The Importance of COI

WHAT IS A COI AND WHY DOES IT MATTER?

One of the main reasons we wanted to try to put together a more complete pedigree database for Nigerians was to be able to see an accurate COI.

A COI is a coefficient of inbreeding, sometimes referred to simply as F. It is a measure developed by pioneering geneticist Sewall Wright and has been in use for almost a hundred years; it is often referred to as Wright's Coefficient. It is the standard calculation used by dog, cat, horse, cattle, sheep and you-name-it breeders, and also by geneticists researching human diseases and DNA. Wright's Coefficient is the calculation used by adgagenetics.

What does it do? Basically it measures the common ancestors and alleles shared by buck and doe in any given mating. In an article for the Institute of Canine Biology Dr. Carol Beuchat explains it very clearly:

"The coefficient of inbreeding is the probability of inheriting two copies of the same allele from an ancestor that occurs on both sides of the pedigree. These alleles are "identical by descent". The inbreeding coefficient is also the fraction of all of the genes of an animal that are homozygous (two copies of the same allele). So, for a mating that would result in offspring with an inbreeding coefficient of 10%, there is a one in 10 chance that any particular locus would have two copies of the same allele, and 10% of all of the genes in an animal will be homozygous."

The Nigerian Dwarf, as a breed, got really pretty really fast. This was to a large extent the result of the benefits of inbreeding - a technique which can be used to quickly fix desirable traits, so that they are identical by descent. But no one has really explored the potential pitfalls of inbreeding in the Nigerian Dwarf.

The danger of inbreeding is established science. As COI goes up, litters get smaller and include more stillbirths, diseases and syndromes linked to recessive autosomal conditions proliferate, the immune system becomes less robust, there is a higher - sometimes much higher - incidence of cancer, and life spans are shorter. Sometimes much shorter. In Standard Poodles, for example, poodles with a COI under 6.25% live an average four years longer than dogs with a COI of over 25%.

What does a COI of 25% represent?

This is the COI of a father-daughter, mother-son, full brother-full sister breeding. There are a number of dog registries which will not accept an animal for registration when the animal has this level of inbreeding.

So is 25% the highest COI possible? No. The COI should be calculated to at least 10 generations, and the COI can be - and is, in many Nigerians - higher than 25% when animals have been closely bred over multiple generations.

Unfortunately, you cannot get an accurate Nigerian COI at adgagenetics for two reasons. Firstly, for almost all Nigerians, the database does not go back ten generations. Secondly, because of the impact on the server, adgagenetics does not calculate COIs to ten generations, but to eight. So even if the information were there (for the most part, it isn't) it wouldn't be used. Not a big deal for the standard breeds, but a very big deal for Nigerians.

Why is this particularly important for Nigerians? Because Nigerians are a new breed, and because the ADGA herdbook, a purebred-only herdbook, has always been closed. There is no way to outcross. If you are breeding Alpines, you can cross in a Saanen or a grade or an NOA and breed up to American Alpine in a few generations. If you are breeding LaManchas, you can cross in and still breed up to Purebred - the herdbook never closed. But Nigerians are out of luck. You breed out of the original foundation pool of IDGR/AGS animals, which was estimated at about 700 animals. Of those 700, not more than half are still represented - their genes dropped out, for whatever reason.

So every registered Nigerian today goes back to a pool of not more than 350 foundation animals. Of those 350, some are much more widely represented than others. This is the "bottleneck" geneticists refer to - the shallow pool that every ND goat goes back to. To get a remotely accurate Nigerian COI, you need to go back at least 10 generations to those foundation animals.

The effects of inbreeding

One of the reasons we started trying to find a way to trace pedigrees back to the foundation animals was because of what I think is an alarmingly high incidence of cancer in the breed, specifically the well-known "tailfold cancer," usually diagnosed as squamous cell carcinoma. In cattle, horses, and people, squamous has a proven genetic component. Whether it does in Nigerians is unknown, because there is no research, but high rates of cancer are definitely associated with inbreeding, as are such well-documented disorders as G6S, the devastating genetic defect that affects Nubians. G6S is an autosomal recessive disorder, exactly the kind of sneaky syndrome that can wreak havoc in a highly homozygous (inbred) population. How long it had been in the breed no one knows, despite estimates that as many as 25% of Nubians were carriers. It certainly would not have been discovered when it was except for the fact that G6S has a human counterpart, Sanfilippo syndrome - which was known to be an inherited disorder - and the connection between the caprine and the human disease sparked research, experimentation, and the development of a test to identify carriers.

Inbreeding is rising across all dairy goat breeds, and it is rising among Nigerians much more dramatically than this chart shows. Curiously the dip you see in the chart below around 2005 is likely the result of all the Nigerians pouring into the ADGA registry - they would all have come in as 0% inbred - not because they were 0% inbred but because they had no ancestors in the database.