Yes, Kooikers are inbred: population genetics

A few days ago I reposted the Institute of Canine Biology’s article “What Population Genetics Can Tell Us About A Breed,” but substituted in the Kooikerhondje numbers. It has spawned a surprising amount of discussion by those who were unaware of the state of the breed population. Since this is important information, I will reshare in summarized form here. Much of this is based on the work of Dr. Oliehoek, the researcher whose numbers are chronicled in the Institute of Canine Biology article, and myself and the entire breed are indebted to him for undertaking this research.

Founders

Kooikerhondjes were recreated starting in the 1940s from thirty founder individuals (controversially, another founder was added in Italy in recent years, but we are disregarding this for this discussion).  Of these thirty, only thirteen of these founders are still contributing to the current population (effective number of founders, fe): Bobbie (1/3 of the population is descended from Bobbie), Bennie, Tommie, the mother of Biffie, the mother of Piet, Bally, Pluis, Bello, the mother of Polly, Koala, Petit, Peggy, and Sita. The founders are assumed to have been unrelated but that assumption is unlikely to be true, but as we cannot prove otherwise, we must use it as a starting point. These founders contain the extent of the diversity to be found in the breed today. Most of the founder loss occurred through the 60s and 70s and since then the breed has been maintained by breeding as unrelated of pairs as possible, with the understanding that these pairs are not truly UNrelated. Over the last century, the breed ballooned from those first thirty founders and their offspring to a worldwide population today closing in on 10,000 individuals.

Today our “founder genome equivalent” (fg) is 1.45. This is “that number of equally-contributing founders that would be expected to produce the same genetic diversity as observed in the current population.” Very roughly, we are breeding with the genetic equivalent of fewer than one and a half unrelated dogs. (Again, the Institute of Canine Biology has a much better explanation of this metric.)

All Kooikerhondjes are thus extremely closely related. The numbers can seem dire – and should be taken seriously – but recall that the Kooiker database is extremely thorough. Our breed is lucky that breeding has been tracked in such detail over so many years, so we can get these accurate numbers. However, care should be taken to compare these statistics with those of other breeds, especially those that have a spottier history of record-keeping. Kooikers may be no more or less inbred than any other breed, but it’s possible we have the best data with which to determine this.

COIs

Coefficients of inbreeding (COIs) are numerical estimates of the likelihood of offspring inheriting two identical genes that are identical BECAUSE their parents are related (so that gene came from just one ancestor). While COIs are limited in their ability to tell a full story, they are easily understood and often used as “shorthand” to determine relatedness. Kooiker databases like Zooeasy and Breedersoft will calculate known and theoretical COIs, but these are based on a certain number of generations (usually between 4 and 6 is standard, and I always advocate for the generation number to be included next to a COI if discussing it, for it means very little without this qualifier). A lower number is better but there are no official upper limits in breeding rules. When using too many generations to calculate COI, the number is so high that it ceases to have meaning – and as we are aware, we cannot avoid having these thirteen now-interrelated founders represented in the pedigree calculations. A more relevant picture of an individual’s degree of inbreeding is produced by using a mid-range number of generations to calculate COI, as well as establishing the number of unique ancestors in a recent pedigree (how far back can you go before you start getting repeats of individuals).

Across the breed, the average COI going back to all founders is 34.5%. For reference, a mating between a full brother and sister would result in offspring with a COI of 25%. That means that the average Kooiker on the street is nearly 10% MORE inbred than the offspring of full siblings.

Inbreeding

High inbreeding causes “inbreeding depression” resulting in reduced lifespan, higher likelihood of inheriting genetic disorders, reduced immune health, and reduced fertility. We see some evidence of all of these in our population. Average lifespan is just over 12, and in 2019 the average number of surviving puppies in Kooiker litters was four, both of which are lower than one would expect for a dog of this size. We are faced with a variety of disorders in this breed with a genetic component (whether this has been “solved” yet or not) including von Willebrand’s disease, ENM, renal dysplasia and polymyositis – the last bleeding into the autoimmune disorders that crop up devastatingly and mysteriously through the pages of the Register. Fertility problems in both sexes (males particularly are known to face sterility at especially high rates) means the effective breeding population is narrowed even further and the problems only increase at a higher rate.

This means we must be extremely careful about our breeding choices, and steward what little genetic diversity we have left with responsibility and forethought. No litter is bred in a vacuum, so no one producing a litter should disregard the impact their progeny will have on the genetic balance of this small population. Each litter should be planned with respect to its kinship to the rest of the population.

We need to maintain a larger effective population, meaning more individuals should remain reproductively intact (whether or not they have plans to breed, or are in fact ever bred – we mustn’t narrow our options too far via widespread pediatric neutering). More individuals should be bred… fewer times. This means we need to be cognizant of popular sire syndrome – one single male (or that male and his son) siring the majority of puppies in this country in any given year, as is currently occurring, must cease. That male should be used once… and his brother used once, and then his great-uncle instead, even just for one litter each. Repeated pairings of the same male and female should only be allowed if the first litter yielded no offspring that will be bred. And lastly, if none of these strategies are used and we end up with a population so riddled with deleterious alleles that there is no one left to breed to – we should consider outcrossing to another breed. While this is a “sexy” option and generates much discussion, I’d prefer we shepherd our existing genetic diversity with more care, to avoid requiring rescue by another breed.