By Carol Beuchat PhD
One measure of genetic diversity is the fraction of loci with two alleles that are different. There are two expressions of heterozygosity: expected heterozygosity (He) is what we would expect to see if the population is breeding randomly, and observed heterozygosity (Ho) is the actual fraction of loci that are heterozygous.
Because heterozygosity depends on actual allele frequencies, two populations with the same COI can have different levels of observed heterozygosity. I won’t go into the math involved, but suffice it to say that you can’t assume that Ho is necessarily 1-COI; that is, you can’t predict one from the other, especially in small, bottle-necked populations (think purebred dogs).
One tricky thing to warn you about is that inbreeding can vary from 0 to (theoretically) 100 percent. But heterozygosity is measured using SNPs, which are “biallelic”, meaning that for a given locus, there are only two possible states. Say you have two alleles, A and B; some dogs will be AA, some will be BB, and some will be AB. Because AB and BA are the same, at most only half of the dogs can be heterozygous. As a consequence, graphs of heterozygosity scale from 0 to 0.5, not 0 to 1.0.
I have made use of published data for heterozygosity of various breeds of dogs (from Bannasch et al. 2021, and the massive study by Donner et al. 2018; ) to produce histograms that make it easy to compare genetic diversity within and across breeds. Within breeds, the range of values reveals the amount of variation in the sampled population. The Donner study supplied data for individual dogs, so I could display them as a histogram. In the Bannasch et al. study, the information provided was the range (blue line) and median (closed circle). (You can browse through the graphs here - https://www.instituteofcaninebiology.org/heterozygosity_donner.html )
Because heterozygosity depends on actual allele frequencies, two populations with the same COI can have different levels of observed heterozygosity. I won’t go into the math involved, but suffice it to say that you can’t assume that Ho is necessarily 1-COI; that is, you can’t predict one from the other, especially in small, bottle-necked populations (think purebred dogs).
One tricky thing to warn you about is that inbreeding can vary from 0 to (theoretically) 100 percent. But heterozygosity is measured using SNPs, which are “biallelic”, meaning that for a given locus, there are only two possible states. Say you have two alleles, A and B; some dogs will be AA, some will be BB, and some will be AB. Because AB and BA are the same, at most only half of the dogs can be heterozygous. As a consequence, graphs of heterozygosity scale from 0 to 0.5, not 0 to 1.0.
I have made use of published data for heterozygosity of various breeds of dogs (from Bannasch et al. 2021, and the massive study by Donner et al. 2018; ) to produce histograms that make it easy to compare genetic diversity within and across breeds. Within breeds, the range of values reveals the amount of variation in the sampled population. The Donner study supplied data for individual dogs, so I could display them as a histogram. In the Bannasch et al. study, the information provided was the range (blue line) and median (closed circle). (You can browse through the graphs here - https://www.instituteofcaninebiology.org/heterozygosity_donner.html )
For comparison, the distribution of Ho for a mixed breed population of dogs shows that most mixed breed dogs have Ho > 0.4, and in many Ho is > 0.45. As you scan through the graphs for breeds, you can see that there is much variation in Ho, with some showing many dogs with Ho > 0.4, while in other breeds the most dogs are < 0.3 (Basenji). (Note that for some breeds where the sample size is very small, you might see just a few bars that don’t say much about to expect for the breed.)
These data are very interesting to browse, and can reveal a lot about the genetic health of a breed. Breeds with less genetic diversity in the population are shifted to the left. This tells you that if a breed is trying to breed away from an undesirable gene (or towards a favorable one), the low heterozygosity (read “diversity) could make this difficult. For breeders faced with developing a cross-breeding program to introduce new genetic diversity into the gene pool, the best candidates for those crosses will be the ones with high heterozygosity and low COI; the worst choices will be breeds with low diversity, and you want to avoid high levels of inbreeding because all puppies will inherit the same allele from a parent for homozygous loci.
These data are very interesting to browse, and can reveal a lot about the genetic health of a breed. Breeds with less genetic diversity in the population are shifted to the left. This tells you that if a breed is trying to breed away from an undesirable gene (or towards a favorable one), the low heterozygosity (read “diversity) could make this difficult. For breeders faced with developing a cross-breeding program to introduce new genetic diversity into the gene pool, the best candidates for those crosses will be the ones with high heterozygosity and low COI; the worst choices will be breeds with low diversity, and you want to avoid high levels of inbreeding because all puppies will inherit the same allele from a parent for homozygous loci.
www.instituteofcaninebiology.org/hi_low_heterozygosity.html
I made two quick graphs to show this. One graph displays the heterozygosity and inbreeding data for the top breeds for genetic diversity, and the other is the breeds with the highest inbreeding and lowest heterozygosity. If you’re looking for genetic diversity for a genetic rescue program, you might steer away from the breeds on the low diversity (although they might be useful for other reasons). I am also working on some analyses that show how diversity in a breed varies among populations in different countries (coming soon…).
Information about heterozygosity can help us make better breeding choices, and Ho is one of the statistics that will be available for all breeds when the updating of the DogsArk Breeding Tool is finished (soon...).
(Access the graphs for each breed here - )
https://www.instituteofcaninebiology.org/heterozygosity_donner.html
I made two quick graphs to show this. One graph displays the heterozygosity and inbreeding data for the top breeds for genetic diversity, and the other is the breeds with the highest inbreeding and lowest heterozygosity. If you’re looking for genetic diversity for a genetic rescue program, you might steer away from the breeds on the low diversity (although they might be useful for other reasons). I am also working on some analyses that show how diversity in a breed varies among populations in different countries (coming soon…).
Information about heterozygosity can help us make better breeding choices, and Ho is one of the statistics that will be available for all breeds when the updating of the DogsArk Breeding Tool is finished (soon...).
(Access the graphs for each breed here - )
https://www.instituteofcaninebiology.org/heterozygosity_donner.html
REFERENCES
Bannasch, D, and others. 2021. The effect of inbreeding, body size and morphology on health in dog breeds. Canine Medicine and Genetics 8:12. https://doi.org/10.1186/s40575-021-00111-4
Donner, J and others. 2018. Genetic prevalence and clinical relevance of canine Mendelian disease variants in over one million dogs. PLoS Genetics 19:31010651. https://doi. org/10.1371/journal.pgen.1010651
Bannasch, D, and others. 2021. The effect of inbreeding, body size and morphology on health in dog breeds. Canine Medicine and Genetics 8:12. https://doi.org/10.1186/s40575-021-00111-4
Donner, J and others. 2018. Genetic prevalence and clinical relevance of canine Mendelian disease variants in over one million dogs. PLoS Genetics 19:31010651. https://doi. org/10.1371/journal.pgen.1010651
You can learn more about the genetics of dogs in ICB's Online Courses.
*** Population Genetics for Dog Breeders ***
Visit our Facebook Groups
ICB Institute of Canine Biology
...the latest canine news and research
ICB Breeding for the Future
...the science of animal breeding
*** Population Genetics for Dog Breeders ***
Visit our Facebook Groups
ICB Institute of Canine Biology
...the latest canine news and research
ICB Breeding for the Future
...the science of animal breeding
