WOMBAT – A program for Mixed Model Analyses by Restricted Maximum Likelihood

## Fitting X-linked genetic effects

xlink_example.par
   PED pedigree.dat  +SEX
DAT xldata.dat
fixeff 2
animal
xlink
record
end
ANAL UNI
MODEL
RAN animal NRM
RAN xlink SEX
FIX fixeff
TR record
END
VAR animal 1
16
VAR xlink 1
4
VAR error 1
20

WOMBAT has an in-built facility to allow for X-linked genetic effects. In brief, this is fitted as an additional random effect and WOMBAT can calculate the appropriate inbreeding coefficients and set up the inverse of the corresponding relationship matrix directly from the list of pedigree information.

The box on the right shows an example for the parameter file for a univariate analysis fitting X-linked genetic effects. The specific requirements are:

1. The pedigree file needs to have a fourth column with a code of 1 or 2, specifying the number of X chromosomes for this individual (Usually 1=males, 2=females).
The code +SEX after the name of the pedigree file tells WOMBAT to look for this additional column.
2. The data file needs to have a column, here named xlink, which contains the identity of the individual, i.e. which is a duplicate of the column for animal.
3. In the model part of the parameter file xlink needs to be specified as an additional random effect with covariance option SEX.
The latter instructs WOMBAT to set up the inverse of the X-linked relationship matrix from the list of pedigree information.
4. Finally, the parameter file needs to contain a VAR statement for the xlink effect, together with a starting value for the pertaining variance component.
bib
@ARTICLE{fern90,
author = {Fernando, R. L. and Grossman, M.},
title = {Genetic evaluation with autosomal and X-chromosomal inheritance},
journal = {Theor. Appl. Genet.},
volume = {80},
year = {1990},
pages = {75--80},
url = {http://dx.doi.org/10.1007/bf00224018}
}