Documenti di Didattica
Documenti di Professioni
Documenti di Cultura
Maternal Effects-Inherited
Reference: Lynch and Walsh Ch 23
Schaeffer, LR Linear Models and Computing
Strategies in Animal Breeding
Lecture 14
Maternal Effects
Maternal
Genetic (Nuclear DNA)
Mendelian Segregation
Inherited maternal effects
Milking ability
Mothering ability
Permanent Environmental
Non inherited maternal effects
Mastitis
Other maternal infection
Maternal Injuries (Damaged teats)
Lecture 14
Sex
Maternal
Direct
Genetic Genetic
Fixed Effects
Lecture 14
Random
error
Random Effects
Direct effect
A d
d
V m = A d ,m
e 0
A d ,m
2
A m
0
0
2
I e
No
environmental
correlations
Sire
Dam
Year
Sex
Wean Wt
7
4
8
5
9
6
10
11
12
13
14
14
15
15
14
15
15
16
16
16
1
2
3
1
2
4
1
4
5
6
86
86
86
87
87
87
88
88
88
88
M
F
M
F
M
F
M
F
M
F
400
380
410
350
420
360
390
390
430
370
Lecture 14
Pedigree
16
11
13
14
12
15
10
Lecture 14
Year sex
86 87 88 m
1
1
0
0
X=
0
0
0
0
0 0 1
0 0 0
0 0 1
1 0 0
1 0 1
1 0 0
0 1 1
0 1 0
0 1 1
0 1 0
b1
b
B = 2
b3
b4
Lecture 14
Herd
Year
Sex
400
380
410
350
420
Y=
360
390
390
430
370
Animal
An
Sire
Dam
14
14
15
15
14
15
10
15
11
16
12
16
13
16
14 1
0
0
0
0
Z1 =
0
0
0
0
2 15 3 16 7 4
8 5 9
6 10 11 12 13
0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
Lecture 14
An
Sire
Dam
14
14
15
15
14
15
10
15
11
16
12
16
13
16
14 1
0
0
0
0
Z2 =
0
0
0
0
1
0
0
1
2 15 3 16 7 4
8 5 9
6 10 11 12 13
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 0 0 0 0 0 0 0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Lecture 14
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
9
MME
X' Z1
X' X
Z ' X Z ' Z + A 1k
1 1
11
1
Z '2 X Z '2 Z1 + A 1k 21
k11
k
21
k11
k
21
'
X' Z 2
b X y
'
'
1
Z1 Z 2 + A k 12 a = Z1 y
Z '2 y
Z '2 Z 2 + A 1k 22 m
k12
dm 2
=
e
2
k 22 dm m
2
d
k 22 300 1200
.
8441
5
.
6288
Lecture 14
10
proc iml;
start main;
y={400,
380,
410,
350,
420,
360,
390,
390,
430,
370};
X={1 0 0 1,
1 0 0 0,
1 0 0 1,
0 1 0 0,
0 1 0 1,
0 1 0 0,
0 0 1 1,
0 0 1 0,
0 0 1 1,
0 0 1 0};
Z1={0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Z2={ 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
1
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Lecture 14
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
1
0
1
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0,
0,
0,
0,
0,
0,
0,
0,
0,
1};
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0,
0,
0,
0,
0,
0,
0,
0,
0,
0};
11
Ainv={2.5 .5 1 0
.5 2.5 0 1
1 0 2 0
0 1 0 3
0 0 0 .5
0 0 0 0
-1 -1 0 0
-1 0 -1 .5
0 0 0 -1
0 -1 0 -1
-1 0 -1 0
0 0 0 -1
0 -1 0 -1
0 0 0 0
0 0 0 0
0 0 0 0
0 0 -1 -1
0 0 -1 0
0 0 0 -1
.5 0 0 .5
1.5 0 0 0
0 2.5 0 .5
0 0 2 0
0 .5 0 3
-1 0 0 0
0 .5 0 0
0 0 0 0
0 .5 0 -1
0 0 0 0
0 -1 0 -1
0 -1 0 0
0 -1 0 0
0 0
0 -1
0 0
-1 -1
-1 0
0 .5
0 0
0 0
2 0
0 2.5
0 0
0 0
0 0
0 0
0 -1
0 0
-1 0 0 0 0 0,
0 0 -1 0 0 0,
-1 0 0 0 0 0,
0 -1 -1 0 0 0,
0 0 0 0 0 0,
0 .5 0 -1 -1 -1,
0 0 0 0 0 0,
0 -1 0 -1 0 0,
0 0 0 0 0 0,
0 0 0 0 -1 0,
2 0 0 0 0 0,
0 2.5 0 0 0 -1,
0 0 2 0 0 0,
0 0 0 2 0 0,
0 0 0 0 2 0,
0 -1 0 0 0 2};
K11=3.3766;K12=.8441;K21=.8441;K22=5.6288;
LHS=((X`*X)||(X`*Z1)||(X`*Z2))
//((Z1`*X)||(Z1`*Z1+AINV#K11)||(Z1`*Z2+AINV#K12))
//((Z2`*X)||(Z2`*Z1+AINV#K21)||(Z2`*Z2+AINV#K22));
RHS=(X`*Y)//(Z1`*Y)//(Z2`*Y);
C=INV(LHS);
BU=C*RHS;
print BU ;
finish main;run;quit;
Lecture 14
12
Sex
0.09
-3.65
2.68
1.16
0.10
-0.38
-1.64
1.55
0.61
-0.09
1.16
1.00
-0.85
0.36
-0.52
0.43
Animal
14 1 2 15 3 16 7 4 8 5 9 6 10 1112 13
Year
1.567
-2.43
1.79
-3.57
0.07
2.58
-1.34
2.67
-1.65
-3.28
3.15
-1.26
-5.59
4.13
1.56
-0.16
14 1 2 15 3 16 7 4 8 5 9 6 10 1112 13
369.40
363.10
374.56
41.48
Animal
13
I i = w1ai + w2 m i
Weights are dependent on the economic impact of each trait on
overall profits
Lecture 14
14
C 4
B 13
A 9
E 11
12
F 11
H 9
13
10
3
4
Find the best estimate of the environmental trend, genetic worth of each animal,
Maternal Genetic Effect (males are in boxes), assume error variance as
previously estimated in 6.2a and
e2
=1
2
a
Lecture 14
e2
= .5
2
m
a ,m
= .25
2
e
15
Cytoplasmic Effects
Follows Maternal Lines Only
Lecture 14
16
Pedigree
16
11
13
14
12
15
10
Lecture 14
17
Sex
Direct Cytoplasmic
Genetic
Fixed Effects
Lecture 14
Random
error
Random Effects
18
Direct effect
d A d
V m = 0
e 0
0
I
2
m
Lecture 14
0
2
I e
Assumes no
cytoplasmic
nuclear gene
interaction
19
Year sex
86 87 88 m
1
1
0
0
X=
0
0
0
0
0 0 1
0 0 0
0 0 1
1 0 0
1 0 1
1 0 0
0 1 1
0 1 0
0 1 1
0 1 0
b1
b
B = 2
b3
b4
Lecture 14
Herd
Year
Sex
400
380
410
350
420
Y=
360
390
390
430
370
20
Animal
An
Sire
Dam
14
14
15
15
14
15
10
15
11
16
12
16
13
16
14 1
0
0
0
0
Z1 =
0
0
0
0
2 15 3 16 7 4
8 5 9
6 10 11 12 13
0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
Lecture 14
21
Cytoplasmic
An
Sire
Dam
14
14
15
15
14
15
10
15
11
16
12
16
13
16
1
0
1
0
Z2 =
0
1
0
1
0
1
0
0
0
0
1
0
0
0
0
0
0
1
1
0
1
0
1
Maternal Lineages
Lecture 14
22
MME
X' Z1
X' X
Z ' X Z ' Z + A 1 k
11
1 1
1
Z '2 X
Z '2 Z1
k11
k
21
k11
k
21
'
b X y
a = Z ' y
1
Z '2 Z 2 + Ik 22 c Z '2 y
X' Z 2
Z1' Z 2
k12 d2 0 2
=
=
k 22 0 c2
0
e2
d2
2
e
2
c
1 0 0
I = 0 1 0
0 0 0
k12 2000
0
0
3.25
=
6500 =
k 22 0
1200
0
5
.
42
Lecture 14
23
proc iml;
start main;
y={400,
380,
410,
350,
420,
360,
390,
390,
430,
370};
X={1 0 0 1,
1 0 0 0,
1 0 0 1,
0 1 0 0,
0 1 0 1,
0 1 0 0,
0 0 1 1,
0 0 1 0,
0 0 1 1,
0 0 1 0};
Z1={0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Z2={ 1
0
0
1
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0,
0,
1,
0,
0,
0,
0,
0,
0,
0};
Lecture 14
0
0
1
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
1
0
0,
0,
0,
0,
0,
0,
0,
0,
0,
1};
I={1 0 0,
0 1 0,
0 0 1};
24
Ainv={2.5 .5 1 0
.5 2.5 0 1
1 0 2 0
0 1 0 3
0 0 0 .5
0 0 0 0
-1 -1 0 0
-1 0 -1 .5
0 0 0 -1
0 -1 0 -1
-1 0 -1 0
0 0 0 -1
0 -1 0 -1
0 0 0 0
0 0 0 0
0 0 0 0
0 0 -1 -1
0 0 -1 0
0 0 0 -1
.5 0 0 .5
1.5 0 0 0
0 2.5 0 .5
0 0 2 0
0 .5 0 3
-1 0 0 0
0 .5 0 0
0 0 0 0
0 .5 0 -1
0 0 0 0
0 -1 0 -1
0 -1 0 0
0 -1 0 0
0 0
0 -1
0 0
-1 -1
-1 0
0 .5
0 0
0 0
2 0
0 2.5
0 0
0 0
0 0
0 0
0 -1
0 0
-1 0 0 0 0 0,
0 0 -1 0 0 0,
-1 0 0 0 0 0,
0 -1 -1 0 0 0,
0 0 0 0 0 0,
0 .5 0 -1 -1 -1,
0 0 0 0 0 0,
0 -1 0 -1 0 0,
0 0 0 0 0 0,
0 0 0 0 -1 0,
2 0 0 0 0 0,
0 2.5 0 0 0 -1,
0 0 2 0 0 0,
0 0 0 2 0 0,
0 0 0 0 2 0,
0 -1 0 0 0 2};
K11=3.25;K12=0;K21=0;K22=5.42;
LHS=((X`*X)||(X`*Z1)||(X`*Z2))
//((Z1`*X)||(Z1`*Z1+AINV#K11)||(Z1`*Z2))
//((Z2`*X)||(Z2`*Z1)||(Z2`*Z2+I#K22));
RHS=(X`*Y)//(Z1`*Y)//(Z2`*Y);
C=INV(LHS);
BU=C*RHS;
RMSE=(Y`*Y-BU`*RHS)#(1/6);
print BU RMSE;
finish main;run;quit;Lecture 14
25
B
Year
Sex
1.55
-3.45
2.53
-3.40
0.06
2.70
-1.92
3.17
-1.60
-3.20
3.44
-1.10
6.12
4.37
1.95
-0.14
14 1 2 15 3 16 7 4 8 5 9 6 10 1112 13
368.15
361.75
373.55
42.94
Animal
Lecture 14
Animal
-2.81
2.73
0.08
1 2 3
26
I i = w1ai + w2 ci
Weights are dependent on the economic impact of each trait on
overall profits.
Economic impact of cytoplasmic effect changes with the time
horizon. Over a large number of generation could be a very
substantial effect
Lecture 14
27
C 4
B 13
A 9
E 11
12
F 11
H 9
13
10
3
4
Find the best estimate of the environmental trend, genetic worth of each animal,
and cytogenetic effects. Assume error variance as previously estimated in 6.2a
and
e2
=1
2
a
e2
= .5
2
c
Lecture 14
28