If all individuals belong to one genetic group, then use 0 as the identity of the parents of base individuals. However, if base individuals belong to various genetic groups this is indicated by the!GROUPSqualifier and the pedigree file must begin by identifying these groups. All base individuals should have group identifiers as parents. In this case the identity 0will only appear on the group identity lines, as in the following example where three sire lines are fitted as genetic groups.
Genetic group example animal !P sire 9 !A dam lines 2 damage adailygain
harveyg.ped !ALPHA !MAKE !GROUP 3 harvey.dat adailygain ∼ mu !r animal 02.5 !GU G1 0 0 G2 0 0 G3 0 0 SIRE 1 G1 G1 SIRE 2 G1 G1 SIRE 3 G1 G1 SIRE 4 G2 G2 SIRE 5 G2 G2 SIRE 6 G3 G3 SIRE 7 G3 G3 SIRE 8 G3 G3 SIRE 9 G3 G3 101 SIRE 1 G1 102 SIRE 1 G1 103 SIRE 1 G1 . . . 163 SIRE 9 G3 164 SIRE 9 G3 165 SIRE 9 G3
It is usually appropriate to allocate a genetic group identifier where the parent
Important
is unknown.
Table 9.1: List of pedigree file qualifiers
qualifier description
!ALPHA indicates that the identities are alphanumeric with up to 225 characters;
otherwise by default they are numeric whole numbers < 200,000,000. If
using long alphabetic identities, use!SLNFORMto see the full identity in the
.slnfile.
!DIAG causes the pedigree identifiers, the diagonal elements of the Inverse of the Relationship and the inbreeding coefficients for the individuals (calculated
9 Command file: Genetic analysis 169
List of pedigree file qualifiers
qualifier description
!FGEN [f]
ASReml3
indicates the pedigree file contains a fourth field indicating the level of selfing or the level of inbreeding in a base individual. In the fourth field, 0 indicates a simple cross, 1 indicates selfed once, 2 indicates selfed twice, etc.. A value between 0 and 1 for a base individual is taken as its inbreeding value. If the pedigree has implicit individuals (they appear as parents but not in the first field of the pedigree file), they will be assumed base non-
inbred individuals unless their inbreeding level is set with !FGEN f where
0< f <1 is the inbreeding level of such individuals.
!GIV instructs ASRemlto write out the A-inverse in the format of.giv files. If
!GROUPSis also specified, this.givfile will include the!GROUPSDFqualifier on its first line.
!GOFFSET o
ASReml3
An alternative to group constraints (see !GROUP below) is to shrink the
group effects by adding the constanto (>0) to the diagonal elements of
A−1pertaining to groups. When a constant is added, no adjustment of the
degrees of freedom is made for genetic groups.
Use!GOFFSET -1to add no offset but to suppress insertion of constraints where empty groups appear. The empty groups are then not counted in the DF adjustment.
!GROUPS g includes genetic groups in the pedigree. The first g lines of the pedigree identify genetic groups (with zero in both the sire and dam fields). All other lines must specify one of the genetic groups as sire or dam if the actual parent is unknown.
You may insert Groups with no members to define constraints on groups, that is to associate groups into supergroups where the supergroup fixed ef- fect is formally fitted separately in the model. A constraint is added to the inverse which causes the preceding set of groups which have members to have effects which sum to zero. The issue is to get the degrees of freedom correct and to get the correct calculation of the Likelihood, especially in bivariate cases where DF associated with groups may differ between traits. The!LASTqualifier (see page 85) is designed to help as without it, reorder-
ing may associate singularities in theAmatrix with random effects which
at the very least is confusing. When theAmatrix incorporates fixed effects,
the number of DF involved may not be obvious, especially if there is also a sparsely fitted fixed HYS factor. The number of Fixed effects (degrees of freedom) associated with GROUPS is taken as the declared number less twice the number of constraints applied. This assumes all groups are rep- resented in the data, and that degrees of freedom associated with group constraints will be fitted elsewhere in the model.
!INBRED
ASReml2
generates pedigree for inbred lines. Each cross is assumed to be selfed several times to stabilize as an inbred line as is usual for cereals such as wheat, before being evaluated or crossed with another line. Since inbreeding is usually associated with strong selection, it is not obvious that a pedigree assumption of covariance of 0.5 between parent and offspring actually holds.
9 Command file: Genetic analysis 170
List of pedigree file qualifiers
qualifier description
!LONGINTEGER
ASReml3
indicates the identifiers are numeric integer with less than 16 digits. The de- fault is integer values with less than 9 digits. The alternative is alphanmeric
identifiers with up to 255 character indicated by!ALPHA.
!MAKE tells ASReml to make theA-inverse(rather than trying to retrieve it from theainverse.binfile).
!MEUWISSEN
ASReml3
The default method for formingA−1is based on the algorithm of Meuwissen
and Luo (1992).
!MGS indicates that the third identity is the sire of the dam rather than the dam.
!QUAAS
ASReml3
The original routine for calculating A−1 inASReml was based on Quaas
(1976)
!REPEAT tells ASReml to ignore repeat occurrences of lines in the pedigree file.
Warning Use of this option will avoid the check that animals occur in chronological order, but chronological order is still required.
!SARGOLZAEI
ASReml3
an alternative procedure for computing A−1 was developed by Sargolzaei
et al.(2005).
!SELF s ASReml2
allows partial selfing when third field is unknown. It indicates that progeny from a cross where the second parent (male parent) is unknown, is assumed
to be from selfing with probabilitysand from outcrossing with probability
(1−s). This is appropriate in some forestry tree breeding studies where
seed collected from a tree may have been pollinated by the mother tree or pollinated by some other tree (Dutkowski and Gilmour, 2001). Do not use the!SELFqualifier with the!INBREDor!MGSqualifiers.
!SKIP n allows you to skipnheader lines at the top of the file.
!SORT
ASReml2
causes ASRemlto sort the pedigree into an acceptable order, that is par-
ents before offspring, before forming the A-Inverse. The sorted pedigree is
written to a file whose name has.srtappended to its name.
!XLINK
ASReml3
requests the formation of the (inverse) relationship matrix for the X chro- mosome as described by Fernando and Grossman (1990) for species where the male is XY and the female is XX. This NRM inverse matrix is formed
in addition to the usualA−1and can be accessed asGIV1or as specified in
the output. The pedigree must include a fourth field which codes the SEX of the individual. The actual code used is up to the user and deduced from the first line which is assumed to be a male. Thus, whatever string is found in the fourth field on the first line of the pedigree is taken to mean MALE and any other code found on other records is taken to mean FEMALE.
9 Command file: Genetic analysis 171