The inbreeding calculation has been enhanced in two key areas. Firstly, from looking at a lot of the data that is out there its
not unusual to see "self parenting" type errors in a database. These can be particularly
difficult to detect because it can occur after say 40 generations. To solve this
problem the Inbreeding Calculation function will automatically check for self parenting
errors with the number of generations specified by the user.
The second big change is that IC now has its own grid for displaying results as shown below: The grid displays:
- the minimum and maxium generations at which an ancestor appears
- the number of times it occurs
- the COI (Coefficient of Inbreeding)
- COR (Coefficient of Relationship).
- Percentage of Blood
- Line Breeding
Toolbar buttons provide the ability to sort on any of the fields making it easy to see which ancestors have the greatest influence (COR) or occur the most times.
There's also a copy button for copying the grid contents to other applications like Excel.
We also have a Breed Planner which provides two
side-by-side tables as above and also allows printing.
We get a lot of queries about inbreeding coefficient and to a lesser extent the relationship coefficient.
BreedMate calculates the Wrights Inbreeding Coefficient.
To verify BreedMate's calculations we recommend you try "Pedigree Viewer" which is a free Win32
application available from Dr Brian Kinghorn's web site http://www-personal.une.edu.au/~bkinghor.
Brian is the Twynam Chair of Animal Breeding Technologies, Division of Animal Science,
University of New England, Australia. It is relatively easy to generate a file that will read into "Pedigree Viewer" -
just follow the steps listed here.
Wright's Inbreeding Coefficient (IC)
Inbreeding can be defined by either of the following two statements:
1. The probability that both genes of a pair in an individual are identical by descent, ie homozygous
2. The probable proportion of an individual's loci containing genes that are identical by descent Wright's Coefficient of Relationship (RC)
A measure of pedigree relationship. The probable proportion of one individual's genes that are identical
by descent to genes of a second individual The correlation between the breeding values of tw
individuals due to pedigree relationship alone.
Number of generations used in calculation
BreedMate allows you to select the number of generations used in the calculation. The way this
is done has changed between V4.6 and V5.1+. The difference is about which ancestors
are included when you specify N generations. In earlier versions it included ancestors only if they
appeared within N generations. In 5.1+, if an ancestor appeared within N generations then it
was also included if it appeared past N generations. For example, in 5.1+, if you calculate COI for
8 generations and ancestor "A" appears at gen 7, 10, 11 then all those "appearences will
be included" whereas in 4.6 only its appearence at 7 is included.
Note if you set the generations large enough the COI will be the same for both 4.6 and 5.1+.
There are many articles relating to inbreeding coefficient on the internet. Note we do not necessarily
approve or recommend any of the links listed:
Converting BreedMate data for Pedigree Viewer
You will need at least V5.0. The steps are as follows:
- Open your BMX file
- Use the Tools-Export to Pedigree Viewer command
- Click on "Export" button - a File Save dialog appears
- Save the file to the PedigreeViewer directory (which is normally C:\Program Files\Pedigree Viewer) and give it a name like "MyPed.txt" (actual
name is not important)
- Using Windows Explorer, double click on the MyPed.txt file - Notepad starts and
opens the file for editing - insert "ID, SireID, DamID" as the first line of the
- Save and exit Notepad
- Change the name of the file so that it has a .PED extension
- Run Pedigree Viewer and use its File-Open Pedigree File command to open MyPed.ped.