Re: Abridged summary of chinook-pedigree-project@googlegroups.com - 9 updates in 1 topic
Carol Beuchat PhD
We can determine the genetic relationships among the dogs using the Embark DNA, which essentially reconstructs the pedigree. We can also determine the genetic similarity between any pair of individuals (and predict average COI of their offspring) and also identify the dogs that are genetically most valuable.
These are some simple data for Malamutes. The red arrows indicate
that there are two main genetic groups, and the shorter the
branches between individuals the more closely related they are
(e.g., yellow arrow). Below that is the genomic kinship matrix
that is color coded by kinship coefficient (which we can set to
whatever levels we want). A dog compared with itself has a kinship
coefficient of 1 (red), dogs that are "unrelated" are green, and I
set 0.065 to yellow (K for first cousins). From these it is easy
to identify the clusters of dogs and choose pairs that will
produce the most diversity in the puppies.
We can also identify blocks of homozygosity on the chromosomes
(each row is a dog, across the top the chromosomes are lined up
end-to-end and numbered 1-38). Using this, you can avoid mating
dogs with blocks of homozygosity in the same place. We can also
tell the difference between recent and old inbreeding - recent
inbreeding produces larger blocks that get broken up during
meiosis each generation, so the bottom chart shows the recent
inbreeding, the top chart also shows the old inbreeding in which
the blocks have been broken up by crossover into smaller and
smaller runs. You can easily see blocks that line up across all
the dogs (red arrows on two large, obvious ones on chromosome 12).
Carol Beuchat
-------------- Carol Beuchat PhD 949-632-5762 Scientific Director Institute of Canine Biology www.InstituteofCanineBiology.org ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Karen Hinchy <kcc...@gmail.com>: Apr 14 12:13PM -0400
Hi all,
Some additional information from the DNA tests on Chinook sirelines from
the 90s has come in, and it is....puzzling. As noted previously, paternal
haplogroups and type come solely from ...more
Mary Malkiel <laughing...@comcast.net>: Apr 14 10:23AM -0600
Hi All,
Perhaps, since we now know that the pedigrees are incorrect, we just start from a place that (maybe) we know the pedigrees to be true and move forward from there?
Perhaps this also ...more
Susan E Bragg <ross...@yahoo.com>: Apr 14 06:11PM
THANK you, Mary. For even though I too am no pro geneticist; I for sure have studied all of these pedigrees for 20plus years already; Just to finally be able to say today-- REALITY is- ...more
Susan E Bragg <ross...@yahoo.com>: Apr 14 06:50PM
re: prior DNA exclusion between NW Kodiac & dam of record G Sheena
Most conservative approach I guess would be to also remove his Dam to OPEN finally. Unless you think that beg's the question ...more
Cheryl Brown <dogr...@comcast.net>: Apr 14 01:34PM -0600
Maybe this means we have more diversity in the breed than we thought :). Who knows who was bred to who! Trying to think positively
Cheryl Brown
...more
Mary Jo Crance <mjc....@gmail.com>: Apr 14 07:52PM
The genetics test we have now show that the Chinook breed is not diverse,
in fact. So even if the sireline pedigrees/paperwork are inaccurate, we
still are no more diverse than the genetic facts we ...more
Cheryl Brown <dogr...@comcast.net>: Apr 14 12:55PM -0700
I understand genetics tell us where we are today. I guess I meant if the pedigrees were correct we could be in even worse shape genetically today :)
Cheryl Brown
...more
Susan E Bragg <ross...@yahoo.com>: Apr 14 08:21PM
Where we stand today would already be a lot closer to 'extinct' without both MARS OS and Embark, agreed.
Regarding pedigrees, bear in mind how even within this sire line(s) review(s); at least 3 ...more
Mary Jo Crance <mjc....@gmail.com>: Apr 14 08:37PM
😀
...more
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