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2007 Paul VanRaden 1, Curt Van Tassell 2, George Wiggans 1, Tad Sonstegard 2, Jeff O’Connell 1, Bob Schnabel 3, Jerry Taylor 3, and Flavio Schenkel 4,

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Presentation on theme: "2007 Paul VanRaden 1, Curt Van Tassell 2, George Wiggans 1, Tad Sonstegard 2, Jeff O’Connell 1, Bob Schnabel 3, Jerry Taylor 3, and Flavio Schenkel 4,"— Presentation transcript:

1 2007 Paul VanRaden 1, Curt Van Tassell 2, George Wiggans 1, Tad Sonstegard 2, Jeff O’Connell 1, Bob Schnabel 3, Jerry Taylor 3, and Flavio Schenkel 4, 1 Animal Improvement Programs Lab and 2 Bovine Functional Genomics Lab, USDA Agricultural Research Service, Beltsville, MD, USA, 3 U. Missouri, Columbia, 4 U. Guelph, ON, Canada Paul.VanRaden@ars.usda.gov 2008 Reliability of Genomic Predictions for North American Dairy Bulls

2 FASS annual meeting, July 2008 (2) Paul VanRaden 2008 Sequencing and Genotyping  Cattle genome sequenced in 2004 30 chromosome pairs (including X,Y) 3 billion letters from each parent  Illumina BovineSNP50 BeadChip 58,000 genetic markers in 2007 38,416 used in genomic predictions Current cost < $250 per animal

3 FASS annual meeting, July 2008 (3) Paul VanRaden 2008 Experimental Design  Compute genomic evaluations and parent averages from 2003 data 3576 older Holstein bulls born 1952-1998  Compare ability to predict daughter deviations in 2008 data 1759 younger bulls born 1999-2002  Test results for 27 traits: 5 yield, 5 health, 16 conformation, and Net Merit

4 FASS annual meeting, July 2008 (4) Paul VanRaden 2008 Genotyped Animals (n=6005) As of April 2008

5 FASS annual meeting, July 2008 (5) Paul VanRaden 2008 Genomic Methods  Direct genomic evaluation Inversion for linear prediction, REL Iteration for nonlinear prediction  Combined genomic evaluation 3 x 3 selection index combining direct genomic PTA, traditional PA or PTA, and subset PA or PTA by REL

6 FASS annual meeting, July 2008 (6) Paul VanRaden 2008 Marker Effects for Net Merit

7 FASS annual meeting, July 2008 (7) Paul VanRaden 2008 Significance Tests for Net Merit

8 FASS annual meeting, July 2008 (8) Paul VanRaden 2008 Major Gene on Chromosome 18 Net Merit, Productive Life, Calving Ease, Stature, Strength, Rump Width

9 FASS annual meeting, July 2008 (9) Paul VanRaden 2008 Marker Effects for Milk

10 FASS annual meeting, July 2008 (10) Paul VanRaden 2008 Marker Effects for Final Score

11 FASS annual meeting, July 2008 (11) Paul VanRaden 2008 Linear and Nonlinear Predictions  Linear model Infinitesimal alleles model in which all loci have non-zero effects  Nonlinear models Model A: infinitesimal alleles with a heavy-tailed prior Model B: finite locus model with normally-distributed marker effects Model AB: finite locus model with a heavy-tailed prior

12 FASS annual meeting, July 2008 (12) Paul VanRaden 2008 Nonlinear and Linear Regressions for marker allele effects

13 FASS annual meeting, July 2008 (13) Paul VanRaden 2008 R 2 for linear and nonlinear predictions

14 FASS annual meeting, July 2008 (14) Paul VanRaden 2008 R 2 vs. Reliability  Adjust the observed genomic R 2 Daughter deviations contain error – Divide by REL of 2008 deviations Parents are selected – Add difference of PA R 2 from expected  Adjust theoretical genomic REL Genotypes contain a few errors QTLs are located between SNPs

15 FASS annual meeting, July 2008 (15) Paul VanRaden 2008 R 2 and Reliabilities for Traditional and Genomic Predictions Squared corr (x100) Reliability TraditionalGenomic Trait PAGenomicPARealizedGain Net Merit 1128305323 Milk 2849355823 Fat 1544356833 Protein 2747355722 Fat % 2563357843 Protein % 2858356934

16 FASS annual meeting, July 2008 (16) Paul VanRaden 2008 R 2 and Reliabilities for Traditional and Genomic Predictions Squared corr (x100) Reliability TraditionalGenomic Trait PAGenomicPARealizedGain Longevity 1727 4518 SCS 2338305121 Fertility 2029254116 S.calf ease 272928313 D.calf ease 1422254015 Final score 2336244218

17 FASS annual meeting, July 2008 (17) Paul VanRaden 2008 Reliability Gains for Proven Bulls  Bulls included in test had: >10 daughters in August 2003 >10% increase in reliability by 2008 Numbers of bulls in test ranged from 104 to 735 across traits Predicted the change in evaluation  Significant increase in R 2 (P <.001) for 26 of 27 traits

18 FASS annual meeting, July 2008 (18) Paul VanRaden 2008 Net Merit by Chromosome for O Man Top bull for Net Merit

19 FASS annual meeting, July 2008 (19) Paul VanRaden 2008 SNPs on X Chromosome  Each animal has two evaluations: Expected genetic merit of daughters Expected genetic merit of sons Difference is sum of effects on X SD =.1 σ G, smaller than expected  Correlation with sire’s daughter vs. son PTA difference was significant (P<.0001), regression close to 1.0

20 FASS annual meeting, July 2008 (20) Paul VanRaden 2008 X, Y, Pseudo-autosomal SNPs 487 SNPs 35 SNPs 0 SNPs 35 SNPs

21 FASS annual meeting, July 2008 (21) Paul VanRaden 2008 Clones and Identical Twins 21HO2121, 21HO2125, 21HO2100, CAN6139300, CAN6139303 TraditionalGenomic BullDtrsNM$RELNM$REL Triton - ETN98-36382-37191 Triad - ETN26-30668-37091 Trey - ETN108-39583-37191 Loyalty108-18578-19687 Lauriet83-20376-19687

22 FASS annual meeting, July 2008 (22) Paul VanRaden 2008 Value of Genotyping More SNP 9,604 (10K), 19,208 (20K), and 38,416 (40K) SNP REL of PA Genomic REL Trait10K20K40K Net Merit $30485053 Milk yield35535658 Fat yield35646668 Protein yield35545657 Productive Life27384145 SCS (mastitis)30454751 Dtr Preg Rate25373941

23 FASS annual meeting, July 2008 (23) Paul VanRaden 2008 Value of Genotyping More Bulls BullsR 2 for Net Merit PredictorPredicteePAGenomicGain 11512518124 21302618179 260951082113 35761759112817

24 FASS annual meeting, July 2008 (24) Paul VanRaden 2008 Simulated Results World Holstein Population  15,197 older and 5,987 younger bulls in Interbull file  40,000 SNPs and 10,000 QTLs  Provided timing, memory test  Reliability vs parent average REL REL = corr 2 (EBV, true BV) 80% vs 34% expected for young bulls 72% vs 30% observed in simulation

25 FASS annual meeting, July 2008 (25) Paul VanRaden 2008 Brown Swiss Results  Nearly all proven bulls genotyped Data from 225 bulls born before 1999 Predict 118 bulls born during or after 1999  Gains in young bull reliability Expected to be 1% to 3% Actual gains were about 2% for yield Little or no gain for other traits  Cooperation with Europe is needed

26 FASS annual meeting, July 2008 (26) Paul VanRaden 2008 Jersey Genotypes  Same experimental design DNA available for 766 bulls Total of 594 genotyped as of June Results not available yet  Gains in reliability expected to be proportional to number of bulls genotyped

27 FASS annual meeting, July 2008 (27) Paul VanRaden 2008 Expected vs Observed Reliability Holsteins  Reliability for predictee bulls Traditional PA: 27% average across traits Genomic: 63% expected vs. 50% observed Observed range 78% (fat pct) to 31% (SCE) PTA regressions.8 to.9 of expected  Multiply genomic daughter equivalents by.7 to make expected closer to observed For example, 16 *.7 = 11 Include polygenic effect, less than 5%

28 FASS annual meeting, July 2008 (28) Paul VanRaden 2008 Genetic Progress Holsteins  Assume 60% REL for net merit Sires mostly 2 instead of 6 years old Dams of sons mostly heifers with 60% REL instead of cows with phenotype and genotype (66% REL)  Progress could increase by >50% 0.37 vs. 0.23 genetic SD per year Reduce generation interval more than accuracy

29 FASS annual meeting, July 2008 (29) Paul VanRaden 2008 Genetic Evaluation Advances and increases in genetic progress YearAdvance% Gain 1935Daughter-dam comparison100 1962Herdmate comparison50 1973Records in progress10 1974Modified cont. comparison5 1977Protein evaluated4 1989Animal model4 1994Net merit, PL, and SCS50 2008Genomic selection>50

30 FASS annual meeting, July 2008 (30) Paul VanRaden 2008 How Related are Relatives? Correction  Example: Full sibs Share 50% ± 5% of their DNA on average (in cattle) SD 3.5% reported previously was low For any diploid species, general formula is 50% ± 50% / [2(C + L)].5, where C is number of chromosomes and L is genome length in Morgans

31 FASS annual meeting, July 2008 (31) Paul VanRaden 2008 Conclusions  Genomic predictions significantly better than parent average (P <.0001) for all 26 traits tested  Gains in reliability equivalent on average to 11 daughters with records Analysis used 3576 historical bulls April data included 5285 proven bulls  High REL requires many genotypes

32 FASS annual meeting, July 2008 (32) Paul VanRaden 2008 Acknowledgments  Genotyping and DNA extraction: BFGL, U. Missouri, U. Alberta, GeneSeek, GIFV, and Illumina  Computing: AIPL staff (Mel Tooker, Leigh Walton, etc.)  Funding: National Research Initiative grants – 2006-35205-16888, 2006-35205-16701 Agriculture Research Service Contributors to Cooperative Dairy DNA Repository (CDDR)

33 FASS annual meeting, July 2008 (33) Paul VanRaden 2008 CDDR Contributors  National Association of Animal Breeders (NAAB, Columbia, MO) ABS Global (DeForest, WI) Accelerated Genetics (Baraboo, WI) Alta (Balzac, AB) Genex (Shawano, WI) New Generation Genetics (Fort Atkinson, WI) Select Sires (Plain City, OH) Semex Alliance (Guelph, ON) Taurus-Service (Mehoopany, PA)

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