1. George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD george.wiggans@ars.usda.gov 2008 Genetic trends in dairy cattle over the next 25 years … where are we headed and how will we get there

2. G.R. Wiggans 2008 National Breeders Roundtable (2) National Dairy Genetic Evaluation Program AIPL CDCB NAAB PDCA DHI Universities AIPL Animal Improvement Programs Lab., USDA CDCBCouncil on Dairy Cattle Breeding DHIDairy Herd Improvement (milk recording organizations) NAABNational Association of Animal Breeders (AI) PDCAPurebred Dairy Cattle Association (breed registries)

3. G.R. Wiggans 2008 National Breeders Roundtable (3) DHI statistics (2007) l 4.4 million cows w 98% fat recorded w 95% protein recorded w 94% somatic cell count recorded l 23,500 herds l 184 cows per herd l 23,560 pounds milk per cow w 3.69% fat w 3.09% (true) protein

4. G.R. Wiggans 2008 National Breeders Roundtable (4) Traits evaluated l Yield (milk, fat, protein volume; component percentages) l Type/conformation l Productive life/longevity l Somatic cell score (SCS)/mastitis resistance l Fertility w Daughter pregnancy rate (DPR; cow) w Estimated relative conception rate (bull) l Calving ease/dystocia (service sire, daughter)

5. G.R. Wiggans 2008 National Breeders Roundtable (5) Evaluation methods l Animal model (linear)Heritability w Yield (milk, fat, protein)25–40% w Type (Ayrshire, Brown Swiss, 7–54% Guernsey, Jersey) w Productive life8.5% w SCS12% w DPR4% l Sire-maternal grandsire model (threshold) w Service sire calving ease8.6% w Daughter calving ease3.6%

6. G.R. Wiggans 2008 National Breeders Roundtable (6) Dairy cattle breeding l Long generation interval – 5 years l High value of individuals – $2,000 per cow l Intensive management – milking 2–3 times per day l Bull semen suitable for dilution – 500 doses per collection day)

7. G.R. Wiggans 2008 National Breeders Roundtable (7) U.S. progeny-test bulls (2006) l Major and marketing-only AI organizations plus breeder proven l Breeds w Ayrshire – 13 w Brown Swiss – 30 w Guernsey – 12 w Holstein – 1,493 w Jersey – 151 w Milking Shorthorn – 8 l 260 new bulls returned to service per year

8. G.R. Wiggans 2008 National Breeders Roundtable (8) Genetic-economic indexes Trait Relative value (%) Cheese merit Net merit Fluid merit Protein (lb)36339 Fat (lb)1822 Milk (lb)–10024 Productive life (mo)911 SCS (log base 2)–7–9 Udder composite677 Feet/legs composite344 Body size composite–2–3 DPR (%)577 Service sire calving difficulty (%)–2 Daughter calving difficulty (%)–2

9. G.R. Wiggans 2008 National Breeders Roundtable (9) Index changes PTA traits included Relative emphasis on traits in index (%) PD$ 1971 MFP$ 1976 CY 1984 NM 1994 NM 2000 NM 2003 Milk (lb) 5227–2650 Fat (lb)484645252122 Protein (lb)…2753433633 Productive life………201411 SCS………–6–9 Udder composite…………77 Feet/legs composite…………44 Body size composite…………–4–3 DPR……………7 Service sire calving difficulty ……………–2 Daughter calving difficulty ……………–2

10. G.R. Wiggans 2008 National Breeders Roundtable (10) International reach l Semen and embryos marketed internationally l Interbull Evaluation Centre (Sweden) ranks all bulls for each participating country l Correlations between countries of <1 accommodated l Some foreign bulls used as sires of sons l U.S. and Canadian semen used widely in South America l Red breeds more popular in Europe than in North America

11. G.R. Wiggans 2008 National Breeders Roundtable (11) PTA milk prediction

12. G.R. Wiggans 2008 National Breeders Roundtable (12) Net merit prediction

13. G.R. Wiggans 2008 National Breeders Roundtable (13) PTA DPR prediction (curvilinear)

14. G.R. Wiggans 2008 National Breeders Roundtable (14) PTA DPR prediction (linear)

15. G.R. Wiggans 2008 National Breeders Roundtable (15) Holstein milk yield

16. G.R. Wiggans 2008 National Breeders Roundtable (16) Goals beyond increased yield l Improve fertility l Increase herdlife l Improve disease resistance l Reduce calving difficulty l Improve efficiency

17. G.R. Wiggans 2008 National Breeders Roundtable (17) Options for increasing progress l Crossbreeding l Increased selection intensity l Adoption of new technologies

18. G.R. Wiggans 2008 National Breeders Roundtable (18) Crossbreds l Increasing interest l Way to increase fertility l Scandinavian Red breeds proposed l Hybrid vigor observed

19. G.R. Wiggans 2008 National Breeders Roundtable (19) All-breed animal model l Purebreds and crossbreds together l Unknown parents grouped by breed l Variance adjustments by breed l Age adjusted to 36 months, not maturity

20. G.R. Wiggans 2008 National Breeders Roundtable (20) Genomics l Genotype calves l Calculate genomic evaluation l Select intensively l Reduce cost of finding top bulls l Increase rate of genetic progress

21. G.R. Wiggans 2008 National Breeders Roundtable (21) Getting started l Select animals to genotype l Assign identification to animals l Collect tissue samples l Extract DNA l Check DNA quality and standardize concentration l Begin 3-day genotyping process

22. G.R. Wiggans 2008 National Breeders Roundtable (22) Genomic evaluation workflow l Check genotypes for inheritance errors l Calculate genomic relationships l Infer missing genotypes l Estimate single-nucleotide polymorphism (SNP) effects

23. G.R. Wiggans 2008 National Breeders Roundtable (23) Evaluation workflow – cont. l Combine genomic information with parent average w Based on gain from genomics over parent average for animals with genotypes l Apply to all traits l Distribute results

24. G.R. Wiggans 2008 National Breeders Roundtable (24) First genomic evaluation l 750 animals nominated for genotyping l Over 5,285 predictor bulls from United States and Canada l Embryo flushes w AI organization that arranged for genotyping have first choice l More information at http://aipl.arsusda.gov/reference/changes/eval0804.html http://aipl.arsusda.gov/reference/changes/eval0804.html

25. G.R. Wiggans 2008 National Breeders Roundtable (25) Reliabilities and squared correlations Squared correlation × 100 Reliability (%) Tradi- tionalGenomic Trait PAGenomicPARealizedGain Net merit 1128305323 Milk (lb) 2849355823 Fat (lb) 1544356833 Protein (lb) 2747355722 Fat (%) 2563357843 Protein (%) 2858356934 Productive life 1727 4518 SCS 2338305121 DPR 2029254116 Service sire calving ease 272928313 Daughter calving ease 1422254015 Final score 2336244218

26. G.R. Wiggans 2008 National Breeders Roundtable (26) Marker effects for net merit

27. G.R. Wiggans 2008 National Breeders Roundtable (27) SNP density comparison PA reliability (%) Genomic reliability (%) Trait10K20K40K Net merit30485053 Milk (lb)35535658 Fat (lb)35646668 Protein (lb)35545657 Productive life27384145 SCS30454751 DPR25373941

28. G.R. Wiggans 2008 National Breeders Roundtable (28) Conclusions l Genomic predictions significantly better than parent average (P <.0001) for all 26 traits tested l Gains in reliability equivalent on average to 11 daughters with records w Analysis used 3,576 historical bulls w Current data includes 5,285 proven bulls l Larger populations require more SNPs

29. G.R. Wiggans 2008 National Breeders Roundtable (29) Current status l Field test results distributed for 750 nominated animals l Extension to Jersey and Brown Swiss in progress l Transition to commercial genotyping labs l Extension to cows planned for June

30. G.R. Wiggans 2008 National Breeders Roundtable (30) SNP project outcomes l Genome-wide selection l Parentage verification and traceability panels l Enhanced mapping for quantitative trait loci and gene discovery

31. G.R. Wiggans 2008 National Breeders Roundtable (31) Future plans l Evaluations of animals not genotyped updated using genomic information (3 times per year) l Genomic evaluations calculated and released more frequently (monthly? weekly?) l Bull evaluations made public when bull enrolled with NAAB l Cow evaluations made public immediately at USDA web site l January 2009 target for public release

32. G.R. Wiggans 2008 National Breeders Roundtable (32) Genomic selection (New Zealand) l Identify top 30,000 bull calves annually based on parent average l Genotype by 6 days old with 768 SNP l Genotype top 500 bull calves with 50K SNP chip l Keep top 100 bull calves

33. G.R. Wiggans 2008 National Breeders Roundtable (33) Genomic selection (NZ) – cont. l At 1 year, limited progeny test to check for undesirable recessives l At 2 years, market as part of DNA team l When progeny tested, graduate best to progeny-proven team

34. G.R. Wiggans 2008 National Breeders Roundtable (34) Research topics l Differential inclusion of X-chromosome effects to predict bulls versus cows l Contribution of cows to accuracy of genomic prediction l Benefit of genotyping more predictor bulls l Optimum methods for combining genomic and current evaluation

35. G.R. Wiggans 2008 National Breeders Roundtable (35) Research topics – cont. l Practicality of screening and parentage verification with low-cost, low-SNP number assay l Potential of freely sharing enough SNP for accurate parentage discovery l Computational methods to improve accuracy, such as haplotyping

36. G.R. Wiggans 2008 National Breeders Roundtable (36) Summary l Genomic prediction has great promise l Extensive changes in bull acquisition and marketing and in cow selection expected l Routine genotyping and validation will become industry rather than research responsibilities

37. G.R. Wiggans 2008 National Breeders Roundtable (37) Where do we go from here l Economic indexes adjusted as conditions change l Traits added as their collection becomes feasible and value demonstrated l Dairies increase in size and technological sophistication l Selection adapts the cow to meet human needs

38. G.R. Wiggans 2008 National Breeders Roundtable (38) Senior research staff