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

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

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

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?

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?

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

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

G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (8) TraitYearTraitYear Milk, fat yield1926Calving ease Protein yield1978Dtr. preg. rate2003 Conformation1978Stillbirth2006 Productive life1994Bull CR SCS (mastitis)1994Cow, heifer CR Sire calving ease evaluated by Iowa State U Estimated relative conception rate evaluated by Traits Evaluated by AIPL

G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (9) Phenotypic base = 11,638 kg Holstein birth year Breeding value (kg) sires cows Genetic Trend – Milk

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

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

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

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?

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?

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

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

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

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

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)

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

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

G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (22) Genotype Data for Elevation Chromosome 1

G.R. Wiggans 2009 Croatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour (23) Chromosome 24 of Megaster Genotype Data from Inbred Bull

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

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

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

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

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

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

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

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

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

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