Reliability of Genomic Predictions for North American Dairy Bulls

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Reliability of Genomic Predictions for North
American Dairy Bulls
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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 lt 250 per animal

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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

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Genotyped Animals (n6005)As of April 2008
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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

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Marker Effects for Net Merit
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Significance Tests for Net Merit
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Major Gene on Chromosome 18Net Merit, Productive
Life, Calving Ease, Stature, Strength, Rump Width
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Marker Effects for Milk
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Marker Effects for Final Score
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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

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Nonlinear and Linear Regressions for marker
allele effects
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R2 for linear and nonlinear predictions
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R2 vs. Reliability

• Adjust the observed genomic R2
• Daughter deviations contain error
• Divide by REL of 2008 deviations
• Parents are selected
• Add difference of PA R2 from expected
• Adjust theoretical genomic REL
• Genotypes contain a few errors
• QTLs are located between SNPs

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R2 and Reliabilities for Traditional and Genomic
Predictions
Squared corr (x100) Squared corr (x100) Reliability Reliability Reliability
Squared corr (x100) Squared corr (x100) Traditional Genomic Genomic
Trait PA Genomic PA Realized Gain
Net Merit 11 28 30 53 23
Milk 28 49 35 58 23
Fat 15 44 35 68 33
Protein 27 47 35 57 22
Fat 25 63 35 78 43
Protein 28 58 35 69 34
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R2 and Reliabilities for Traditional and Genomic
Predictions
Squared corr (x100) Squared corr (x100) Reliability Reliability Reliability
Squared corr (x100) Squared corr (x100) Traditional Genomic Genomic
Trait PA Genomic PA Realized Gain
Longevity 17 27 27 45 18
SCS 23 38 30 51 21
Fertility 20 29 25 41 16
S.calf ease 27 29 28 31 3
D.calf ease 14 22 25 40 15
Final score 23 36 24 42 18
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Reliability Gains for Proven Bulls

• Bulls included in test had
• gt10 daughters in August 2003
• gt10 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 R2 (P lt .001) for 26 of
  27 traits

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Net Merit by Chromosome for O ManTop bull for
Net Merit
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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 sG, smaller than expected
• Correlation with sire