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New Genomic Predictions Combine DNA and DHIA Data

New Genomic Predictions Combine DNA and DHIA Data. Traditional Pedigree. Genomic Pedigree. Example of SNP Haplotypes. SNP. SNP. SNP. Chr1. caacg t at. …. atccg c at. …. tct a ggat. …. Chr2. caacg g at. …. atccg a at. …. tct c ggat. …. Haplotype 1. tca. Haplotype 2. gac.

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New Genomic Predictions Combine DNA and DHIA Data

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  1. New Genomic PredictionsCombine DNA and DHIA Data

  2. Traditional Pedigree

  3. Genomic Pedigree

  4. Example of SNP Haplotypes SNP SNP SNP Chr1 caacgtat … atccgcat … tctaggat … Chr2 caacggat … atccgaat … tctcggat … Haplotype 1 tca Haplotype 2 gac Haplotype is a set of single nucleotide polymorphisms (SNPs) on a chromosome.

  5. SNP Pedigree atagatcgatcg ctgtagcgatcg ctgtagcttagg agatctagatcg agggcgcgcagt cgatctagatcg ctgtctagatcg atgtcgcgcagt cggtagatcagt agagatcgcagt agagatcgatct atgtcgctcacg atggcgcgaacg ctatcgctcagg

  6. Haplotype Pedigree atagatcgatcg ctgtagcgatcg ctgtagcttagg agatctagatcg agggcgcgcagt cgatctagatcg ctgtctagatcg atgtcgcgcagt cggtagatcagt agagatcgcagt agagatcgatct atgtcgctcacg atggcgcgaacg ctatcgctcagg

  7. Haplotypes Sum to Genotypes ctgtagcgatcg agatctagatcg 111211120200

  8. Genotype PedigreeCount number of second allele 0 = homozygous for first allele (alphabetically) 1 = heterozygous 2 = homozygous for second allele (alphabetically)

  9. 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. • Combine genotype and pedigree data to determine exact fractions

  10. 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

  11. Genotyped Bulls from Cooperative Dairy DNA Repository • DNA of bulls stored in Beltsville (BFGL) • Genotypes of 2560 proven bulls included in computing predictions • Bulls born 1994-1996 with >75% reliability of Net Merit • Plus ancestor bulls born 1952-1993 • Genotypes of 659 later bulls used to test predictions • Born 2001 with >75% reliability of Net Merit

  12. Contributors of DNACDDR bulls to predict born in 2001

  13. Birth Years of Bulls Genotyped Data cutoff

  14. Simulated ResultsActual pedigrees and 10,000 SNPs • Normally distributed QTLs, n = 100 • Reliability vs parent average REL • 58% vs 36% if QTLs are between SNPs • 71% vs 36% if QTLs are located at SNPs • Higher REL if major loci and Bayesian methods used, lower if many loci (>100) affect trait

  15. Actual Results • Predict January 2008 daughter deviations for 569 younger bulls from August 2003 PTAs for 2650 older bulls • Results computed for 5 yield traits, 5 health traits, 16 conformation traits, and Net Merit

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

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

  18. Conclusions • Genomic predictions significantly better than parent average (P < .0001) for all 26 traits tested • Gains in reliability equivalent on average to 9 daughters with records

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