Genetic groups
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Genetic groups


I have been trying to fit genetic groups, without luck.

I have data from an apple tree breeding population consisting of open
pollinated families. The mother trees were divided into genetic group based
on species, region and era of development. There are 36 genetic groups.
Because the mother trees were planted in tree repositories surrounded by
unkown trees, potentially from any of the 36 genetic groups, I have assumed
that each family has 2-3 unknown pollen donors. I have tried the analysis
with pollen donors set to 0 (unknown genetic group) and with pollen donors
set to genetic group37.

An example of the program file:

Title:  Univariate variance component estimation - Apple data
 TreeID !P
 Site 2 !A
 Row 40
 Tree 400
 Family 225 !A
 Block 257
 Origin 100 !A
pedigree.txt !ALPHA !MAKE !GROUPS 36 !NEW
data.txt !filter 2 !select 1 !skip 1 !maxit 10
Weight ~ mu Block !r Family

I have tried two pedigree files. The first has zeros for the pollen donor
as it could belong to any of the 36 genetic groups:

group1 0 0 
group2 0 0 
group36 0 0 
fam1 0 group1
fam2 0 group1
fam225 0 group36
ID1 0 fam1
ID2 0 fam1
ID4000 0 fam5

The second pedigree file has group37 assigned to the pollen donors.

group1 0 0 
group37 0 0 
fam1 group37 group1
fam2 group37 group1
fam225 group37 group36
ID1 group37 fam1
ID2 group37 fam1
ID4000 group37 fam5

However, the answers I get are the same as if I run the program without the
pedigree file and !P option. The first question is how do I fit genetic
groups ? The second question is can I fit genetic groups to only the dams,
leaving the pollen donors unknown, or do I have to fit a genetic group to
the unknown pollen donors?

Thanks in advance for any suggestions,
Alastair Currie