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

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)

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

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)

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%

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)

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

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

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) Protein (lb)… Productive life……… 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

G.R. Wiggans 2008 National Breeders Roundtable (25) Reliabilities and squared correlations Squared correlation × 100 Reliability (%) Tradi- tionalGenomic Trait PAGenomicPARealizedGain Net merit Milk (lb) Fat (lb) Protein (lb) Fat (%) Protein (%) Productive life SCS DPR Service sire calving ease Daughter calving ease Final score

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

G.R. Wiggans 2008 National Breeders Roundtable (27) SNP density comparison PA reliability (%) Genomic reliability (%) Trait10K20K40K Net merit Milk (lb) Fat (lb) Protein (lb) Productive life SCS DPR

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

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

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

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

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

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

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

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

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

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

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