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2	National Dairy Genetic Evaluation Program
3	DHI statistics (2007) 4.4 million cows 98% fat recorded 95% protein recorded 94% somatic cell count recorded 23,500 herds 184 cows per herd 23,560 pounds milk per cow 3.69% fat 3.09% (true) protein
4	Traits evaluated Yield (milk, fat, protein volume; component percentages) Type/conformation Productive life/longevity Somatic cell score (SCS)/mastitis resistance Fertility Daughter pregnancy rate (DPR; cow) Estimated relative conception rate (bull) Calving ease/dystocia (service sire, daughter)
5	Evaluation methods Animal model (linear) Heritability Yield (milk, fat, protein) 25–40% Type (Ayrshire, Brown Swiss, 7–54% Guernsey, Jersey) Productive life 8.5% SCS 12% DPR 4% Sire-maternal grandsire model (threshold) Service sire calving ease 8.6% Daughter calving ease 3.6%
6	Dairy cattle breeding Long generation interval – 5 years High value of individuals – $2,000 per cow Intensive management – milking 2–3 times per day Bull semen suitable for dilution – 500 doses per collection day)
7	U.S. progeny-test bulls (2006) Major and marketing-only AI organizations plus breeder proven Breeds Ayrshire – 13 Brown Swiss – 30 Guernsey – 12 Holstein – 1,493 Jersey – 151 Milking Shorthorn – 8 260 new bulls returned to service per year
8	Genetic-economic indexes
9	Index changes
10	International reach Semen and embryos marketed internationally Interbull Evaluation Centre (Sweden) ranks all bulls for each participating country Correlations between countries of <1 accommodated Some foreign bulls used as sires of sons U.S. and Canadian semen used widely in South America Red breeds more popular in Europe than in North America
11	PTA milk prediction
12	Net merit prediction
13	PTA DPR prediction (curvilinear)
14	PTA DPR prediction (linear)
15	Holstein milk yield
16	Goals beyond increased yield Improve fertility Increase herdlife Improve disease resistance Reduce calving difficulty Improve efficiency
17	Options for increasing progress Crossbreeding Increased selection intensity Adoption of new technologies
18	Crossbreds Increasing interest Way to increase fertility Scandinavian Red breeds proposed Hybrid vigor observed
19	All-breed animal model Purebreds and crossbreds together Unknown parents grouped by breed Variance adjustments by breed Age adjusted to 36 months, not maturity
20	Genomics Genotype calves Calculate genomic evaluation Select intensively Reduce cost of finding top bulls Increase rate of genetic progress
21	Getting started Select animals to genotype Assign identification to animals Collect tissue samples Extract DNA Check DNA quality and standardize concentration Begin 3-day genotyping process
22	Genomic evaluation workflow Check genotypes for inheritance errors Calculate genomic relationships Infer missing genotypes Estimate single-nucleotide polymorphism (SNP) effects
23	Evaluation workflow – cont. Combine genomic information with parent average Based on gain from genomics over parent average for animals with genotypes Apply to all traits Distribute results
24	First genomic evaluation 750 animals nominated for genotyping Over 5,285 predictor bulls from United States and Canada Embryo flushes AI organization that arranged for genotyping have first choice More information at http://aipl.arsusda.gov/reference/changes/eval0804.html
25	Reliabilities and squared correlations
26	Marker effects for net merit
27	SNP density comparison
28	Conclusions Genomic predictions significantly better than parent average (P < .0001) for all 26 traits tested Gains in reliability equivalent on average to 11 daughters with records Analysis used 3,576 historical bulls Current data includes 5,285 proven bulls Larger populations require more SNPs
29	Current status Field test results distributed for 750 nominated animals Extension to Jersey and Brown Swiss in progress Transition to commercial genotyping labs Extension to cows planned for June
30	SNP project outcomes Genome-wide selection Parentage verification and traceability panels Enhanced mapping for quantitative trait loci and gene discovery
31	Future plans Evaluations of animals not genotyped updated using genomic information (3 times per year) Genomic evaluations calculated and released more frequently (monthly? weekly?) Bull evaluations made public when bull enrolled with NAAB Cow evaluations made public immediately at USDA web site January 2009 target for public release
32	Genomic selection (New Zealand) Identify top 30,000 bull calves annually based on parent average Genotype by 6 days old with 768 SNP Genotype top 500 bull calves with 50K SNP chip Keep top 100 bull calves
33	Genomic selection (NZ) – cont. At 1 year, limited progeny test to check for undesirable recessives At 2 years, market as part of DNA team When progeny tested, graduate best to progeny-proven team
34	Research topics Differential inclusion of X-chromosome effects to predict bulls versus cows Contribution of cows to accuracy of genomic prediction Benefit of genotyping more predictor bulls Optimum methods for combining genomic and current evaluation
35	Research topics – cont. Practicality of screening and parentage verification with low-cost, low-SNP number assay Potential of freely sharing enough SNP for accurate parentage discovery Computational methods to improve accuracy, such as haplotyping
36	Summary Genomic prediction has great promise Extensive changes in bull acquisition and marketing and in cow selection expected Routine genotyping and validation will become industry rather than research responsibilities
37	Where do we go from here Economic indexes adjusted as conditions change Traits added as their collection becomes feasible and value demonstrated Dairies increase in size and technological sophistication Selection adapts the cow to meet human needs
38	Senior research staff