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Brenda Bonnett

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The Downside of Inbreeding - It’s Time For a New Approach

by C.A. Sharp

First published in Double Helix Network News, Winter 1999

 

I am pulling together a presentation for the Embrark Canine Health Summit and came across an article I have cited before... an oldie but a goldie!  This article is by the very knowledgeable C.A. Sharp, expert and person behind ASGHI (Australian Shepherd Genetics and Health Institute) and one of our collaborating partners.

Good news - she gives a great coverage of this important topic.  Of concern - this was written in 1999 and it is still a hot topic today. READ it here: https://www.ashgi.org/home-page/genetics-info/breeding/breeding-genetic-diversity/the-downside-of-inbreeding

Embark has been regularly publishing Coeffiecients of Inbreeding (COI's) on genetic samples from various breeds on its Embark for Breeders facebook page.

These are genomic NOT pedigree based COIs (learn about the difference here) and understandably but unfortunately we do not know how many dogs were included in the calculations.  Presumably it is an international sample.  Notwithstanding this limitation, these are useful to consider.

Firstly, remember that a brother-sister mating results in a COI of 25%.  That is inbreeding.  Look at these values from Embark, as examples.

Both the German Shepherd Dog and the Bulldog have average COIs above that level... meaning that many of the dogs have values that are higher still. On average, dogs with a COI >25% share more genetic material from common ancestors than would arise from a brother-sister mating.

 

Embark COI gsd.png          Embark COI Bulldog.png

 

Results for the Cattle Dog and the Husky below show lower values for COIs.  Not surprisingly, perhaps, given a focus on performance in these breeds?

 

Embark COI Aus Cattle dog.png      Embark COI Siberian Husky.png

 

Protecting the future of your breed depends on Genetic Diversity.  Make sure you understand how breeding practices like line-breeding result in reduced diversity and over time may create health problems like poor reproductive capacity, lowered longevity and more.

Other reading:  Linebreeding vs. Inbreeding – Let’s be perfectly clear.

 

 

 

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I have no doubt that inbreeding leads to problems and that loss of genetic variation is a problem in dog breeds.

However, Brenda points out that the genetic COI (or genomic COI) are not pedigree-based but then continues to say that a 25% COI (F) is what you get from a full-sib mating. That is correct when you talk about pedigree-based F. For the genetic COI from Embark we do not have a benchmark. We know that they use runs of homozygosity (ROH) and it seems that they allow also very short ROHs. This increases the general level of COI. Going to the extreme limit, you come down to single-snp based COI, i.e., overall homozygosity. This is no longer a measure of identity by descent (IBD) but rather identity by state (IBS). Now, remember that with only 2 alleles the proportion of homozygotes (if we have Hardy-Weinberg equilibrium) is p2 + q2, where p and q are the allele frequencies. If they are equal, we have 50% homozygosity. If allele frequencies are unequal, the homozygosity increases. If minor allele frequency is 0.25 then the expected homozygosity is 0.625 (without inbreeding). 

So, presumably, the genetic COI are somewhere in-between pedigree-based IBD inbreeding coefficients and the IBS homozygosity F, but where on the spectrum is hard to know. 

As an example, in a snp-dataset I have available, with settings that only allow rather long ROH (hardly any ROHs shorter than 4 mill. base pairs, average of 6.7 Mbp) I get an F_ROH average of 0.05. If I allow shorter ROHs (average 1.7 Mbp) I get an average F_ROH of 0.16 for the same group of animals. (Total homozygosity is 0.65)

I think it would be very useful to benchmark the genomic COI (from Embark or elsewhere) against known pedigree-based average relationships and total homozygosity before we draw the conclusion that all German shepherds, say, are full sibs in the IBD sense.

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