Page 301 - Linear Models for the Prediction of Animal Breeding Values 3rd Edition

DATA ARRANGEMENT
The pedigree file is set up as described in Section 17.4.1 but only for animals that are
parents. The pedigree file for the example data is:

Animal Code Sire or progeny Dam or mate
1 1 0 0
1 2 5 2
1 2 9 6
2 1 0 0
2 2 5 1
2 2 6 3
3 1 0 0
3 2 6 2
3 2 8 5
4 1 0 0
4 2 7 6
5 1 1 2
5 2 8 3
6 1 3 2
6 2 7 4
6 2 9 1
7 1 4 6
8 1 3 5
9 1 1 6
A data file is set up consisting of a code to identify parents and non-parents. For
non-parents, one record is set up for each parent, comprising the parent, a code indicat-
ing it is a non-parent, the animal that has the yield record, the other parent (mate), the
sire and dam of the animal with the yield record, fixed effects, covariates (if any) and
traits. A single record is set up for parents, comprising the animal, a code indicating it is
a parent, the animal again, a field set to zero corresponding to the column for the other
parent in non-parents’ records, the sire and dam of the animal, fixed effects, covariates
(if any) and traits. The data file may be sorted in three sequences if there is a major fixed
effect in the model: sorted by major fixed effect, such as HYS (file A); sorted by animal
(file B); and third sorted by dam code (file C). For the example, file A is:

Parent/ Birth
animal Code a Animal Mate Sire Dam Herd Sex weight (kg)

5 0 5 0 1 2 1 Male 35.0
6 0 6 0 3 2 1 Female 20.0
7 0 7 0 4 6 1 Female 25.0
8 0 8 0 3 5 1 Male 40.0
9 0 9 0 1 6 2 Male 42.0
3 1 10 2 3 2 2 Female 22.0
2 1 10 3 3 2 2 Female 22.0
3 1 11 7 3 7 2 Female 35.0
7 1 11 3 3 7 2 Female 35.0
8 1 12 7 8 7 3 Female 34.0
Continued

Solving Linear Equations 285