!FGEN [f]
indicates the individuals in the pedigree are inbred to some degree.
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| ltf | lt1 is the inbreeding level of such individuals.
!GIV
or
!SAVE
instructs ASReml to write out the A-inverse in the format of
.giv
files.
!Goffset o
An alternative to group constraints
(see !GROUP below) is to shrink the group effects by
adding the constant o (gt0.0)
to the diagonal elements of A inverse pertaining to groups.
When a constant is added, no adjustment of the degrees of freedom is made for
genetic groups. Typically, o is small as it represents genetic variance relative to group variance.
Use !Goffset -1 to 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 effect 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
!LAST qualifier
is designed to help as without it, reordering
may associate singularities in the A matrix with random effects
which at the very least is confusing. When the A matrix 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 represented in the data, and that
degrees of freedom associated with group constraints will
be fitted elsewhere in the model.
!INBRED
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, 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.
Do not use the
!INBRED
qualifier with the
!MGS
or
!SELF
qualifiers.
!LONGINTEGER
indicates the identifiers are numeric integer with less than 16 digits. The default is
integer values with less than 9 digits.
The alternative is alphanmeric identifiers with
up to 20 character indicated by !ALPHA.
!MAKE
tells ASReml to make the
A-inverse
(rather than trying to retrieve it from the
ainverse.bin
file).
!MGS
indicates that the third identity is the sire of the dam rather than the dam.
!MEUWISSEN
The default method for forming A inverse is based on the algorithm of
Meuwissen and Luo (1992).
!QUASS
The original routine for calculating A inverse in ASReml was based on Quass ()
!REPEAT
tells ASReml to ignore
repeat occurrences of lines in the pedigree file.
Use of this option will avoid the check that animals occur in chronological order, but chronological order is still required.
!SARGOLZAEI
invokes an alternative procedure for computing A inverse developed by
Sargolzaei etal (2005).
!SELF s
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 probability s and
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.
Do not use the
!SELF
qualifier with the
!INBRED
or
!MGS
qualifiers.
!SKIP n
you to skip n header lines at the top of the file.
!SORT
causes ASReml to sort the pedigree into an acceptable order,
that is parents before offspring,
before forming the A-Inverse. The sorted pedigree is written to
a file whose name has
.srt
appended to its name.
A pdf file
pedigree.pdf
contains details of these options.
!XLINK
requests the formation of the (inverse)
relationship matrix for the X chromosome 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 usual A inverse and can be accessed as
GIV1 or 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.
Genetic groups
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
!GROUP
qualifier and the pedigree file must
begin by identifying these groups. All base individuals should have
group identifiers as parents. In this case the identity
0
will 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
Sire1 G1 G1
Sire2 G1 G1
Sire3 G1 G1
Sire4 G2 G2
Sire5 G2 G2
Sire6 G3 G3
Sire7 G3 G3
Sire8 G3 G3
Sire9 G3 G3
101 Sire1 G1
102 Sire1 G1
103 Sire1 G1
...
163 Sire9 G3
164 Sire9 G3
165 Sire9 G3
It is usually
appropriate to allocate a genetic group identifier where the parent is unknown.
Two pedigree terms!
ASReml only provides directly for a single pedigree factor. For some crops, breeding is
based on distinct beeding families, crossed in the last stage to produce hybrid production lines.
To handle this, we need two runs of ASReml. The first run saves one NRM file as a GRM file for use
in the second run as in the following code.
!PART 1
Mline !P
Fline !A
...
Mline.ped !GIV !DIAG !ALPHA
#!GIV generates the file Hybrid1A.giv
#!DIAG generates Hybrid1.aif which contains the identifier names
!PART 2 #reads in inverse additive relationship matrix generated in !PART 1
Mline !A !L Hybrid1.aif !LSKIP 1 #associates identifier names with levels of Mline
Fline !P #used in giv file
...
Fline.ped !GIV !DIAG !ALPHA
Hybrid1_A.giv # Formed in part 1 from Mline.ped
Hybrid.asd !SKIP 1
...
... grm1(Mline) nrm(Fline)} #using new synonyms and functions
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