Transcript Document 7729587

Update on Inbreeding, Herd by
Sire Effects, and New Traits
Paul VanRaden, John Cole, Duane Norman, Mel
Tooker, and Jan Wright
Animal Improvement Programs Laboratory
Agricultural Research Service, USDA, Beltsville, MD
[email protected]
2005
Topics

Inbreeding adjustments

Herd by sire interaction variance

PTA’s for potential traits of interest
•
•
•
•
•

Maturity (lactations 1-3 before 1999, animal model)
Persistency (13 mil records, animal model)
Age at 1st calf (1.1 mil records, 5109 sires)
Gestation length (1.2 mil records, 3451 sires)
Milking speed (survey of AI company PTA’s)
Definition of productive life
2005
NAAB DSEC 2005 (2)
VanRaden, Cole, Norman, Tooker, Wright
Expected and Actual Inbreeding
1998
Dtrs
2005
Dtrs
1998
Dtr F
2005
Dtr F
1998
EFI
2005
EFI
Winchester
59
27744
2.9
4.1
4.2
5.1
Fred
63
24332
3.2
5.4
7.0
6.6
Rubytom
52
20762
3.3
4.6
5.2
4.9
Jolt
50
18310
3.5
5.0
5.8
5.8
Zebo
55
18115
2.8
3.2
3.7
3.8
Marty
54
17628
4.4
5.2
6.2
6.1
Top 100 Avg
63
8220
3.2
4.4
5.2
5.3
Bull
2005
NAAB DSEC 2005 (3)
VanRaden, Cole, Norman, Tooker, Wright
Elite Cows

Nov 2004 compared to March 2005
•
•
•
•
Cow F increased from 5.0% to 5.2%
Cow EFI decreased from 5.5% to 5.4
Sample cow EFI = 5.0% for 600 Holsteins
Base EFI (cows born in 2000)
–
–
–

4.7% +- .6% for Holsteins
5.7% +- 1.0% for Brown Swiss
6.7% +- 1.4% for Jerseys
EFI in selection and mating programs
2005
NAAB DSEC 2005 (4)
VanRaden, Cole, Norman, Tooker, Wright
Inbreeding of US Daughters
(Proven Holstein bulls born since 1994)
Bull Origin
USA
Canada
Netherlands
France
Great Britain
Italy
Denmark
Bulls
8941
355
39
25
8
6
6
Pedigree
Compl. Dtr F
99.9
4.2
99.5
4.3
99.9
4.3
99.4
4.5
99.5
4.5
98.0
4.7
100.0
4.4
EFI
5.1
5.0
4.8
4.7
5.1
5.1
5.6
2005
NAAB DSEC 2005 (5)
VanRaden, Cole, Norman, Tooker, Wright
Inbreeding Math

Subtract regression (b) from y
•
•

Add expected future inbreeding (EFI)
•
•
•

YD0 = y - m - p - c - b (Fcow)
DYD0 = Σ w (YD0 - mate PTA0) / Σ w
PTAEFI = PTA0 + b (EFI - EFIbase)
PAEFI = PA0 + b (EFI - EFIbase)
DYDEFI = DYD0 + b (EFI - EFIbase)
Account for F in w and in reliability?
2005
NAAB DSEC 2005 (6)
VanRaden, Cole, Norman, Tooker, Wright
Interactions for Famous Old Bulls
(Milk pounds, from VanRaden et al 1992 JDS 75:2892)
Mars
Tony
Bell Elevation Astronaut
Mars Tony
-1430
+79
-871
Bell
+79
-1371
+97
Elevation
-871
+97
-1560
+174
+344
Astronaut
+26
-88
+174
-1250
-400
MGS effect
+442
+857
+172
-200
Bull
+26
Sire
effect
+884
-88 +1714
2005
NAAB DSEC 2005 (7)
VanRaden, Cole, Norman, Tooker, Wright
Number of Cows per Interaction
(from VanRaden et al 1992 JDS 75:2892)
Mars
Tony
Bull
Mars Tony
Bell
18
Bell Elevation Astronaut
811
167
634
13
1997
351
34
4215
Elevation
Astronaut
(half stored)
35
2005
NAAB DSEC 2005 (8)
VanRaden, Cole, Norman, Tooker, Wright
Herd × Sire Var: Daughters / Herd
Effective Daughters
14
5% H×S
12
10
7% H×S
8
10% H×S
6
4
2
0
0
5
10
15
20
25
30
35
40
45
50
Actual Daughters
2005
NAAB DSEC 2005 (9)
VanRaden, Cole, Norman, Tooker, Wright
Maximum Daughters / Herd
Trait
h2
c2
p2
Maximum
Yield
30
10
15
9
(new)
30
7
18
12
DPR
4
1
8
98
(new)
4
4
5
25
PL
8
5
0
19
SCS
12
5
18
19
h2 = heritability, c2 = herd by sire interaction, p2 = permanent environment variance
2005
NAAB DSEC 2005 (10)
VanRaden, Cole, Norman, Tooker, Wright
Age at First Calf: Best Bulls (99% R)
Age at 1st
calf (days)
-9
Avg. Age
(mo)
26
DPR
+0.8
Rudolph
-9
26
+2.1
Indy
-8
26
+0.1
Duster
-7
26
+2.2
Sand
-7
26
- 0.5
Spencer
-7
27
0.0
Top Gun
-7
27
+1.7
Bull
Merv
2005
NAAB DSEC 2005 (11)
VanRaden, Cole, Norman, Tooker, Wright
Age at First Calf: Worst Bulls (99% R)
Age at 1st
calf (days)
+9
Avg. Age
(mo)
27
DPR
+2.0
Marksman
+8
27
- 1.3
Skybuck
+8
27
+1.2
Activate
+7
27
- 2.7
Man
+7
27
- 2.0
Sandwater
+7
27
+1.6
Choice
+7
27
- 1.1
Bull
Raider
2005
NAAB DSEC 2005 (12)
VanRaden, Cole, Norman, Tooker, Wright
Longest Gestation Length
(as trait of daughters, 99% REL bulls)
Bull
Stylist
Gestation
Length
2.1
Sire
Daughter
C. Ease C. Ease
10
13
Dixie
1.9
8
9
Manager
1.8
8
11
Benefit
1.8
8
11
Mark Star
1.7
9
8
Caveman
1.7
9
10
Mandel
1.7
9
9
2005
NAAB DSEC 2005 (13)
VanRaden, Cole, Norman, Tooker, Wright
Shortest Gestation Length
(as trait of daughters, 99% REL bulls)
Bull
Echo
Gestation
Length
- 2.4
Sire
Daughter
C. Ease C. Ease
5
8
Script
- 2.3
7
7
Goliath
- 2.0
7
10
Magician
- 2.0
7
11
Elite
- 2.0
6
5
Wine
- 1.9
5
9
Billy
- 1.9
5
9
2005
NAAB DSEC 2005 (14)
VanRaden, Cole, Norman, Tooker, Wright
High Maturity PTA Bulls
(500 dtrs by 1999 and 5000 dtrs by 2005)
Bull
Langs
Milk Maturity
PTA 1,2,3 – 1
+619
PTA
Milk
+462
PTA
PL
1.1
Cash
+510
+16
2.8
Whamo
+395
-492
2.1
Black Jack
+372
-935
.6
Labelle
+372
+611
.8
Horton
+361
-492
-.9
Mich
+358
-605
.1
2005
NAAB DSEC 2005 (15)
VanRaden, Cole, Norman, Tooker, Wright
Low Maturity PTA Bulls
(500 dtrs by 1999 and 5000 dtrs by 2005)
Milk Maturity
PTA 1,2,3 – 1
-453
PTA
Milk
+27
PTA
PL
-1.1
Bellwood
-436
+1085
-.8
Mascot
-397
-179
-3.3
Mister Bova
-369
-32
+.6
Jackpot
-339
-529
-.9
Nick
-335
-586
-.1
Emory
-290
+497
+.1
Bull
Mason
2005
NAAB DSEC 2005 (16)
VanRaden, Cole, Norman, Tooker, Wright
PTA Persistency of
Top Net Merit Bulls (99% REL)
Bull
R Boone
Protein
Persistency
- .17
JC Fagan
NM$
522
DPR
- 0.5
+.14
426
+2.9
BW Marshall
- .23
425
- 2.0
Orion
- .18
404
+0.1
Addison
- .10
403
- 2.1
Mtoto
- .13
397
+0.9
Manfred
+.14
375
+2.0
2005
NAAB DSEC 2005 (17)
VanRaden, Cole, Norman, Tooker, Wright
Cow with Average Persistency
60
Pounds
50
40
30
Best Prediction
20
Standard Curve
10
Test Days
0
0
30
60
90
120 150 180 210 240 270 300
Days in Milk
2005
NAAB DSEC 2005 (18)
VanRaden, Cole, Norman, Tooker, Wright
Highest Cow Persistency
250
Best Prediction
Standard Curve
Test Days
Pounds
200
150
100
50
0
0
30
60
90
120 150 180 210 240 270 300
Days in Milk
2005
NAAB DSEC 2005 (19)
VanRaden, Cole, Norman, Tooker, Wright
Lowest Cow Persistency
250
Best Prediction
Standard Curve
Test Days
Pounds
200
150
100
50
0
0
30
60
90
120
150
180
210
240
270
300
Days in Milk
2005
NAAB DSEC 2005 (20)
VanRaden, Cole, Norman, Tooker, Wright
Milking Speed Survey

Current US AI evaluations
•
•
•
•

Select Sires: 1-9 scale
Genex CRI: 1-9 scale
Accelerated Genetics: 1-5 scale
Alta Genetics: actual time, 4.5 +- .2
Milking speed in foreign indexes
•
DNK 6%, AUS 3%, CAN <1%
2005
NAAB DSEC 2005 (21)
VanRaden, Cole, Norman, Tooker, Wright
Current PL Credits
140
Percent
Credit
120
100
80
60
1
40
2
3
20
0
0
1
2
3
4
5
YEARS
2005
NAAB DSEC 2005 (22)
VanRaden, Cole, Norman, Tooker, Wright
Possible PL Credits
140
Percent
Credit
120
100
80
60
1
40
2
3
20
0
0
1
2
3
4
5
YEARS
2005
NAAB DSEC 2005 (23)
VanRaden, Cole, Norman, Tooker, Wright
Proposed PL Credits
Month of Lactation
Lac
1
3
5
7
9
11
13
15
.80
.88
.89
.85
.80
.74
.68
.62
2
1.15 1.13 1.06
.96
.84
.73
.67
.60
3+
1.22 1.20 1.13 1.02
.89
.76
.69
.62
1
2005
NAAB DSEC 2005 (24)
VanRaden, Cole, Norman, Tooker, Wright
Productive Life Research

Upper limits on lactation length
and age can be removed

New projection factors derived

36 month PL vs final PL
•
•
Genetic correlation = .87
Genetic corr with protein .14 vs .00
–
–
–
Has declined rapidly in recent years
Phenotypic correlations are fairly stable
Adjustment for yield may be needed
2005
NAAB DSEC 2005 (25)
VanRaden, Cole, Norman, Tooker, Wright