1. G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD george.wiggans@ars.usda.gov 2009 G.R. WiggansInner Mongolia Livestock Improvement Training (1) US Genetic Improvement Program: Methods and Results

2. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (2) AIPL Mission Conduct research to discover, test, and implement improved genetic evaluation techniques for economically important traits of dairy cattle and goats Genetically improve efficiency of dairy animals for yield and fitness

3. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (3) AIPL Research Objectives Maintain a national database with animal identification, production, fitness, reproduction, and health traits to support research on dairy genetics and management Provide data to others researchers submitting proposals compatible with industry needs

4. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (4) AIPL Research Objectives (cont.) Increase accuracy of genetic evaluations for traits through improved methodology and through inclusion and appropriate weighting of deviant data Develop bioinformatic tools to automate data processing in support of quantitative trait locus detection, marker testing, and mapping methods

5. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (5) AIPL Research Objectives (cont.) Improve genetic rankings for overall economic merit by evaluating appropriate traits and by determining economic values of those traits in the index Improved profit functions are derived from reviewing incomes and expenses associated with each trait available for selection

6. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (6) AIPL Research Objectives (cont.) Characterize dairy industry practices in milk recording, breed registry, and artificial- insemination to document status and changes in data collection and use and in observed and genetic trends in the population

7. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (7) U.S. Dairy Statistics (2009) 9.2 million cows 48% milk recorded through Dairy Herd Information (DHI) 22,246 DHI herds 200 cows/herd 22,200 lb (10,070 kg)/cow ~93% Holsteins, ~5% Jerseys ~75% bred AI

8. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (8) U.S. Dairy Population and Yield

9. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (9) U.S. Progeny-test Bulls born 2007 Major and marketing-only AI organizations Breed # Bulls Ayrhire7 Brown Swiss24 Guernsey9 Holstein1207 Jersey98 Milking Shorthorn3

10. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (10) Dairy Genetic Evaluation Program AIPLCDCB NAAB PDCA DHI Universities AIPL Animal Improvement Programs Lab., USDA CDCBCouncil on Dairy Cattle Breeding DHIDairy Herd Information (milk recording organizations) NAABNational Association of Animal Breeders (AI) PDCAPurebred Dairy Cattle Association (breed registries)

11. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (11) Genetic Evaluation Advances YearAdvance% Gain 1862USDA established 1895USDA begins collecting dairy records 1926Daughter-dam comparison 100 1962Herdmate comparison 50 1973Records in progress 10 1974Modified cont. comparison 5 1977Protein evaluated 4 1989Animal model 4 1994Net merit, PL, and SCS 50 2008Genomic selection >50

12. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (12) Daughter-Dam Difference 1926-1961 Introduced by:  R. R. Graves  1926 USDA Bulletin #1372 Advantages:  Allowed progeny testing of bulls  Adjusted for herd effect via dam  (Over) adjusted for merit of mates

13. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (13) Herdmate Comparison 1962-1973 Introduced by:  Robert Miller  Rankings in Hoards Dairyman (1964) Advantages:  Sire effect random (informative prior) High rank requires more daughters, n / (n + k)  Did not require records on dam  More data, less bias, 1st cow index (1964)

14. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (14) Modified Contemporary Comparison 1974-1989 Introduced by:  Duane Norman, Ben McDaniel, Rex Powell, and Frank Dickinson Advantages:  Ancestor and daughter merit combined Sire-MGS pedigree introduced 1 year before Henderson’s relationship inverse Genetic group effects inherited (similar to Westell et al., 1988)  Adjusted for merit of competing sires  Cow indexes included more relatives

15. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (15) Animal Model 1989-present Introduced by:  George Wiggans and Paul VanRaden Advantages:  Use of all relatives  Adjusts for merit of mates  Uniform procedures for males and females  Best prediction given the model (BLUP)  Revised to include crossbreds (2007)

16. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (16) Models Borrowed from Others Calving ease threshold model  Berger and Freeman (Iowa State, 1978) Service sire conception rate  Clay (NC State, 1986), programs by Misztal (Georgia) Somatic cell score  Shook (U. WI, 1980), Boettcher et al (U. MN, 1992) Multi-trait productive life  Weigel et al (Holstein USA, 1994) Multi-trait linear type  Programs by Gengler (Belgium)

17. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (17) Genomic Selection Use many markers to track inheritance of chromosomal segments Estimate the impact of each chromosomal segment on each trait Combine estimates with traditional evaluations to produce genomic evaluation (GPTA) Select animals shortly after birth using GPTA Replaces searching for individual genes of large effect (Major Genes)

18. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (18) Genomic Evaluation System Provides timely evaluations of young bulls for purchasing decisions Increases accuracy of evaluations of bull dams Assists in selection of service sires, particularly for low-reliability traits

19. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (19) Traits Evaluated by AIPL TraitYearTraitYear Milk, fat yield1926Calving ease 1 2000 Protein yield1978Dtr. preg. rate2003 Conformation1978Stillbirth2006 Productive life1994Bull CR 2 2006 SCS (mastitis)1994Cow, heifer CR2009 1 Sire calving ease evaluated by Iowa State U. 1978-1999 2 Estimated relative conception rate evaluated by DRMS@Raleigh 1986-2005

20. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (20) Evaluation Methods l Animal model (linear)  Yield (milk, fat, protein)  Type (Ayrshire, Brown Swiss, Guernsey, Jersey)  Productive life  SCS  Daughter pregnancy rate l Sire – maternal grandsire model (threshold)  Service sire calving ease  Daughter calving ease  Service sire stillbirth  Daughter stillbirth Heritability 25 – 40% 7 – 54% 8.5% 12% 4% 8.6% 3.6% 3.0% 6.5%

21. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (21) Type Traits Stature Strength Body Depth Dairy Form Rump Angel Thurl Width Rear Legs (side) Rear Legs (rear) Foot Angle Feet and Leg Score Fore Udder Attachment Rear Udder Height Rear Udder Width Udder Cleft Udder Depth Front Teat Placement Rear Teat Placement Teat Length

22. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (22) Genetic Trend – Milk Phenotypic base = 11,638 kg -3500 -3000 -2500 -2000 -1500 -1000 -500 0 500 1000 19601970198019902000 Holstein birth year Breeding value (kg) sires cows

23. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (23) Genetic Trend – Fat Phenotypic base = 424 kg sires cows

24. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (24) Genetic Trend – Protein Phenotypic base = 350 kg sires cows

25. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (25) Genetic Trend – Productive Life (mo) Phenotypic base = 24.6 months sires cows

26. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (26) Genetic Trend – Somatic cell score Phenotypic base = 3.08 (log base 2) sires cows

27. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (27) Genetic Trend – Daughter preg. rate Phenotypic base = 21.53% sires cows

28. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (28) Genetic Trend – calving ease SCE Phenotypic base = 8.47% DBH DCE Phenotypic base = 7.99% DBH service sire daughter

29. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (29) Genetic Trend – stillbirth Phenotypic base = 8% SBH service sire daughter

30. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (30) Genetic-economic Indices Trait Relative value (%) Net merit Cheese merit Fluid merit Milk (lb)0-1224 Fat (lb)231823 Protein (lb)23280 Productive life (mo) (PL)171317 Somatic cell score (log 2 ) (SCS)–9–7-9 Udder composite (UDC)656 Feet/legs composite (FLC)333 Body size composite (BSC)–4–3-4 Daughter pregnancy rate (%) (DPR)978 Calving ability ($) (CA$)646

31. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (31) Index Changes Trait Relative emphasis on traits in index (%) PD$ (1971) MFP$ (1976) CY$ (1984) NM$ (1994) NM$ (2000) NM$ (2003) NM$ (2006) Milk5227–26500 Fat48464525212223 Protein…275343363323 PL………20141117 SCS………–6–9 UDC…………776 FLC…………443 BDC…………–4–3–4 DPR……………79 SCE……………–2… DCE……………–2… CA$………………6

32. G.R. Wiggans 2009 Inner Mongolia Livestock Improvement Training (32) Summary Evaluation procedures have improved Fitness traits have been added Effective selection has produced substantial annual genetic improvement Indexes enable selection for overall economic merit Increased weight on fertility necessary to prevent continued decline AIPL serves the dairy industry with reliable evaluations and research to improve procedures