2007 Paul VanRaden, Curt Van Tassell, George Wiggans, Tad Sonstegard, and Jeff O’Connell Animal Improvement Programs Laboratory and Bovine Functional Genomics.

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Presentation transcript:

2007 Paul VanRaden, Curt Van Tassell, George Wiggans, Tad Sonstegard, and Jeff O’Connell Animal Improvement Programs Laboratory and Bovine Functional Genomics Laboratory, USDA Agricultural Research Service, Beltsville, MD, USA 2008 Genomic Prediction Results

NAAB DSEC April 2008 (2) Paul VanRaden 2008 Measuring Genetic Similarity  Cattle genome sequenced in chromosome pairs (including X,Y) 3 billion letters from each parent  Illumina Bovine SNP50 TM Chip 58,000 genetic markers in ,835 used in genomic predictions Cost about $200 per animal

NAAB DSEC April 2008 (3) Paul VanRaden 2008 How Related are Relatives?  Example: Full sibs are expected to share 50% of their DNA on average, with SD of 5% may actually share 40% to 60% of their DNA because each inherits a different mixture of chromosome segments from the two parents. SD 3.5% reported previously was low

NAAB DSEC April 2008 (4) Paul VanRaden 2008 Simulated Results (Apr 2007)  1777 older and 500 younger bulls  10,000 SNPs and 100 QTLs  Reliability vs parent average REL 58% vs 36% for young bulls Higher REL if major loci and Bayesian methods used, lower if many loci (>100) affect trait

NAAB DSEC April 2008 (5) Paul VanRaden 2008 Simulated Results (2008)  8271 older and 1984 younger bulls  40,000 SNPs and 500 QTLs  Provided timing, memory test  Reliability vs parent average REL 79% vs 37% expected for young bulls 76% vs 37% observed in simulation

NAAB DSEC April 2008 (6) Paul VanRaden 2008 Genotyped Bulls (Feb 2007) from Cooperative Dairy DNA Repository  DNA of bulls stored in Beltsville (BFGL)  2560 proven bulls used to computed predictions Bulls born with >75% reliability of Net Merit Plus ancestor bulls born  659 later bulls used to test predictions Born 2001 with >75% reliability of Net Merit

NAAB DSEC April 2008 (7) Paul VanRaden 2008 Proposed Genotyping (Apr 2007) Data cutoff

NAAB DSEC April 2008 (8) Paul VanRaden 2008 Current Genotyped Animals (n=6005)

NAAB DSEC April 2008 (9) Paul VanRaden 2008 Acknowledgments  Funding: NRI grants , CDDR Contributors (NAAB, Semex)  Genotyping and DNA extraction: BFGL, U. Missouri, U. Alberta, GeneSeek, GIFV, and Illumina  Computing from AIPL staff

NAAB DSEC April 2008 (10) Paul VanRaden 2008 Genomic Methods  Direct genomic evaluation Inversion for linear prediction, REL Iteration for nonlinear prediction  Combined genomic evaluation Traditional PA or PTA, subset PA or PTA, and direct genomic combined by REL in 3 x 3 selection index Nonlinear genomic predictions used

NAAB DSEC April 2008 (11) Paul VanRaden 2008 Nonlinear and Linear Regressions for marker allele effects

NAAB DSEC April 2008 (12) Paul VanRaden 2008 Actual Results (Feb 2007 data)  August 2003 PTAs for 2650 older bulls to predict January 2008 daughter deviations for 569 younger bulls (total = 3119 bulls)  Results computed for 27 traits: 5 yield, 5 health, 16 conformation, and Net Merit  Nonlinear A used, B didn’t work

NAAB DSEC April 2008 (13) Paul VanRaden 2008 Marker P-Values for Net Merit

NAAB DSEC April 2008 (14) Paul VanRaden 2008 Marker Effects for Net Merit

NAAB DSEC April 2008 (15) Paul VanRaden 2008 Marker Effects for Milk

NAAB DSEC April 2008 (16) Paul VanRaden 2008 Marker Effects for Final Score

NAAB DSEC April 2008 (17) Paul VanRaden 2008 Reliabilities and R-square values comparing traditional to genomic predictions Squared corr (x100) Reliability TraditionalGenomic Trait PAGenomicPARealizedGain Net Merit Milk Fat Protein Fat % Protein %

NAAB DSEC April 2008 (18) Paul VanRaden 2008 Reliabilities and R-square values comparing traditional to genomic predictions Squared corr (x100) Reliability TraditionalGenomic Trait PAGenomicPARealizedGain Prod Life SCS DPR SCE DCE Final Score

NAAB DSEC April 2008 (19) Paul VanRaden 2008 Expected vs Observed Reliability  Reliability for predictee bulls Average across traits: 57% expected vs. 48% observed vs. 30% PA Observed range 72% (fat pct) to 36% PTA regressions.8 to.9 of expected  Redo 2003 cutoff using April data  Develop REL and PTA adjustments

NAAB DSEC April 2008 (20) Paul VanRaden 2008 Clones and Identical Twins 21HO2121, 21HO2125, 21HO2100, CAN , CAN TraditionalGenomic BullDtrsNM$RELNM$REL Triton - ETN Triad - ETN Trey - ETN Loyalty Lauriet

NAAB DSEC April 2008 (21) Paul VanRaden 2008 X, Y, Pseudo-autosomal SNPs 487 SNPs 35 SNPs 0 SNPs 35 SNPs

NAAB DSEC April 2008 (22) 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

NAAB DSEC April 2008 (23) Paul VanRaden 2008 SNP Density Comparison 2130 older and 261 younger bulls REL of PA Genomic REL Trait10K20K40K Net Merit Milk Fat Protein Productive Life SCS Dtr Preg Rate

NAAB DSEC April 2008 (24) Paul VanRaden 2008 Genetic Evaluation Advances and increases in genetic progress YearAdvance% Gain 1935Daughter-dam comparison Herdmate comparison Modified cont. comparison5 1977Protein evaluated4 1973Records in progress Animal model4 1994Net merit, PL, and SCS Genomic selection>40

NAAB DSEC April 2008 (25) Paul VanRaden 2008 Conclusions  Genomic predictions significantly better than parent average (P <.0001) for all 26 traits tested  Gains in reliability from 2650 bulls (Feb data) equivalent on average to 9 daughters with records  April data included 5285 proven bulls, more analysis needed