Comparing levels of inbreeding in dogs and horses

By Carol Beuchat PhD

Inbreeding is part of the process of breed formation in domestic animals and is used to produce homozygosity in the genes most responsible for type and breed-typical traits. But inbreeding is also blamed for the high rates of genetic disorders in purebred dogs (OMIA). Is the level of inbreeding in purebred dogs higher than in other types of domestic animal breeds? How much inbreeding is necessary to produce a domestic animal breed?

First, we need to define "breed". We can take as a general definition that the animals in the specified group have a set of recognizable characteristics that make them unique from other breeds and that are reproduced reliably in their offspring. This definition applies both to breeds that are strictly "purebred" (i.e., bred within a closed gene pool) as well as to landraces.

In my previous post (Inbreeding of purebred dogs determined from DNA), I presented a summary of the average levels of inbreeding in dog breeds, taken from a recently published compilation based on direct measurement from DNA (Dreger et al 2016). These data show that most breeds of dogs are highly inbred, with average values that exceed the inbreeding level that results from the mating of half-siblings (12.5%). In fact, more than half of the breeds had average inbreeding coefficients greater than 25%, equal to mating full siblings from unrelated parents. This means that for many breeds, most breedings involve a sire and dam that are more similar genetically than full siblings. 

The race horse Eclipse, who is found in the pedigrees of most modern Thoroughbreds.

The question we want to ask is whether the levels of inbreeding that are typical of purebred dogs are similar to those of other domestic animals.

To address this question, I used data from a paper that documented levels of inbreeding in nearly 40 breeds of horses (Petersen et al 2013) using the same methods used for the dog data (i.e., heterozygosity of thousands of SNP markers). The breeds included everything from modern sport horses, to draft breeds with history going back hundreds of years, and even landrace breeds.

I plotted these data on the same axes I used for the dog data, and did separate graphs for both the mean level of inbreeding as well as the maximum for each horse breed. (Unfortunately, the maximum values were not reported for the dog data.) As before, I included reference lines for inbreeding levels of 6.25% (green; the result of mating first cousins), 12.5% (yellow; mating of half-siblings), and 25% (red; mating of full siblings).

There are three graphs below. First are the dog data, using the same graph presented in my earlier blog post, but turned horizontally so it's easier to compare to the horse data. (See that blog post for a larger, vertical version of this graph).  Below the graph for dogs, there are two graphs for horses: one with the mean inbreeding coefficient for each breed (comparable to the dog data) and a second one with the maximum. 

​Inbreeding Coefficients in Dogs
(Data from Dreger et al 2016)
(From the blog post Inbreeding of purebred dogs determined from DNA)

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​Inbreeding Coefficients in Horses
(Data from Petersen et al 2013)

• Mean (top)
• Maximum (bottom)

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In horses, only one breed, the Clydesdale, has an average level of inbreeding exceeding 25% (top, red line), whereas in comparision, about 75% of dog breeds were greater than 25%. Inbreeding is less than 12.5% (yellow) in about half of the horse breeds, while only a handful of dogs are this low. 

In horses, even the maximum inbreeding values were greater than 25% in only about a third of the breeds (bottom, red line). 

These data are compelling evidence that inbreeding is much higher in dogs than should be necessary to produce a population of animals with the consistency of traits necessary to be considered a "breed". 

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References

Dreger DL, M Rimbault, BW Davis, A Bhatnagar, HG Parker, & EA Ostrander. 2016. Whole genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic trait mapping. http://dmm.biologists.org/lookup/doi/10.1242/dmm.027037.

Petersen JL, JR MIckelson, EG Cothran, and others. 2013. Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLoS One 8(1): e54997. doi:10.1371/journal.pone.0054997.

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