Genetic evaluation using combined data from all breeds and crossbred cows

2007

Paul VanRadenPaul VanRaden

Animal Improvement Programs Laboratory, USDAAgricultural Research Service, Beltsville, MD, [email protected]

2007

Genetic evaluation using Genetic evaluation using combined data from all breeds combined data from all breeds

and crossbred cowsand crossbred cows

Petersen Symposium 2007 (2) P.M. VanRaden200

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USDA Yearbook of Agriculture 1947Jersey Jersey Holstein Holstein

Cow #

Pounds of Milk

% Butterfat

Pounds of Butterfat

X-1 9,784 4.85 475

X-3 13,065 4.71 615

X-17 13,837 3.85 533

From USDA research herd at Beltsville, MD


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Crossbreds averaged 12,904 pounds of milk and 588 pounds of butterfat, outperforming dams by more than sire proof predictions (Fohrman,1947).

Advanced register Holsteins averaged 13,833 pounds of milk and 493 pounds of fat in 1945.

USDA Yearbook of Agriculture 1947Red Dane Red Dane Jersey Jersey


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GoalsGoals

Evaluate crossbred animals without biasing purebred evaluations

Accurately estimate breed differences

Compare crossbreeding strategies

Compute national evaluations and examine changes

Display results without confusion


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All-Breed AnalysesAll-Breed Analyses

Crossbred animals• Will have PTAs, only 3% did before if in

breed association grading-up programs• Reliable PTAs from both parents

Purebred animals• Information from crossbred relatives• More herdmates (other breeds, crossbreds)

Routinely used in other populations• New Zealand (1994), Netherlands (1997)• USA goats (1989), calving ease (2005)


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MethodsMethods

All-breed animal model• Purebreds and crossbreds together• Relationship matrix among all• Unknown parents grouped by breed• Variance adjustments by breed• Age adjust to 36 months, not mature

Within-breed-of-sire model examined but not used


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DataData

Numbers of cows of all breeds• 22.6 million for milk and fat • 16.1 million for protein• 22.5 million for productive life• 19.9 million for daughter pregnancy rate• 10.5 million for somatic cell score

Type traits are still collected and evaluated in separate breed files


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Purebred and Crossbred DataPurebred and Crossbred DataUSA milk yield recordsUSA milk yield records

Breed % of total Cows born 2003

Holstein 90.5 642,354

Jersey 6.4 45,151

Brown Swiss .8 5,960

Guernsey .4 2,563

Ayrshire .3 1,926

F1 Crossbred 1.2 8,647


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Crossbred CowsCrossbred Cowswith 1with 1stst parity records parity records

Fresh year

F1 (%)

F1 cows

Back-cross

Het > 0

XX cows

2006 1.4 10153 3422 15365 6099

2005 1.2 8647 2495 12621 4465

2004 1.1 7863 1983 11191 3947

2003 .9 6248 1492 9051 3111

2002 .7 4689 1467 7338 2564


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Number of Cows with RecordsNumber of Cows with Records (with > 50% heterosis; March 2007)

Dam Sire Breed

Breed AY BS GU JE MS XX HO

AY — 29 29 221 48 43 1796

BS 20 — 50 294 42 13 2619

GU 46 96 — 288 32 16 3256

JE 181 357 155 — 116 56 3718

MS 281 52 10 71 — 5 965

XX 489 1544 308 3568 323 — 8859

HO 1843 13993 1721 35193 1858 675 —


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Number of Cows with RecordsNumber of Cows with Records (with > 50% heterosis; March 2007)

Sire Breed

Dam Breed #

Sire Breed

Dam Breed #

BS SM 25 HO DL 47

DL HO 109 HO LD 195

MO HO 73 HO MI 60

NO HO 38 HO NR 21

NR HO 23 HO RE 22

SR HO 118 HO SM 16


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Crossbred Daughters AddedCrossbred Daughters Addedfor sires in top 10 NM$ within breedfor sires in top 10 NM$ within breed

Sire

breed

Daughters

Sire Name Feb ‘07 Added

Legacy AY 157 33

Agenda BS 35 21

Excite BS 144 57

Q Impuls JE 241 20

Stetson MS 36 31


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Heterosis for Yield TraitsHeterosis for Yield Traits Percent of Parent Breed Average

Milk Fat Protein

BreedHO Sire

HO Dam

HO Sire

HO Dam

HO Sire

HO Dam

Ayrshire 2.4 -2.0 2.7 -1.8 2.9 -2.4

Brown Swiss 5.6 3.2 4.8 4.5 4.7 3.8

Guernsey 5.2 2.4 7.1 4.4 5.5 4.0

Jersey 7.5 1.6 6.6 4.5 7.2 4.1

M. Shorthrn 2.8 0.3 3.2 1.3 3.6 1.2

Heterosis 3.4 4.4 4.1


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Breed Effects and HeterosisBreed Effects and Heterosis

Three estimates of breed differences: • From phenotypic breed differences• From herds containing crossbred cows• From all-breed model using all data• All three estimates were similar

Estimates of general heterosis from 2001 and 2003 studies were used in the current research and not re-estimated


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Unknown Parent GroupsUnknown Parent Groups

Look up PTAs of known parents Estimate averages for unknowns Group unknown parents by

• Birth year • Breed • Path (dams of cows, sires of cows,

parents of bulls)• Origin (domestic vs other countries)


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All- vs Within-Breed EvaluationsAll- vs Within-Breed EvaluationsCorrelations of PTA MilkCorrelations of PTA Milk

Breed99% REL bulls

Recent bulls

Recent cows

Holstein >.999 .994 .989Jersey .997 .988 .972Brown Swiss .990 .960 .942Guernsey .991 .988 .969Ayrshire .990 .963 .943

Milking Shorthorn .997 .986 .947


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Display of PTAsDisplay of PTAs

Genetic base• Convert all-breed base to within-breed

bases (or vice versa)• PTAbrd = (PTAall – meanbrd) SDbrd/SDHO

• PTAall = PTAbrd (SDHO/SDbrd) + meanbrd

Heterosis and inbreeding• Both effects removed in the animal model• Heterosis added to crossbred animal PTA• Expected Future Inbreeding (EFI) and merit

differ with mate breed


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Milk (kg)Milk (kg)Genetic trend on all-breed baseGenetic trend on all-breed base

-6000

-5000

-4000

-3000

-2000

-1000

0

1000

1960 1970 1980 1990 2000

Birth Year

Bre

ed

ing

Va

lue Ayrshire

Brwn Sws

Guernsey

Holstein

Jersey

Mlk Shrtn


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Fat (kg)Fat (kg)Genetic trend on all-breed baseGenetic trend on all-breed base

-200

-150

-100

-50

0

50

1960 1970 1980 1990 2000

Birth Year

Bre

ed

ing

Va

lue Ayrshire

Brwn Sws

Guernsey

Holstein

Jersey

Mlk Shrtn


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Protein (kg)Protein (kg)Genetic trend on all-breed baseGenetic trend on all-breed base

-125

-100

-75

-50

-25

0

25

1976 1980 1984 1988 1992 1996 2000

Birth Year

Bre

edin

g V

alu

e Ayrshire

Brwn Sws

Guernsey

Holstein

Jersey

Mlk Shrtn


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Somatic Cell ScoreSomatic Cell ScoreGenetic trend on all-breed baseGenetic trend on all-breed base

-0.4

-0.3

-0.2

-0.1

0

0.1

0.2

1985 1990 1995 2000

Birth Year

Bre

ed

ing

Va

lue Ayrshire

Brwn Sws

Guernsey

Holstein

Jersey

Mlk Shrtn


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Productive LifeProductive LifeGenetic trend on all-breed baseGenetic trend on all-breed base

-20

-15

-10

-5

0

5

1960 1970 1980 1990 2000

Birth Year

Bre

ed

ing

Va

lue Ayrshire

Brwn Sws

Guernsey

Holstein

Jersey

Mlk Shrtn


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Daughter Pregnancy RateDaughter Pregnancy RateGenetic trend on all-breed baseGenetic trend on all-breed base

-1012345678

1960 1970 1980 1990 2000

Birth Year

Bre

ed

ing

Va

lue Ayrshire

Brwn Sws

Guernsey

Holstein

Jersey

Mlk Shrtn


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EBV differences from Holstein EBV differences from Holstein estimated from an all-breed modelestimated from an all-breed model

Difference from Holstein (pounds)

Milk Fat Protein

AY -5269 -134 -130

BS -4213 -79 -71

GU -6120 -82 -137

JE -6530 -75 -104

MS -7121 -245 -198


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Phenotypic breed differences from Phenotypic breed differences from Holstein from an all-breed modelHolstein from an all-breed model

Difference from Holstein (pounds)

Milk Fat Protein

AY -6587 -207 -176

BS -4555 -97 -82

GU -7286 -143 -179

JE -6956 -99 -119

MS -8419 -320 -240

HO 23104 842 694


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EBV differences from Holstein EBV differences from Holstein estimated from an all-breed modelestimated from an all-breed model

Difference from Holstein

SCS PL (mo) DPR (%)

AY -0.16 0.3 2.4

BS -0.10 0.8 1.1

GU 0.07 -8.5 0.8

JE 0.19 3.2 5.5

MS -0.07 -2.2 4.5


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Phenotypic breed differences from Phenotypic breed differences from Holstein from an all-breed modelHolstein from an all-breed model

Difference from Holstein

SCS PL (mo) DPR

AY -0.11 3.3 0.8

BS -0.15 1.9 -0.6

GU 0.29 -1.3 -1.1

JE 0.26 4.9 5.0

MS 0.12 1.5 3.3

HO 3.07 28.1 25.5


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Net Merit Relative EmphasisNet Merit Relative EmphasisIn cooperation with Dr. Tony Seykora et al.In cooperation with Dr. Tony Seykora et al.

Trait 2003 2006 Trait 2003 2006

Protein 33 23 Udder 7 6

Fat 22 23 F&L 4 3

Milk 0 0 Size 3 4

PL 11 17 DPR 7 9

SCS 9 9 CA$ 4 6

DPR = daughter pregnancy rate (fertility), CA$ is index of calving ease and stillbirth


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NM$, FM$, CM$ Economic ValuesNM$, FM$, CM$ Economic Values

NM$ FM$ CM$

Milk 0.00 0.11 −0.07

Fat 2.70 2.70 2.70

Protein 3.55 0.00 5.73

Other values are same in each index:

PL 29, SCS -150, Size -14, Udder 28, F&L 13, DPR 21, CA$ 1


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Other Trait EstimatesOther Trait Estimates Calving ease and stillbirth estimated

from breed means• 7.3 million HO, 37000 JE, 17000 BS,

2000 GU, 2000 AY, 300 MS

Body size composite estimated from mature weight

Udder composite, Feet / Leg composite extrapolated from regressions on other traits within Holsteins• Size, PL, milk, DPR, SCS


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Correlations used in PredictionsCorrelations used in Predictions

Corr with Size PL SCS DPR Milk

Udder .26 .30 −.33 .03 −.20

F&L .22 .19 −.02 −.04 −.02

Canada now scores linear conformation traits of all breeds on the same scale


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Assumed Effects – Other TraitsAssumed Effects – Other TraitsTransmitting ability differences from HolsteinTransmitting ability differences from Holstein

Size Udder F&LCalving Difficulty

Still-birth

Jersey −10.4 −1.4 −2.1 −7.1 −1.5

B. Swiss 0.0 0.7 0.3 −3.2 −0.7

Guernsey −7.3 −0.5 −1.3 −4.6 1.1

Ayrshire −5.8 −1.6 −0.9 −3.5 −1.2

M. Short. −4.2 0.1 −0.6 −0.1 −2.4

Heterosis 0.9 0.0 0.0 0.0 0.0


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Merit of FMerit of F11 Holstein Crossbreds Holstein Crossbreds

Second Breed NM$ CM$ FM$

Ayrshire −304 −261 −364

Brown Swiss 55 139 −78

Guernsey −408 −405 −503

Jersey 31 153 −158

M. Shorthorn −498 −461 −547

Compared to 2005 genetic base for Holstein


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Later Generation CrossesLater Generation Crosses

Holstein backcross or

multi-breed NM$ CM$ FM$

HO x (BS x HO) +28 +70 −39

HO x (JE x HO) +16 +77 −79

BS x (JE x HO) −32 +109 −251

JE x (BS x HO) −44 +116 −292

HO x (BS x JE) +44 +147 −118

Compared to 2005 genetic base for Holstein


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Butterfat yield of three breed crosses was greater than from their F1 crossbred dams.

Three breed crosses averaged 14,927 pounds of milk and 641 pounds of butterfat as 2-year-olds in 1947.

USDA Yearbook of Agriculture 1947Three-Breed CrossesThree-Breed Crosses


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Scandinavian and French BreedsScandinavian and French Breeds

AIPL has pedigree records for other breeds (NR, SR, MO); but few production records yet

For further information:• Interbull conversions to Ayrshire

base• U. Minnesota scientists (Heins et al.)


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ConclusionsConclusions


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Conclusions (1)Conclusions (1)

All-breed model accounts for:• Breed effects and general heterosis• Unequal variances within breed

May 2007 implementation expected• PTA converted back to within-breed

bases, crossbreds to breed of sire• PTA changes larger in breeds with

fewer animals


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Breed effects were estimated• Yield, PL, SCS, DPR by all-breed model• Calving ease and stillbirth breed means• Udder, F&L composites from other traits

Lifetime Net Merit formula for August 2006 applied

Holsteins still superior for FM$


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BS x HO and JE x HO crosses had higher NM$ and CM$ than HO

BS x JE had higher CM$ than HO

Three-breed crosses (HO, BS, JE) are higher than HO backcrosses for CM$, similar for NM$

Use best bulls within each breed


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AcknowledgmentsAcknowledgments

Several others at AIPL contributed greatly to this project, including Mel Tooker, George Wiggans, John Cole, Jay Megonigal, and Ashley Sanders

Genetic evaluation using combined data from all breeds and crossbred cows

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