overview of the dairy genetic evaluation system

G.R. WiggansAnimal Improvement Programs LaboratoryAgricultural Research Service, USDA Beltsville, [email protected]

2009G.R. WiggansCroatian Holstein Breeders Federation and MOA/Veterinary Affairs study tour(1)

Overview of the Dairy Genetic Evaluation System

G.R. Wiggans 2009Croatian 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


05

1015202530

40 50 60 70 80 90 00Year

Cows

(mill

ions

)

0

2,000

4,000

6,000

8,000

10,000 Milk yield (kg/cow)U.S. Dairy Population and Yield


• 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?


• 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?


AIPL CDCB

NAAB

PDCA DHI

UniversitiesAIPL Animal Improvement Programs Lab., USDA

CDCBCouncil on Dairy Cattle BreedingDHI Dairy Herd Information (milk recording organizations)NAAB National Association of Animal Breeders (AI)PDCAPurebred Dairy Cattle Association (breed registries)

Dairy Genetic Evaluation Program


Year Advance % Gain1926 Daughter-dam comparison 1001962 Herdmate comparison 501973 Records in progress 101974 Modified cont. comparison 51977 Protein evaluated 41989 Animal model 41994 Net merit, PL, and SCS 502008 Genomic selection >50

Genetic Evaluation Advances


Trait Year Trait YearMilk, fat yield 1926 Calving ease1 2000Protein yield 1978 Dtr. preg. rate 2003Conformation 1978 Stillbirth 2006Productive life 1994 Bull CR2 2006SCS (mastitis) 1994 Cow, heifer CR 2009

1Sire calving ease evaluated by Iowa State U. 1978-19992Estimated relative conception rate evaluated by DRMS@Raleigh 1986-2005

Traits Evaluated by AIPL


Phenotypic base = 11,638 kg

-3500-3000-2500-2000-1500-1000-500

0500

1000

1960 1970 1980 1990 2000Holstein birth year

Bree

ding

val

ue (

kg)

sires cows

Genetic Trend – Milk


-2-1012345

1960 1970 1980 1990 2000Holstein birth year

Bree

ding

val

ue (%

)

Phenotypic base = 21.53%

sires cows

Genetic Trend – Daughter preg. rate


• 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


• 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


• 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?


• 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?


• Estimated Breeding value (EBV) Animal’s own genetic value

• Predicted Transmitting ability (PTA) ½ EBV Expected contribution to progeny

Expressing Evaluations


• 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


• 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


Whole-genome Selection in Dairy Cattle


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)


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


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


Genotype Data for ElevationGenotype Data for Elevation

1000111220020012111011112111101111001121100020122002220111 1202101200211122110021112001111001011011010220011002201101 1200201101020222121122102010011100011220221222112021120120 2010020220200002110001120201122111211102201111000021220200 0221012020002211220111012100111211102112110020102100022000 2201000201100002202211022112101121110122220012112122200200 0200202020122211002222222002212111121002111120011011101120 0202220001112011010211121211102022100211201211001111102111 2110211122000101101110202200221110102011121111011202102102 1211011022122001211011211012022011002220021002110001110021 1021101110002220020221212110002220102002222121221121112002 0110202001222222112212021211210110012110110200220002001002 0001111011001211021212111201010121202210101011111021102112 2111111212111210110120011111021111011111220121012121101022 202021211222120222002121210121210201100111222121101

Chromosome 1


1021222101021021011102110112112211211002202000222020002020220 0000220020222202202000020020222222000020222200000220200002002 2002000000222200022220000000000020222022002000222020222220002 2022222222200002002202022202000200022000000002202220000002200 2020002222002020020020202220222222220222020002022022022220202 2202020202200022002220220022200000220200002002002000200222220 0022220202002220022202000020200000022222020200002002002222000 2022022220022000222202200222202020002202202222002220022000200 2202000002200220222000022000022000222202002222000220020020202 2020002220002220022202202200000220220020020020220002000222202 2002220020220200222202220000020220002020020202000220022000002 2022200202220200022002000200022002002000200220222220022022000 2000020002000020220020220200200002220000222002000200222000022 0220020022002202202020202020200022202000220200202202220220000 2020200002020200022222200222200020022022220000020220020200202 022022020200002000200220220002200

Chromosome 24 of Megaster

Genotype Data from Inbred BullGenotype Data from Inbred Bull


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


Parent-Progeny Verification

Parent

10212002101201211001020120100

Progeny

10202010100200221001120120220


X Chromosome

Bull

202220200002022220002020222020202

Cow

1201201212222010111022210210212022


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


Data & Evaluation Flow

Animal Improvement

Programs Laboratory,

USDA

AI organizations,

breed associations

Dairyproducers

DNAlaboratories

samples

samples

samples

genotypes

nominationsevaluations


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


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


• 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


• 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


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

overview of the dairy genetic evaluation system

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