A beginners guide to inbreeding and line breeding

My thanks to Sue Bowling for allowing me to quote extensively from her article


First and foremost I should emphasise that line breeding is the cornerstone of selective breeding. Selective breeding has given us cows that give the maximum amount of milk, sheep that give the maximum amount of wool, chickens that lay eggs almost every day and the most beautiful dogs in the world. There is nothing wrong with line breeding but it is like using a satellite navigation device – if it is not used intelligently you land up in Richmond, North Yorkshire when you intended to go to Richmond in London! If you are to use line breeding intelligently you have to know the basics. I hope that this short article will help.

What are inbreeding and line breeding, and what effect do they have?

In genetic terminology, inbreeding is the mating of two animals who are related to each other. In its opposite, out crossing, the two parents are totally unrelated. Since all pure breeds of animal (including humans) trace back to a relatively limited number of foundation ancestors, all pure breeding is, by this definition, inbreeding though the term is not generally used to refer to matings where a common ancestor does not occur within a five-generation pedigree.

Breeders of purebred livestock have introduced the term ‘line breeding’, to cover the milder forms of inbreeding. Exactly what the difference is between line breeding and inbreeding tends to be defined differently for each species for there is no ‘formal’ definition. Inbreeding at its closest applies to what would be considered incest in human beings – parent to offspring or a mating between full siblings. However, uncle-niece, aunt-nephew, half sibling matings, and first cousin matings are called inbreeding by some people and line breeding by others. Under normal circumstances if this was the only example of close breeding in a five-generation pedigree what is called the ‘inbreeding coefficient’, expressed as a percentage, would be so low as not to be significant. But three things need to be taken into account. The closer this relationship is to the first generation of the pedigree, the more often it occurs and the relationships of the other sires and dams in the pedigree all result in an increased percentage.

What does inbreeding (in the genetic sense) do? Basically, it increases the probability that the two copies of any given gene will be identical and derived from the same ancestor. The higher the inbreeding coefficient the more likely this is to happen. The technical term is ‘homozygous’ for that gene. The ‘heterozygous’ animal has some differences in the two copies of the gene. Remember that each animal (or plant, for that matter) has two copies of any given gene (two alleles at each locus, if you want to get technical), one derived from the father and one from the mother. If the father and mother are related, there is a chance that the two genes in the offspring are both identical copies contributed by the common ancestor.

This is neither good nor bad in itself – but consider, for instance, the gene for PRA (Progressive Retinal Atrophy), which causes progressive blindness. Carriers have normal vision, but statistically, if one is mated to another carrier it is likely that one in four of the puppies will have PRA and go blind. Inbreeding will increase both the number of affected dogs (1 in 4) and the number of genetically normal dogs (3 in 4) so inbreeding can thus bring these undesirable recessive genes to the surface, where they could be removed from the breeding pool – you do not breed from the dogs which go blind – although a proportion of other dogs in the litter will be carriers. This will only matter if they are mated to another carrier, of course, but it demonstrates the complexity of the problems

Unfortunately, it is still much more complicated for we cannot breed animals based on a single gene – the genes come as just two packages: one in the sperm and one in the egg. So you may be able to eliminate one undesirable pair but the very fact that the animals will be becoming increasingly homozygous (which may quickly improve some characteristics) is also likely to bring other undesirable combinations to the surface.

Sewell Wright developed what is called the ‘inbreeding coefficient’ in the 1920s. This is related to the probability that both copies of any given gene are derived from the same ancestor. A total outcross (in dogs, probably a first-generation cross between two purebreds of different, unrelated breeds would be the best approximation) would have an inbreeding coefficient of 0. As we have seen, they would still have common ancestors many generation back so would still be homozygous for some genes shared by all dogs so even though the inbreeding coefficient = 0 even matings between unrelated pairs can still throw up genetic disease.

An inbreeding coefficient of 100% is rare in mammals and would result if the only matings practiced over many generations were between full brother and full sister. A mating between a brother and sister from unrelated parents would result in an inbreeding coefficient of 50%. A mother/son (or vice versa) or father/daughter (or vice versa) mating would result in a breeding coefficient of 25% assuming that there were no other related matings in the preceding generations. A cousin-to-cousin mating actually gives a relatively low percentage (6.25) but other related matings would affect this figure – perhaps substantially. However, Dr Malcolm Willis, one of the most experienced geneticists in the world of dogs, has said that the average inbreeding coefficient in pedigree dogs registered with the Kennel Club is actually only between 4 and 5% but, of course, the long term effect of many generations of a breed on the same register will mean that today’s dogs do have a higher chance of passing on deleterious genes simply because, as explained at the beginning of this article, there were relatively limited number of foundation ancestors.

As a general rule, very close inbreeding in domestic animals cannot be maintained for many generations because it generally results in loss of fertility – apart from any other genetic disease which may become apparent. .

To ensure genetic health breeders need to select pairs in such a way that the inbreeding coefficient of the offspring is kept as low as possible commensurate with the adherence of stock to the breed standard. One way of doing this is to use the method often adopted in other countries: that is breed from animals which ‘look’ the same (heterozygous) as distinct from what we tend to do in the UK which is to breed from animals which are genetically similar (homozygous).

Another key is to constantly move away from families known for possessing deleterious genes – a method practiced by knowledgeable dog breeders for generations.

You can download a programme from the Internet called GENEs which was written by Dr Robert Lacy which will enable you to calculate the inbreeding coefficient of any mating (assuming you have the full five generation pedigree) quite easily. The programme is free but has some restrictions. Go to http://www.vortex9.org/genes.html to download it.

Genetics is an immensely complex subject and this is but a simplistic introduction. Much more can be found at http://www.highflyer.supanet.com/coefficient.htm including the formula for working out inbreeding coefficients. It is:


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19 Comments on “A beginners guide to inbreeding and line breeding”

  1. Dear Mr. Cavill,

    may I make some rmarks on your article (and some I read from you otherwhere:
    According to latest studies inbreeding leads to inbreeding depression which is a genetic stress owing to defective genes and is comparable e.g. to aging, not just to increase of recessive defect genes. Part of those genes do not lead to diseases but have more or less deleterious effects (genetic load). A smaller part of the causes for inbreeding depression is overdominance, i.e. the better effectiveness of “cooperation” of two different genes on the same site (locus).

    If inbred mice are wanted for the lab, a great number of pairs is bred, each offspring being inbred. Within about ten generations all the lines will be extinct owing to infertility, but the remaining will be purged, appear healthy and can
    be bred on for hundreds of generations. However, when they are outcrossed, they will show outcrossing vigour due to overdominance.

    Owing to inbreeding depression in purebreds, mongrels are on average more longlived and healthier. If you like, I can send you the result of my literature research on it. This is the result of being exempt of inbreeding depression and carrying the same defect gene less often. Only purebreds non in/linebred for over five generations will be in the same range of longevity.

    In the long run, dogs cannot be successfully bred without maintaining or achieving very low inbreeding coefficient (if necessary, an outcross to a similar breed must be made,) and working use or fitness tests.

    I you wish, I can send you the list of comparative studies.


    Hellmuth Wachtel

    Dr. Hellmuth Wachtel
    Speisinger Str. 220
    A 1230 Vienna Austria
    p. +43 1 8892025
    f. +43 1 889 7058

  2. Please forward the above comment.

    Hellmuth Wachtel

  3. davidcavill Says:

    Thank you for your comment, Hellmuth. I am, of course, well aware of your work but as I said in this article ‘it is but a simplistic introduction’.

    However, I know your comments will be appreciated by readers and I would appreciate it if you could post a link here to the research to which you refer.

  4. Simon Roff Says:

    What percentage would you consider to high when breeding dogs ?

    • davidcavill Says:

      There are no hard and fast rules – and with pedigree dogs there is a degree of in/line breeding by definition. I have (once) bred mother to son. They were both near perfect specimins of the breed and the resultant litter was superb. There were no short or long term problems and many of the best dogs for almost twenty years had those puppies in their pedigree – some of the best still do.

      But I think you miss the point. You do not in/line breed for the sake of it. You find the best examples of the breed you can that have the characteristics you want and which (as far as you can be aware) do not have intrinstic genetic or health problems) and mate them. You examine the puppies carefully and select the best. It is called selective breeding and it is how all species(us included) have come to exist. The difference with dogs that it is not random (which is slow) but deliberate (which can be very quick) but which if done thoughtlessly can lead to difficulties. Remember that when random slection does not work the examples of that branch of the species die out. We have a tendency to look after our pets and keep them alive if they are not perfect so entrenching any mistakes.

  5. Julie Says:

    Pehaps a more specific question is in order. Is there a generally excepted guideline on what percentage of inbreeding coefficient (on the low end) would still be considered linebreeding. Thank you in advance.

    • davidcavill Says:

      Thank you for your comment Julie. As usual in these matters the the answer is not simple. Almost by definition, pedigrees include a great deal of inbreeding even when in the preceding five generations looks quite open. A good example is in Golden Retrievers where virtually all those that now exist can be traced back to just two dogs – one dog and one bitch. So even when you have what looks like an open pedigree in some breeds there is still a significant amount of inbreeding. However, over the years most breeders in most breeds have behaved very sensibly and rationally. It is where they havethat breeds have problems. In a breed where pedigrees are relatively open my recommendation has always been that you can breed reasonably closely twice in succession but then you must move out from that pedigree as far as possible. Close means grandfather to granddaughter or grandmother to grandson but clearly the closer the line breeding already in the pedigree, the further away from close relatives you need to get. One of the things that people forget is that selective breeding is designed to improve characteristics. The problems arise when accompanying that improvement stray genes begin to double up and it is essential that breeders recognise when this is beginning to happen. The way out of all the deleterious situation that some breeds find themselves in is actually better quality selective breeding. I hope that this helps.

  6. Tamra Says:

    Does inbreeding really make a difference in chickens?
    Thanks Tamra

  7. Robert Selby Says:

    Hi,my name is Robert.My female German shepard got hooked up with her son accidently.She had 8 pups.The 8th one was still born,the 7th was barely breathing,I tried nursing him but he only made it 22 hours after birth.The remaining 6 look healthy and strong.Its only been 4 days now,so I am not sure about the outcome yet.My friend knows a reproductive specialist who has said some of the most gorgous dogs have come from inbreed litters.I will say I am very nervous about them and how they are going to be later on in there lives.

    • davidcavill Says:

      If both dogs are healthy I would just wait and see for the reproductive specialist is quite rightis right. On the other hand, I would not try to ‘save’ any puppies which are failing – let htem go

  8. ulric spears Says:


    Mr David could you tell me how is this dog bred is he line bread or in bread
    and your over all opinion

  9. kscate Says:

    I have just found your weblog and it has helped me a lot. Being new in the dog show world, I have been blessed with a great dog who has done well and who I have now bred successfully. Her full sister was also bred to a completely different male. Her litter was born about 6 weeks ago. Two of her sister’s puppies have a slight entropia in one eye that may require a couple of stitches temporarily until their heads grow out. I have also found out that two puppies in my dog’s and her sister’s litter had to have two stitches in one eyelid for two weeks and then they were removed and the dogs had no more trouble and were homed with restricted registrations. So this apparently has a genetic component, although the breeder’s vet said it was not genetic. None of the puppies required surgery and none have had any further issues. But now that it has shown up in two litters and we have heard of other incidences of this, we are thinking it may indeed be genetic. So my bitch is going to have puppies in two weeks. I am wondering how to tell if this type of thing is genetic or a developmental issue as the vet has asserted. I don’t know how to find out. Also, if it is a minor type of genetic entropia, do both parents have to have the gene for it to show up or can it come from just one parent. We have a relatively rare breed with a smaller gene pool. So if it is genetic, how do we eliminate it, Neither of the mothers of these litters had this issue and neither did mine. It just showed up in their puppies. I wonder how likely it is that siblings will carry the same defect. Any suggestions or comments would be appreciated. We are trying to do the right thing for the breed.

    • davidcavill Says:

      This is a very interesting question although difficult to answer although knowing the breed might provide a clue. However, I would not expect this problem to have a simple solution as, I suspect, several, if not very many, genes are likely to be involved. You need to contact Catherine Mellersh (cathryn.mellersh@aht.org.uk) at the Animal Health Trust explaining the problem as above and giving the breed. Good luck

  10. kscate Says:

    Thank you for responding so quickly and giving me Ms. Mellersh’ contact information. The breed is the korthals griffon. This has been an extremely healthy breed, but problems are starting to pop up. We do have a foundational sire, imported from another country years ago, that seems (but is not proven) to be connected to all the cases we know of. So if it is a genetic issue, line breeding is involved with its appearance in the population. It seems to affect only male puppies. In one litter there were 8 puppies with 6 males. Two males were affected. One litter had a singleton male and he was affected. One little had 11 with about half males and half females. Two males were affected. The other two instances we have heard about, we don’t know the sex. Both my bitch and her sister were bred completely away from this sire, but not because of this issue. We did not know it was an issue until my dog’s littermate had her pups a few weeks ago and the breeder began asking questions of other breeders. So my bitch’s sister and mother have had two male pups each with this issue. I understand that if it is polygenomic and the mother is not affected by it, but is a carrier, there is a 50% chance that the unaffected siblings will be carriers too. So there is a 50% chance mine is a carrier as well. Then there is the question of does it always show up in every litter? If none of my puppies have it, does that mean my bitch is clear and therefore her offspring are clear or is it something that randomly appears in one litter and then not in another. Also, the question of whether both sire and dam must carry the defective genes for it to occur will be important in trying to figure out how to breed it out of the population. So I have tried researching it and have written to a genetics expert at a large university veterinary college and received no response. So I was very grateful to run across your site. Thank you again. I will contact Ms. Mellersh at your suggestion and try to give all the relevant details that I know of. If you have any other thoughts i would appreciate your sharing them. You have been very helpful.

  11. kscate Says:

    On of the breeders mentioned above, wrote about it to the AKC. The AKC responded that dogs who have comfort stitches for a few weeks and grow out of the need for them are not barred from showing. Whereas dogs requiring surgery to correct entropia are barred from showing. They did not weigh in on whether they considered this genetic or developmental.

    All of the breeders I have mentioned are members in good standing with the AWPGA and report health data to the AWPGA health and genetics database, including me. This is so new that there is no consensus about whether it is genetic or growth related. We don’t have enough information yet to make a designation. Which is why we are trying to reach out to experts in this area. I have emailed Ms. Mellersh. Thank you so much.

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