Does your breed need genetic rehabilitation? Here's where to start

By Carol Beuchat PhD

I am often contacted by breeders that are concerned about inbreeding and loss of genetic diversity in their breed. They recognize that these things matter over both the short and long term, and that they affect the burden of genetic health issues in the breed. The question from the breeder is "What do we do about this?"

Invariably, they bring up the issue of what dogs they should cross to, either individuals in the breed, or other dogs that are completely unrelated (e.g., another breed, mixed breed, etc.)

Breeders always want to discuss this right from the start. But, for a genetic rehabilitation project, you need to identify the specific problems you need to solve before you make decisions about what to do. The "What do we do" questions will get answered after we first ask "What are the genetic problems that need to be solved?"

The first thing you need is information about the genetics of your breed. At the top of list will be information about the inbreeding and genetic diversity of the breed. You can determine these using either pedigree databases or DNA genotypes.

To make a decision about whether to analyze pedigrees or genotypes, you need to know what information each can produce. Both have limitations and advantages, and there are also considerations of cost and whether the information is even available.

​When you get to this step, it's worth evaluating both options very carefully so you make the best decision to suit your purposes. In fact, however, having information from both pedigree and DNA analyses will be more powerful than either alone. If you are expecting to do the "whole enchilada" analysis,  then you can simply prepare to do both.

The Norwegian Lundehund is undergoing genetic restoration through a crossbreeding program that is now producing dogs of good type that are healthy and fertile.  (Melis et al 2022).

Genetic analyses, whether from pedigrees or DNA, will produce information containing a bunch of terms you are probably not familiar with. To use this information, you will need to understand the vocabulary and what the data produced can tell you. Do not think you can learn this stuff from chats in Facebook groups. If you're going to put in the time and make an investment in doing these analyses for your breed, please take the ICB online courses. I am not aware of any other educational resources that are developed specifically for dog breeders and that cover the essential information while requiring no background in science. You need to invest some time in your own education or you won't know how to use the information from data analyses. Remember, the goal here is to figure out what breeders need to do to solve specific genetic problems in the breed. For this, you will need to understand the information provided. Take the courses. 

I have created a table (below) with some information about the types of basic information that you can extract from both pedigree data and genotypes. In general, I would advise breeders that only intend to use data from one of these sources to use pedigrees. It might seem that DNA should be better because it uses "high tech" techniques to provide information about chromosomes and genes. But, in fact, you will find that a pedigree analysis provides all the information you need to do a good job of genetic management of a breed. It requires no effort (or cost) from breeders to keep it up to date, and it will provide critical information for you generation after generation, forever. There is some overlap in what can be extracted from pedigree versus DNA data, but pedigrees might be better for some things and DNA better for others. Again, if you have the option of doing both, that is the most useful thing to do.

If you want to use DNA genotype data for your breed, you should use SNP (single nucleotide polymorphism) analysis, not microsatellites (or single tandem repeat markers, STR). Embark uses the most popular, research grade analysis based on high-density SNPs. Their output can be combined with data produced by any research lab using the same chip (e.g., data from a study). Wisdom also uses SNPs but they have a lower resolution chip of their own design and their data cannot be combined with Embark's. Also (and more importantly) they do not make the genotype data available to the user, so third-party analysis (as I am describing here) is not possible. Microsattelite data cannot be combined with SNPs, and they do not provide the resolution needed for planning a genetic rehabilitation program for a breed. However, STRs can provide data for the genes for the immune system (DLA, dog leucocyte antigen), and this is useful to know so you can breed for high diversity in these genes specifically.

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The table below includes some additional information about the convenience and logistics of obtaining and managing data from pedigrees versus DNA genotypes. 

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Armed with the information from analysis of your pedigree database or DNA genotyping, you are ready to start summarizing the issues that need to be addressed. For this, you will also need to know some other things - the actual number of living dogs, how many of these can be used in a breeding program (i.e, not spayed or neutered), and how many breeders there are and where they live (e.g., country). This is also the time to pull out all the information you have about phenotypic traits that you care about (e.g., coat color, variety, etc.) as well as known health issues and associated genotypes when known.

All of this is information that should be available about your breed anyway, but usually the motivation for getting things together is the realization by breeders that there are issues about genetic health that need to be addressed. With some information extracted from pedigrees or DNA genotypes, we can take a lot of the guesswork out of making breeding decisions. A little effort invested now in data preparation will yield benefits for the breed far into the future.

I have provided the reference for a nice paper by Mabunda et al (see References) about using pedigree and molecular data to evaluate genetic health of dog breeds. It contains a useful summary of the information provided by pedigree and genotype analyses and how to use it. You will see some jargon that might be new to you, so you can start here to become familiar with meanings and concepts. There is much more to know about how to set up a genetic rehabilitation program for your breed, but this is the place to start.

If you would like to know more about the genetic status of your breed and what can be done to improve it, contact me and we can discuss where to start.

Watch this space for more information about genetic rehabilitation of dog breeds coming soon...

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REFERENCES

Mabunda et al 2022. Evaluation of genetic diversity in dog breeds using pedigree and molecular analysis: a review. Diversity 14: 1054. https://doi.org/10.3390/d14121054.
https://www.mdpi.com/1424-2818/14/12/1054

Melis et al 2022. Genetic rescue of the highly inbred Norwegian Lundehund. Genes 13: 163. https://doi.org/10.3390/ genes13010163.
https://www.mdpi.com/2073-4425/13/1/163

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