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Mixed linear models with polygenic effects

Model

See the textbook for details.

Files and solutions for SNP-BLUP

First, we perform the SNP-BLUP analysis. The data file (mr117a.dat) is from the previous example, Example 11.1. We can use the same pedigree file as before (mr117.ped).

The parameter file contains 10 SNP effects and residual polygenic effects.

DATAFILE
mr117a.dat
NUMBER_OF_TRAITS
1
NUMBER_OF_EFFECTS
12
OBSERVATION(S)
6
WEIGHT(S)

EFFECTS:
 4  1 cross   # general mean
 1 26 cross   # residual polygenic effects
 7  1 cov     # SNP effect 1
 8  1 cov     # SNP effect 2
 9  1 cov     # SNP effect 3
10  1 cov     # SNP effect 4
11  1 cov     # SNP effect 5
12  1 cov     # SNP effect 6
13  1 cov     # SNP effect 7
14  1 cov     # SNP effect 8
15  1 cov     # SNP effect 9
16  1 cov     # SNP effect 10
RANDOM_RESIDUAL VALUES
245.0
RANDOM_GROUP  # polygenic effect
2
RANDOM_TYPE
add_animal
FILE
mr117.ped
(CO)VARIANCES
3.5241
RANDOM_GROUP  # jointly considering independent 10 SNP effects
3 4 5 6 7 8 9 10 11 12
RANDOM_TYPE
diagonal
FILE

(CO)VARIANCES
8.9636 0 0 0 0 0 0 0 0 0
0 8.9636 0 0 0 0 0 0 0 0
0 0 8.9636 0 0 0 0 0 0 0
0 0 0 8.9636 0 0 0 0 0 0
0 0 0 0 8.9636 0 0 0 0 0
0 0 0 0 0 8.9636 0 0 0 0
0 0 0 0 0 0 8.9636 0 0 0
0 0 0 0 0 0 0 8.9636 0 0
0 0 0 0 0 0 0 0 8.9636 0
0 0 0 0 0 0 0 0 0 8.9636
OPTION solv_method FSPAK

You can check the solutions against the reference values in the textbook (pp. 199–200).

Files and solutions for GBLUP

The author has already prepared a text file for \(\mathbf{G}^{-1}\). The animal codes in the file are aligned with the original animal codes; therefore, you do not need to use any tricks with PREGSF90.

The data file (mr117b.dat) is the same as the previous one, except that the marker covariates have been removed. The pedigree file (mr117.ped) is the same as the one used for SNP-BLUP.

The parameter file is shown below.

DATAFILE
mr117b.dat
NUMBER_OF_TRAITS
1
NUMBER_OF_EFFECTS
3
OBSERVATION(S)
6
WEIGHT(S)

EFFECTS:
4  1 cross
1 26 cross
1 26 cross
RANDOM_RESIDUAL VALUES
245.0
RANDOM_GROUP
2
RANDOM_TYPE
add_animal
FILE
mr117.ped
(CO)VARIANCES
3.5241
RANDOM_GROUP
3
RANDOM_TYPE
user_file
FILE
mr117b.Gi
(CO)VARIANCES
31.717
OPTION solv_method FSPAK

The solutions can be obtained by running BLUPF90+.

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