1. G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD george.wiggans@ars.usda.gov 2009 G.R. WiggansCroatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour(1) Overview of the Dairy Genetic Evaluation System

2. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (2) 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 AIPL Mission

3. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (3) U.S. Dairy Population and Yield

4. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (4) A valuable tool for genetic selection Allows for comparison of animals in different environments Can include all of the information available for each animal Greatest impact on progress is from selection of males Why genetic evaluations?

5. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (5) Phenotype is measurable  Pounds of milk produced  Stature An evaluation is an estimate of merit of the Genotype Phenotype = Genotype + Environment What is an evaluation?

6. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (6) 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) Dairy Genetic Evaluation Program

7. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (7) YearAdvance% Gain 1926Daughter-dam comparison100 1962Herdmate comparison50 1973Records in progress10 1974Modified cont. comparison5 1977Protein evaluated4 1989Animal model4 1994Net merit, PL, and SCS50 2008Genomic selection>50 Genetic Evaluation Advances

8. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (8) 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 Traits Evaluated by AIPL

9. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (9) Phenotypic base = 11,638 kg -3500 -3000 -2500 -2000 -1500 -1000 -500 0 500 1000 19601970198019902000 Holstein birth year Breeding value (kg) sires cows Genetic Trend – Milk

10. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (10) Phenotypic base = 21.53% sires cows Genetic Trend – Daughter preg. rate

11. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (11) An index combines evaluations for a group of traits based on their contribution to a selection goal  Net Merit $  Cheese Merit  Fluid Merit  TPI – Total production Index (Holstein) Economic Indexes

12. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (12) Completeness of ID and parentage reporting Years herd has collected data Size of herd Frequency of testing and component determination Factors Affecting Value of Data

13. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (13) Reliability measures the amount of information contributing to an evaluation Increases at a decreasing rate as daughters are added Also affected by:  Number of contemporaries  Reliability of parents’ evaluations  Heritability of the trait How Accurate are Evaluations?

14. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (14) Evaluations are predictions  The true value is unknown The predictions rank animals relative to one another using a defined base The base is the zero- or center-point for evaluations  For example: the performance of animals born in a given year What do the Numbers Mean?

15. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (15) Estimated Breeding value (EBV)  Animal’s own genetic value Predicted Transmitting ability (PTA)  ½ EBV  Expected contribution to progeny Expressing Evaluations

16. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (16) Heritability is the portion of total variation due to genetics  Milk: 30%  Daughter Pregnancy Rate: 4% Rate of genetic improvement is determined by:  Generation interval  Selection intensity  Heritability Factors in Genetic Improvement

17. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (17) Purchase promising young bulls for progeny test (PT) Select only the best of the PT bulls for widespread use  Only about 1 in 10 PT bulls enter active service Remove bulls from active service as better new bulls become available  Bulls remain active only a few years Bull Selection

18. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (18) Whole-genome Selection in Dairy Cattle

19. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (19) What is Whole-Genome Selection Use many markers to track inheritance of chromosomal segments Estimate the impact of each 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)

20. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (20) What is a SNP? Single-nucleotide polymorphism Place on the chromosome where animals differ in the nucleotides (A, C, T, or G) they have Usually not part of the gene that controls a trait – quantitative trait locus (QTL) With enough SNPs, association between SNP alleles and QTL alleles gives useful evaluations SNPs chosen to be distributed evenly and have both alleles well represented in population

21. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (21) Source of Genomic Evaluations DNA extracted from blood, hair, or semen ~43,400 genetic markers (SNPs) evaluated Genotypes represented as 0, 1, 2; number of A alleles (5 indicates missing) Genomic evaluation combines SNP effect estimates with existing PA or PTA Genomic data contribute ~11 daughter equivalents to reliability

22. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (22) Genotype Data for Elevation 1000111220020012111011112111101111001121100020122002220111 1202101200211122110021112001111001011011010220011002201101 1200201101020222121122102010011100011220221222112021120120 2010020220200002110001120201122111211102201111000021220200 0221012020002211220111012100111211102112110020102100022000 2201000201100002202211022112101121110122220012112122200200 0200202020122211002222222002212111121002111120011011101120 0202220001112011010211121211102022100211201211001111102111 2110211122000101101110202200221110102011121111011202102102 1211011022122001211011211012022011002220021002110001110021 1021101110002220020221212110002220102002222121221121112002 0110202001222222112212021211210110012110110200220002001002 0001111011001211021212111201010121202210101011111021102112 2111111212111210110120011111021111011111220121012121101022 202021211222120222002121210121210201100111222121101 Chromosome 1

23. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (23) 1021222101021021011102110112112211211002202000222020002020220 0000220020222202202000020020222222000020222200000220200002002 2002000000222200022220000000000020222022002000222020222220002 2022222222200002002202022202000200022000000002202220000002200 2020002222002020020020202220222222220222020002022022022220202 2202020202200022002220220022200000220200002002002000200222220 0022220202002220022202000020200000022222020200002002002222000 2022022220022000222202200222202020002202202222002220022000200 2202000002200220222000022000022000222202002222000220020020202 2020002220002220022202202200000220220020020020220002000222202 2002220020220200222202220000020220002020020202000220022000002 2022200202220200022002000200022002002000200220222220022022000 2000020002000020220020220200200002220000222002000200222000022 0220020022002202202020202020200022202000220200202202220220000 2020200002020200022222200222200020022022220000020220020200202 022022020200002000200220220002200 Chromosome 24 of Megaster Genotype Data from Inbred Bull

24. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (24) What Can Go Wrong Sample doesn’t provide adequate DNA quality or quantity Genotype has many SNPs that can’t be determined (90% call rate required) Parent-Progeny conflicts  Pedigree error  Sample ID error  Laboratory error  Unrelated animal qualifies as parent or progeny

25. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (25) Parent-Progeny Verification Parent 10212002101201211001020120100 Progeny 10202010100200221001120120220

26. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (26) X Chromosome Bull 202220200002022220002020222020202 Cow 1201201212222010111022210210212022

27. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (27) Genomic vs. Traditional PTA Genotype can be thought of as source of information like parents, progeny, and records Indicator added to official PTA that include a genomic contribution An animal’s one genotype can be used to calculate its genomic evaluations for all 29 traits Genomic evaluations used the same as traditional PTA Expected to increase rate of genetic improvement because of a large decrease in generation interval

28. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (28) Data & Evaluation Flow Animal Improvement Programs Laboratory, USDA AI organizations, breed associations Dairy producers DNA laboratories samples genotypes nominations evaluations

29. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (29) Impact on Producers Young-bull evaluations with accuracy of early 1st- crop evaluations AI organizations marketing genomically evaluated 2- year-olds Bull dams likely to be required to be genotyped Rate of genetic improvement likely to increase by up to 50% Progeny-test programs changing

30. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (30) International Implications All major dairy countries investigating genomic selection Interbull meeting January 2009 discussed how genomic evaluations should be integrated AI organizations may see benefits in wider sharing of genotypes Importing countries must change rules to allow for genomically evaluated young bulls

31. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (31) US bulls recognized as siring high yield Genetic evaluation system perceived as unbiased Large program offers bulls with a wide range of strengths Effective international marketing effort Leader in genomic selection Large population of high producing cows offers many selection candidates Intense competition among bull studs yields good value for customer World Market Competitiveness

32. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (32) Evaluation procedures have improved Selection is the basis of genetic improvement Effective selection has produced substantial annual genetic improvement Indexes enable selection for overall economic merit Increased weight on fertility necessary to prevent continued decline Genomic evaluations are rapid and allow the use of young bulls AIPL serves the dairy industry with reliable evaluations and research to improve procedures Competitive in the world market Summary

33. G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (33) Financial Support National Research Initiative grants, USDA NAAB (Columbia, MO) ABS Global (DeForest, WI) Accelerated Genetics (Baraboo, WI) Alta (Balzac, AB) Genex (Shawano, WI) New Generation Genetics (Fort Atkinson, WI) Select Sires (Plain City, OH) Semex Alliance (Guelph, ON) Taurus-Service (Mehoopany, PA) Holstein Association USA (Brattleboro, VT) American Jersey Cattle Association (Reynoldsburg, OH) American Brown Swiss Association (Beloit, WI) Agricultural Research Service, USDA