Dairy Cattle Genomic Evaluation Program Update G R

Dairy Cattle Genomic Evaluation Program Update G. R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD george. wiggans@ars. usda. gov 2011 National Breeders Roundtable 1 ()

National Dairy Genetic Evaluation Program l Collaboration between ARS and Dairy industry l Dairy Industry partners w DHI Milk recording w Breed Associations w Artificial Breeding organizations w Other farm service organizations 2011 National Breeders Roundtable 2 () Wiggans

Expanding Industry Role l l l Collaboration of: w ARS - Animal Improvement Programs Lab w Council on Dairy Cattle Breeding Council – Plan to provide staff for data collection, database management, calculation and distribution of evaluations AIPL – Focus on research and Development 2011 National Breeders Roundtable 3 () Wiggans

History of genomic evaluations l Dec. 2007 Bovine. SNP 50 Bead. Chip available l Apr. 2008 First unofficial evaluation released l Jan. 2009 Genomic evaluations official for Holstein and Jersey l Aug. 2009 Official for Brown Swiss l l Sept. 2010 Unofficial evaluations from 3 K chip released Dec. 2010 3 K genomic evaluations official 2011 National Breeders Roundtable 4 () Wiggans

Genomic Evaluations l Genotype calves l Calculate evaluation l Select intensively l Reduces cost of finding top bulls l Increases rate of genetic progress 2011 National Breeders Roundtable 5 () Wiggans

Data & evaluation flow AI organizations, breed associations s ple no m ina tio ns lua tio ns eva sam Dairy producers USDA samples sam ple s Animal Improvement Programs Laboratory, e typ s o n ge DNA laboratories 2011 National Breeders Roundtable 6 () Wiggans

Changes in last 12 Months l l New Chips w Low density 3 K, 2900 SNP w High Density −Illumina 777, 062 SNP −Affymetrics 648, 855 SNP Collaboration with Italy and Great Britain Adjustment of cow evaluations to improve compatibility with those of bulls Improved accuracy of imputation 2011 National Breeders Roundtable 7 () Wiggans

Chip Types HD 50 K 3 K HD - $200 $100 50 K - $100 3 K - $45 $200 2011 National Breeders Roundtable 8 () Wiggans

Cow adjustment – background l l Genotyped cows adjusted starting April 2010 Required to prevent distortions in SNP effect estimates by making genotyped cows and bulls comparable Made PTA of genotyped cows not comparable (lower) than those of non-genotyped cows Industry requested adjustment on nongenotyped cows for April 2011 evaluation. 2011 National Breeders Roundtable 9 () Wiggans

Cow adjustment l l l Make evaluations of non-genotyped cow more like those of genotyped cows Reduce variation to that of bulls Subtract 40% of within year parent average deviation Additional adjustment for genotyped cows Discontinue using foreign cow evaluations in predictor population 2011 National Breeders Roundtable 1 ( 0) Wiggans

Imputation l l Based on splitting the genotype into individual chromosomes (maternal & paternal contributions) Missing SNP approximated by tracking inheritance from ancestors and descendents Imputed Dams increase predictor population 3 K & 50 K genotypes merged by imputing SNP not on 3 K 2011 National Breeders Roundtable 1 ( 1) Wiggans

Imputation improvements l l Use multiple segment lengths to detect common haplotypes Long segments increase chance that matching haplotype came from a common ancestor Shorter segments improve fill in 2 -3 percentage points increase in accuracy achieved 2011 National Breeders Roundtable 1 ( 2) Wiggans

High density (HD) genotypes l Illumina Bovine HD Bead. Chip available 777, 962 SNP w Collaborations with GBR, ITA, & CAN to provide genotypes w Over 400 genotypes from research projects in database w 2011 National Breeders Roundtable 1 ( 3) Wiggans

High density (HD) genotypes l Affymetrics HD w 648, 855 SNP w Research project to determine usefulness w Optimized for genetic coverage w Over 100, 00 SNP in common with. Illumina 2011 National Breeders Roundtable 1 ( 4) Wiggans

Use of HD l l Some increase in accuracy from better tracking of QTL Potential for across breed evaluations Requires few new HD genotypes once adequate base for imputation developed Imputation improvements were particularly beneficial in imputing HD 2011 National Breeders Roundtable 1 ( 5) Wiggans

3 K chip l 2900 SNP mostly from SNP 50 chip w 14 Y Chr SNP included for sex validation w Evenly spaced across 30 Chr l Developed to reduce cost of genotyping l 2614 SNP used after removing poor performers l Rapid adoption, 4, 731 animal genotypes submitted for May genomic evaluation 2011 National Breeders Roundtable 1 ( 6) Wiggans

Genotype processing improvements l Labs submit genotypes for automated checking for: Nomination issues w Genotype calling issues w Sample ID errors w l Reports of conflicts enhanced Excel compatible format w Additional ID information w l Online pedigree correction 2011 National Breeders Roundtable 1 ( 7) Wiggans

Parentage validation and discovery l Parent-progeny conflicts detected Reported to breeds and requesters w Correct sire usually detected w l Maternal Grandsire checking SNP at a time checking w Haplotype checking more accurate w l Breeds moving to accept SNP in place of microsatellites 2011 National Breeders Roundtable 1 ( 8) Wiggans

Genotyped Holsteins Date 04 -10 08 -10 09 -10 10 -10 11 -10 12 -10 01 -11 02 -11 03 -11 04 -11 05 -11 Bulls* 9, 770 10, 430 10, 611 10, 616 10, 619 11, 293 11, 194 11, 196 11, 713 12, 152 12, 429 Cows* 7, 415 9, 372 9, 453 9, 787 10, 175 12, 825 13, 582 13, 935 14, 382 11, 224 11, 834 Young animals** Bulls Heifers 16, 007 8, 630 18, 652 11, 021 19, 389 13, 333 20, 184 15, 288 20, 836 17, 095 21, 161 18, 336 22, 567 22, 999 23, 330 26, 270 24, 505 29, 929 25, 202 36, 545 26, 139 40, 996 All animals 41, 822 49, 475 52, 786 55, 877 58, 727 63, 615 70, 342 74, 731 80, 529 85, 123 91, 398 *Traditional evaluation **No traditional evaluation 2011 National Breeders Roundtable 1 ( 9) Wiggans

Number of Genotyped Animals May Genotypes – Holstein and Jersey 3500 3000 2500 2000 1500 1000 500 0 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 Birth Year Holstein 2011 National Breeders Roundtable 2 ( 0) Jersey Wiggans 2011

Number of Genotyped Holsteins May Genotypes − Holstein 4500 4000 3500 3000 2500 2000 1500 1000 500 0 3 K 50 K Chip Type Males 2011 National Breeders Roundtable 2 ( 1) Females Wiggans

Number of Genotyped Jerseys May Genotypes − Jersey 1000 900 800 700 600 500 400 300 200 100 0 3 K 50 K Chip Type Males 2011 National Breeders Roundtable 2 ( 2) Females Wiggans

Number of Bulls Holstein Bulls 10000 9000 8000 7000 6000 5000 4000 3000 2000 1000 0 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 Birth Year Total 10 Herds 2011 National Breeders Roundtable 2 ( 3) Genotyped Both Wiggans 2011

Determination of Reliability l Sum of genomic relationships with the predictor animals weighted by reliability l Call rate l Expected imputation error rate l Reliability of parent average w Larger impact if dam not genotyped 2011 National Breeders Roundtable 2 ( 4) Wiggans

Reliabilities for young Holsteins* Number of animals 9000 50 K genotypes 3 K genotypes 8000 7000 6000 5000 4000 3000 2000 1000 0 40 45 50 55 60 65 70 75 Reliability for PTA protein (%) *Animals with no traditional PTA in April 2011 National Breeders Roundtable 2 ( 5) Wiggans 80

Use of genomic evaluations l Determine which young bulls to bring into AI service l Use to select mating sires l Pick bull dams l Market semen from 2 -year-old bulls 2011 National Breeders Roundtable 2 ( 6) Wiggans

Use of 3 K genomic evaluations l Sort heifers for breeding w Flush w Sexed semen w Beef bull l Confirm parentage to avoid inbreeding l Predict inbreeding depression better l Precision mating considering genomics(future) 2011 National Breeders Roundtable 2 ( 7) Wiggans

Future 2011 National Breeders Roundtable 2 ( 8) Wiggans

Increase in accuracy l l Genotyped bulls get traditional evaluation when 5 years old Possible genotyping of 10, 000 bulls with semen in CDDR l Collaboration with more countries l Use of more SNP from HD chips l Full sequencing 2011 National Breeders Roundtable 2 ( 9) Wiggans

Application to more traits l l l Animal’s genotype is good for all traits Traditional evaluations required for accurate estimates of SNP effects Traditional evaluations not currently available for heat tolerance or feed efficiency Research populations could provide data for traits that are expensive to measure Will resulting evaluations work in target population? 2011 National Breeders Roundtable 3 ( 0) Wiggans

Summary l l Extraordinarily rapid implementation of genomic evaluations Young-bull acquisition and marketing now based on genomic evaluations Genotyping of many females because of 3 K chip Application of HD chips being developed 2011 National Breeders Roundtable 3 ( 1) Wiggans

2011 National Breeders Roundtable 3 ( 2) Wiggans