Genomic Prediction Results

Methods to Include Foreign Information in National Evaluations

2007Paul VanRaden, Mel Tooker*, and Jan WrightAnimal Improvement Programs Lab, Beltsville, MDPaul.VanRaden@ars.usda.govFASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker20121Animal model (1989 to present)Single-trait milk, fat, and proteinOthers (PL, SCS, DPR) added laterAll-breed animal model 2007Multiple-step genomic model - 2009One step evaluation (future)All breeds, traits, and genotypes might be evaluated together

IntroductionFASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker20122Include foreign phenotypes using MACE EBVs of bullsSingle (ST) or multi-trait (MT) national evaluations7-trait model: yield, SCS, daughter pregnancy rate (DPR), MT and ST productive life (PL)14-trait model with conformationOne Step Evaluation TestsFASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012Foreign portion of deregressed MACE EBV added as daughtersAdapted from Bonaiti, Boichard 1995Subtract domestic portion of MACEAdd 1 observation weighted by EDC instead of adding n daughtersFor multi-trait, multiply by D.5 T-1 D.5Mean included to adjust foreign data to genetic base of solutionsAdding Foreign InformationFASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012To include foreign data, the bulls deregressed proof (DRP) was obtained fromthe MACE EBV as: DRP = PA + (EBV - PA)/REL, where PA is theparent average from MACE. For bulls with both domestic and foreigndaughters, domestic EBV was used instead of PA to compute DRP, anddomestic daughter equivalents (DE) were subtracted from the total.Remaining DE were added to diagonals of the mixed model equationsand were used to compute REL. For multi-trait models, diagonal matrix Dcontained the DE for each trait of a bull. The vector of DRP was premultipliedby D.5T1D.5, where T is the genetic covariance matrix amongtraits, and D.5T1D.5 was added to the mixed model equations.

4Foreign deregressed PTAs for 118,741 bulls (foreign dams not yet included)Deregession: pure foreign or mixedPAIB + ( PTAIB PAIB ) / RELIB-PAPTAdom + ( PTAIB PTAdom ) / RELIB-dom Data (Yield and Health)FASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012Deregress away from PA for foreign bulls;Deregress away from domestic PTA for mixed bulls;RELIB is the difference between mace and domestic.DEIB = DEmace - DEdom;RELIB = DEIB / (DEIB + 1);

5One step model includes:72 million lactation phenotypes50 million animals in pedigree29 million permanent environment7 million herd mgmt groups11 million herd by sire interactions Traits: M, F, P, SCS, PL, DPRGenotypes not yet included

Data (Yield and Health)FASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012Official animal modelData edits and adjustmentsSeparate weight for each observationAll breeds and crossbreds includedInbreeding and heterosis correctionHerd by sire interactionConvert PTAs to within-breed baseHeritability of yield decreasedMimic effect of cow adjustments Previous Features RetainedFASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012Model options now include:Multi-trait modelsMultiple class and regress variablesSuppress some factors / each traitRandom regressionsForeign dataParallel processingGenomic information (Pauls talk)Renumber factors in same program

New Features AddedFASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012Renumber factors in same program8Correlations within breedTraitTrad, STTrad, MTST, MTMilk.986.986.999Fat.985.985.999Protein.986.988.999SCS.998.994.995PL.975.945.972DPR.987.958.970Traditional, ST, and MT EvaluationDomestic bulls ( 10 USA daughters)FASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012When using 95% rel bulls, MT PL and DPR increase correlations to .981 for DPR and .968 for MT PL9Test bulls with no USA daughtersCorr (National EBV, MACE EBV)0.77 before adding foreign data~ 0.99 after adding foreign dataInterbull uses only ST longevityUSA computes both ST and MT in the same one-step program with genetic correlations set = 0 for STForeign Yield, Health Data: ResultsFASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012ST PL is run through the one step multi-trait system as a kludge, otherwise have to run separate program for ST, just for Interbull purposes.10Correlations with MACETraitTradST + MACEMT + MACEMilk.818.993.999Fat.740.991.998Protein.835.994.999SCS.667.988.989PL.568.970.890DPR.612.913.835MACE Data in National EvaluationForeign proven bulls (no USA daughters)FASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012PL correlation with ST+MACE based on using ST PL from the Interbull 037 file.These data are also did not totally converge, DPR for example .0006 11Correlations with officialTraitSTST + MACEMTMT + MACEMilk.986.990.987.990Fat.986.989.986.989Protein.987.989.988.990SCS.998.997.995.991PL.978.979.950.940DPR.989.988.963.951Adding April 2012 MACE Data Domestic bulls (50 USA daughters) FASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012ST and MT correlations with Traditional. ST+ MACE and MT+MACE with official. (note: official includes genomics).12CPU for all-breed model (7 traits)ST: 4 min / round with 7 processors and ~1000 roundsMT: 15 min / round and ~1000 rounds~200 rounds for updates using priorsLittle extra cost to include foreignMemory requiredST or MT: 32 Gbytes (256 available)Computation RequiredFASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012716,645 cows, most with 14 traitsST required 1.75 hours / 1000 rndsMT required 5 hours / 1000 rndsForeign data not added yetConformation traits currently use a multi-trait system.Jersey Conformation EvaluationFASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012Jersey Conformation ResultsCorrelations for 1363 bulls with 50 daughters (April 2012)TraitST, TradMT, TradSTA0.9870.989STR0.9730.984DFM0.9270.985FTA0.9700.983RLS0.9680.984RUA0.9960.996TRL0.9690.990FASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012Jersey Conformation ResultsCorrelations for 1363 bulls with 50 daughters (April 2012)TraitST, TradMT, TradFUA0.9560.981RUH0.9270.967RUW0.9910.978UDP0.9950.977UCL0.9410.965FTP0.9400.979TLG0.9930.960FASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012ConclusionsForeign data can add to national evaluationsIn one step model instead of post-processHigh correlations of national with MACEMulti-trait all-breed model developedReplace software used since 1989Many new features addedCorrelations ~.99 with traditional AMTested with 7 yield and health traitsAlso tested with 14 JE conformation traits

FASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012Future ResearchAdding genomicsAdding foreign damsAdding supporting variables Improving reliability calculationsIntegrating one-step output for routine delivery

FASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012George Wiggans provided advice on algorithms and modeling

AcknowledgmentsFASS joint annual meeting, Phoenix, AZ, July 2012 (#)Mel Tooker2012