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Genomic Prediction Results

This document summarizes the breakthroughs in genomic prediction and genetic similarity in cattle, focusing on the genomic insights gained from the bovine genome sequenced in 2004. It details the significance of using the Illumina Bovine SNP50TM Chip with 58,000 genetic markers, specifically highlighting reliability statistics and the effects of using major loci versus numerous loci in trait predictions. The results show improvements in reliability for both older and younger bulls, indicating that genomic predictions are markedly superior to traditional parent averages across various traits.

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Genomic Prediction Results

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  1. Genomic Prediction Results

  2. Measuring Genetic Similarity • Cattle genome sequenced in 2004 • 30 chromosome pairs (including X,Y) • 3 billion letters from each parent • Illumina Bovine SNP50TM Chip • 58,000 genetic markers in 2007 • 39,835 used in genomic predictions • Cost about $200 per animal

  3. 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

  4. 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

  5. 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

  6. 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 1994-1996 with >75% reliability of Net Merit • Plus ancestor bulls born 1952-1993 • 659 later bulls used to test predictions • Born 2001 with >75% reliability of Net Merit

  7. Proposed Genotyping (Apr 2007) Data cutoff

  8. Current Genotyped Animals (n=6005)

  9. Acknowledgments • Funding: • NRI grants 2006-35205-16888, 16701 • CDDR Contributors (NAAB, Semex) • Genotyping and DNA extraction: • BFGL, U. Missouri, U. Alberta, GeneSeek, GIFV, and Illumina • Computing from AIPL staff

  10. 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

  11. Nonlinear and Linear Regressions for marker allele effects

  12. 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

  13. Marker P-Values for Net Merit

  14. Marker Effects for Net Merit

  15. Marker Effects for Milk

  16. Marker Effects for Final Score

  17. Reliabilities and R-square values comparing traditional to genomic predictions

  18. Reliabilities and R-square values comparing traditional to genomic predictions

  19. 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

  20. Clones and Identical Twins21HO2121, 21HO2125, 21HO2100, CAN6139300, CAN6139303

  21. X, Y, Pseudo-autosomal SNPs 35 SNPs 35 SNPs 0 SNPs 487 SNPs

  22. 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 σG, smaller than expected • Correlation with sire’s daughter vs. son PTA difference was significant (P<.0001), regression close to 1.0

  23. SNP Density Comparison2130 older and 261 younger bulls

  24. Genetic Evaluation Advancesand increases in genetic progress

  25. 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

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