Genetic diversity of the Maine Coon

Is a domestic cat healthier than a Maine Coon?

In the Netherlands, a common thought is that a mixed breed or a domestic cat is healthier than a pedigreed cat because of their higher genetic diversity. Well the median of a domestic cat is indeed a bit higher than the median of a Maine Coon. The bandwidth of a domestic cat is between 35-42% (shown below in orange) and for a Maine Coon between 28-42% (shown below in blue). BUT depending on the breeders goals and the lines the breeder is working with, it is definitely possible to breed Maine Coons that have at least as much genetic diversity as a mixed breed or a domestic cat. Maine Coons that have a genetic diversity higher than 35% have reached that point. Obviously a breeder working with pedigreed cats has more knowledge of the lines and the quality of the genes in terms of health than a breeder who’s cat accidentally got pregnant by some neighbor’s cat we don’t know anything about. Which can make the choice for a pedigreed Maine Coon even safer than a domestic cat who's history of the ancestors is unknown and where no healthtests are done.

How can you use genetic diversity in your breeding program?

When I learned about this test, my first question was: how does the genetic diversity relates to inbreeding levels? You would expect to see a higher genetic diversity of cats who have low inbreeding levels. But is this true for every cat? I had to find out by doing research on the public Maine Coon profiles in mycatdna.com. I looked up the pedigree names in the Pawpedsdatabase in order to find information about the inbreeding levels and clones. Then I have made the charts to visualize the correlation between the indicators that we use:

• total COI%

• inbreeding on 5 generations and 10 generations

• the clones

Below are the results for each indicator and the correlation with genetic diversity. All those charts are based on Population B*.

Genetic diversity correlated to COI%

Let’s have a look at how the genetic diversity relates to the total inbreeding coefficient (COI%). You can see the green line, showing the average COI versus genetic diversity (%). For example a Maine Coon that has a genetic diversity of 39% (these results are rounded) has an average COI of 5%. And a Maine Coon with a genetic diversity of 31% has an average COI of 19%.

The yellow and blue lines show the bandwidth where the COI% can be on an individual level. It shows that there is at least one Maine Coon that has a high genetic diversity of 38% and also has a higher COI than you would expect: 15%. The yellow line also shows an exceptional result of a cat that has a low genetic diversity of 30% and has a COI of 0%. How can this happen? A cat with 0% inbreeding doesn't exist, but (New) Foundation cats are registered as such, since we don't know their parents and inbreedinglevels. This shows that probably not all New Foundation cats (COI 0%) are genetically diverse. But this test can proof if they are! This particular cat probably has related parents (high COI), but could still be very unrelated to the majority of the other cats and bring in new genes to the population.

The black dotted line shows how many Maine Coons fall into the genetic diversity category. The outer edges don’t have as much testresults to draw reliable conclusions here. But the trend (green line) is very visible. In other words, there is a correlation between the COI and the genetic diversity, but it is not as predictable, since there are exceptions.

You can make general predictions here: A Maine Coon with COI of 15% is likely to have a genetic diversity less than 35%, but you can see from the blue line that 38% is still possible also. Maine Coons that have lower inbreeding levels then 10% will probably have a genetic diversity level between 36,5 and 40,5%. In a low COI% pedigree nowadays often one or more New Foundation cats are responsible for the low numbers. But the genetic diversity does depend on the genetic diversity level of the New Foundation cat and how unrelated those genes are to the lines you mix them with. This test adds new information about the genetic diversity of that new line and if it indeed adds something new to the breed.

In case you didn’t already realize that inbreeding is not a good idea health-wise, the breeder tool helps you visualizing the results when you plan to mate related cats.​

Example 1:

Brother – sister mating increases the COI with 25%. What happens with the genetic diversity when you plan such a mating (which is not recommended)? In the breeder tool you can match the profile of Chelles of Macadamia (genetic diversity of 39,2%) with her brother Lyon of Macadamia (genetic diversity of 37,8%). (Note that brother and sister have a difference of 1,4%, which shows that not all siblings have the same genetic diversity.) Their kittens are expected to have a genetic diversity around 29,7%. A decrease of 8,8% in genetic diversity. You don’t get them much lower than that! Obviously a very bad idea.

Example 2:

Grandparent – grandchild mating increases the COI with 12,5%. We take the profile of Chelles of Macadamia (39,2%) again and this time we will select her grandfather So Out Coon’s Mirai (38,5%). Both cats have a very good genetic diversity. The expected genetic diversity of their kittens will be around 34,9%. A decrease of nearly 3,95% in genetic diversity in just one generation. It seems a small number and small step, but don't take a few percent very lightly. It takes you straight to the other side of the chart. Remember the bandwidth of the tested Maine Coon population is only 14% (between 28-42%), so a decrease of 3,95% means you will lose 28% of their genetic diversity in one step!

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Genetic relations

Note that mycatdna database doesn't keep track of any family relationships. The prediction of the genetic diversity for the offspring is purely based by comparing the genomes. If the predicted genetic diversity is lower than both parents, it means their genomes is mostly the same (and they are probably related).

At the genetic relations map of the testresults you can see all the cats of the breed and how they cluster together when their genomes have similarities. Think of this: when you have a Maine Coon with a high genetic diversity, lets say 40%, but it is shown in the graphic in the middle of the blue cluster of dots. It means you will have a hard time finding a good match to further improve genetic diversity, since most of the other cats are close to yours and share most of the same DNA. You will have to look for lines in the outer areas to find unrelated matches, to continue a high genetic diversity for future generations.

Surprisingly the graphic below shows that the domestic long hairs and the Maine Coon mixed cats are all in the same yellow cluster. Showing that their DNA is different from the Maine Coon breed, but within this mixed-breed-category there is not very much diversity at all.

Also notice that the Polydactyl Maine Coons (pink dots) seems to be very diverse. The Polydactyls are registered as a separate breed into Mycatdna and has its own median of 35,9%, which is 1,4% higher than a non-poly Maine Coon (34,5%).