You are on page 1of 28

Lecture 14

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

Genetic (Cytoplasmic DNA)


Transmitted along maternal lines

Permanent Environmental
Non inherited maternal effects
Mastitis
Other maternal infection
Maternal Injuries (Damaged teats)

Lecture 14

Maternal Genetic Effects


yijkmn = ( HY ) i + S j + Dk + M n + eijkmn
Herd Year

Sex

Maternal
Direct
Genetic Genetic

Fixed Effects

Lecture 14

Random
error

Random Effects

Maternal Genetic Effects


y = Xb + Z1d + Z 2m + e
Maternal Genetic

Direct effect

A d
d

V m = A d ,m
e 0

There is a genetic correlation


between the animals direct
and maternal genetic effect

A d ,m
2
A m
0

0
2
I e

No
environmental
correlations

The are inherited and


determined by additive
effects in the mother
Lecture 14

Maternal Effects Example


Schaeffer Table 8.7
Animal

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

The effect of a good or bad mother is


reflected in the performance of the
offspring

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

Animal 1 was the mother of animals 7, 5, 10

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

k12 2000 300


3.3766 .8441
=
6500 =

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

Note that it is possible to estimate a maternal genetic effects for males.


Why?
Lecture 14

13

What to do with the estimates in a


breeding program
Selection Index (to be covered later)
Give a weight to each effect and combine in
an index

I i = w1ai + w2 m i
Weights are dependent on the economic impact of each trait on
overall profits

Lecture 14

14

Lab Problem 14.1


D

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

The effect of a good or bad mother is


reflected in the performance of the
offspring

Lecture 14

17

Model Cytoplasmic Effects


yijkmn = ( HY ) i + S j + Dk + M n + eijkmn
Herd Year

Sex

Direct Cytoplasmic
Genetic

Fixed Effects

Lecture 14

Random
error

Random Effects

18

Cytoplasmic Effects Mixed Model


y = Xb + Z1d + Z 2c + e
Cytoplasmic

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

Animal 1 was the mother lineage of animals 7, 5, 10, 12

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

What to do with the estimates in a


breeding program
Selection Index
Give a weight to each effect and combine in
an index

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

Lab Problem 14.2


D

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

You might also like