has dramatically changed dairy cattle breeding l Rate of gain is increasing primarily because of a large reduction in generation interval 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

Wiggans, 2013China Emerging Markets Program Seminar U.S. genomic evaluation team