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Outline

1	New Genomic Predictions Combine DNA and DHIA Data
2	Traditional Pedigree
3	Genomic Pedigree
4	Example of SNP Haplotypes
5	SNP Pedigree
6	Haplotype Pedigree
7	Haplotypes Sum to Genotypes
8	Genotype Pedigree Count number of second allele
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 SNP50^TM 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 DNA CDDR bulls to predict born in 2001
13	Birth Years of Bulls Genotyped
14	Simulated Results Actual 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