genetic evaluation using combined data from all breeds and crossbred cows
DESCRIPTION
Genetic evaluation using combined data from all breeds and crossbred cows. Jersey Holstein. USDA Yearbook of Agriculture 1947. From USDA research herd at Beltsville, MD. Red Dane Jersey. USDA Yearbook of Agriculture 1947. - PowerPoint PPT PresentationTRANSCRIPT
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
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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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Conclusions (2)Conclusions (2)
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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Conclusions (3)Conclusions (3)
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