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Inbreeding animals on small farms

 
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Hello. I’ve put this topic in the chicken section but it could be relevant to any animal.

I was chatting to the boss at work the other day and was shocked to learn that he doesn’t care about inbreeding in his flock of sheep. He has 10 acres (not permaculture) and only replaces his ram every 3 or 4 years. He doesn’t care about inbreeding between ram replacements.

I was thinking about this and realised that we raised chickens when I was young and I have no recollection of ever replacing the rooster despite many years of breeding. It’s going back a fair few years now so my memory could be wrong but it appears that we were inbreeding our chickens as well. (Or my parents were getting rid of the hens without me noticing).

So, Two questions: Do you care about inbreeding in your farm animals (or you do for some types but not for others) and what steps do you take to prevent inbreeding if you do?


Cheers.
 
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I have no experience with animal.breeding so take this with a cup.of salt.

Basically, fears about inbreeding are (I think) often overblown. There is not any inherent harm that I've ever been shown from inbreeding, it is just that you have no way to.breed out any traits you don't want. Inbreeding has been central to strain/variety formation in plants and animals since forever. Assuming healthy and vigorous starting population, the worst you are doing to yourself by inbreeding is creating a genetic bottleneck that limits the total scope.of traits that are ever available to you
 
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This is a great question.

Some elements of farming, we actually want to inbreed as it helps solidify traits in the flock.  But in many situations, a wide genetic variety is a huge bonus.  

With sheep, I keep a breeding flock, but I don't always keep lambs every year.  That way, I can keep the same ram several years in a row without inbreeding, because very few if any of his offspring are kept.  However, in some situations, it's not only okay, but desirable, to have up to 3 generations of inbreeding in sheep if the results have the traits you are trying to increase in the flock. So 3 years with the same ram is pretty standard, 4 years is pushing it but so long as there are no obvious signs of genetic defects, it's okay.  This goes for most farm mammals.  

With chickens, I finally settled on a barnyard mix, with about 20 different breeds of chicken starting, and adding a few more breeds as time went on.  That way the genetics are varied and I don't have to worry about importing a rooster every few years.  

With ducks, I have half a dozen breeding ducks and two drakes.  These are steady from year to year, only replacing one if another one dies.  When we first started, we had the girls from one line from out of town, the two drakes were from separate parts of the province.  When the drake dies, we will usually import one from another farm, but sometimes, if we feel the genetic variation is still good within the flock, we'll keep a son.  I keep a close eye on genetic defects and the ratio of pigeon toe vs waddle toe offspring as these are the two primary traits of our original drakes.  

Do I care about inbreeding? I am aware of it.  I'm not afraid of it as it makes a good tool for improving qualities in a flock, but I am careful to observe any defects that are obviously genetic and cull accordingly.
 
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I do replace my males so there is no inbreeding. We had a new peacock male every year (mostly because they kept dying to be honest). I kept our boar separate so he wouldn't breed his daughters.
 
r ranson
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A few things to think about when bringing in new replacements.

1. local isn't always good.  With sheep and goats, I find that most breeds only have two male lines and many of these are crossbread.  So getting new livestock from within driving distance isn't always a guarantee you'll get new genetics.  I almost bought a ram this year until I found out it was closer related to my girls than the one we just had.  

2. Every new animal that comes onto your farm is a chance to destroy the farm.  There are some seriously bad STDs, especially in sheep and goats, that can mean culling the entire flock.  Or worse, having the government take an interest in the culling - so that you don't get the money from the meat sales and well, I don't really want to go into that.

 
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So far, with our chickens, it's a non-issue, because hubs doesn't want a roo. With the goats, I have some issues right now, because I'm working toward breed development and advancement. If I allow my buck to breed with his daughter, the breed genetics classification stays at her level (f2). So, we're getting an f2 buckling, this month, to advance to f3 genetic classification. Beyond that... well, time will tell.
We just purchased all our ducklings as a straight run, so I've no clue if any are from the same lineage, and they're only 4 weeks old, at this point. Most will be in the freezer by the end of this month, but in keeping a drake and 2 ducks? Who knows. But, we only want them for eggs and meat - not sales. So, we will likely replace the drake every few years, until the ducks stop laying, then we will replace them, instead. I think.
 
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my current kittens are product of brother and sister, out of 4, 1 seemed very slow doncha no a hawk got it probably fed to its chicks, the three remaining all males are fine rat catchers. I think all the feral cats in the area have been got, well see what happens when momma gets in heat again.
 
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This is correct; however, in livestock, inbreeding is often done in an effort to identify these hidden recessives, which allows the breeder to cull the undesirable gene(s) from the herd and work towards having a bloodline which is homozygous for the desirable genes.
At the same time, outcrossing to an animal from a different line doesn't necessarily lower the chance of getting a "double recessive."
For instance, when I first started breeding rabbits I occasionally had cases of malocclusion show up in my litters, so I culled the stock with bad teeth and the stock that produced bad teeth and the issue was resolved within a few generations.
3-4 years later I brought in a new, unrelated buck and bred to the girls. The second generation after bringing him in I started seeing cases of malocclusion, again, in the animals descended from him. Had I not linebred closely, I would have had the gene circulating through the herd again, just waiting for the right opportunity to show up. While some may feel it's okay when the maladaptive genetics stay hidden, I prefer to identify them and cull them from the gene pool before they get spread out across the herd. Additionally, I don't want to potentially sell an animal that carries something undesirable to someone and end up damaging their line's gene pool by introducing the recessive.
 
r ranson
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It's definitely important to monitor for receive unwanted traits.

The big problem with pure breeds, which is especially evident in dogs and the kind of goats I have, is that they have an hourglass shape genetics.  The goats, for example, at one time went down to a population size of SIX.  That's six goats and from those six goats, all the goats of that breed in Canada are descended.  So even though we have a few hundred now, and there is a second billy-line (boy descendent line) on the far side of the country, this narrow spot in the genetic history makes inbreeding very dangerous.  And yet, to maintain the breed, we still have to inbreed to some extent - although there is a method where you grade-up (you bring in a goat of a different breed, then inbreed the decendents  back into the breed standard.

Choosing starting genetics that are as varied as possible leave more leeway to inbreed without genetic defects.  Like my chickens for example.  So long as I get vast variety in the offspring, I feel confident that I can keep the flock closed (no outside inputs) for probably 10 or 20 more years.  With my sheep, if I want to buy a ram, I need to be careful to choose a ram-line that isn't too closely related to my current sheep as I have a few double descendants from my last ram.  

 
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In the wild, inbreeding is common and used to better survival in most herd species. Take a bull elk that that will be dominant enough to mate with often up to 3 generations of his offspring. Even when replaced by a young aggressive bull it will often be one of his own sons which will still keep the inbreeding intact. This gets repeated over and over through multiple generations.
 
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One thing to remember, though, is that wild animals usually don't survive if they have dangerous recessives. Unlike livestock, no one is going to try to keep them alive if they're weakened. The vast majority of inbred recessives that might be dangerous are sorted out within a few generations as the animals die off before they have offspring.

With animals that are bred for specific traits, they're more likely to be catered to and medicated/treated until they can pass on the damaged genes. Take the elk vs a herd of cows--an elk that can't push out her calf will die. Period. A human will pull the cow's calf, then go ahead and do it again as often as necessary, and keep that cow's descendants who then have the same problem. It becomes normal.
 
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One should never get that attached to homesteader livestock/poultry that they can't cull the poor traits. What nature can't do under these conditions we must.
 
s. lowe
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Jordan Holland,

I think that continuous inbreeding with little to no culling is certainly dangerous and likely to create problems. What I was trying to express was that the simple act of inbreeding isn't a guaranteed source of problems. As long as its paired with a willingness to cull and careful observation I wouldn't be overly stressed about some inbreeding
 
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Natural selection vs, human selection.

When it comes to selecting breeding stock, culling the defective ones is one option but for me, I keep this as a last resort.  The big point is to prevent them from breeding, so what happens to the ones that shouldn't be bred depends on the farmer and their situation.

If the defect doesn't affect the quality of life, there can be quite a bit of value to the ones that shouldn't be bred.  I keep a couple of canaries in each flock - animals that have weak genetics and are more susceptible to illness.  If there's an illness or parasite load in the flock, these animals get sick quick and hard.  They show illness long before the others and by watching my canaries daily, I can see when it's time to give a close health-check on the other members of the flock before the issue gets bad.

Even if they aren't breeding, animals can still serve their function - grow wool, mow lawn, produce eggs, eat slugs, whatever the animal does best - on the farm.  If there isn't enough room on the farm, one can sell it to urban farmers who won't be breeding the livestock.  They just want two chickens to lay breakfast omelettes or a couple of old sheep for mowing the lawn.  

Human selection can be so much kinder than natural selection.  Natural selection is ruthless in the way they rogue out the undesirable characteristics, but humans have kindness.  We can simply choose who to breed and not breed.  

If a ewe cannot push out a lamb unaided, I still help her.  But then I think very hard about breeding her again.  Was it something wrong with the ram (too large a head?) or something wrong with the diet (probably the most common issue with birthing in my part of the world), or something wrong with her genetics.  Is it time for her to go to the retirement flock up the road?
 
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If I ever had livestock, I'd be obsessed about pedigrees for sure. I know how much damage inbreeding did to dogs; although it wasn't inbreeding per se, but rather the purpose (breeding for looks and shows, not for function).
I used to have pet rats and I kept their pedigrees even after they died :D four generations!
It's really such an interesting topic.
I only have plants, and from the generations that repeat (mostly pumpkins) - I collect only the seeds from the healthiest and most tasty fruit, and I exchange seeds with other permaculture gardeners in the area. So they're different each year but also better and more adapted.
 
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There are a lot of good and thought-provoking comments here!

When I think about inbreeding, I think of the permaculture teachers who encourage the planting of trees from seed rather than the commercial practice of grafting everything. One of the issues in our forests is that some were planted not just as mono-cultures, but with seeds from an extremely narrow group of parent trees.

I will also add about living on an Island - getting a divergent blood-line can be hard. I've been trying to get new Khaki-Campbell ducks for at least 3 years without luck. The symptoms are subtle, but livability in young is the most obvious - too many die in the shell or during hatch. I finally decided that this year I'd try crossing with a breed with Khaki in them. It may give me some healthier ducks, but I have no idea where to go from here next year. It's complicated because female khakis all look the same pretty much, and my success with leg bands is less than stellar. I've got two young females in the adult group, and one has lost her band after only a month! All we can do is try.
 
Flora Eerschay
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Genetic diversity is also linked with healthier immune system, so you might want to outcross for that (there is a number of research papers on this topic).
 
Jay Angler
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I've been taught that in the wild, predators prey first on the weak, which replaces the safety system that discourages inbreeding. Along the North American East Coast there are increasing cases of wasting disease in deer and I suspect at least one factor is the shortage of predators. Unlike wolves, when humans fill the predator roll, they often kill the "biggest and the best" and avoid an animal that looks sick.

One domestic example is from an acquaintance that breeds "pug" dogs - the puppies are all delivered by C-section because their heads are too large. Nature would not put up with that crap!

A second domestic example is how humans are incubator hatching so much of our poultry that we're at some risk of eggs not being naturally successful. That's fine so long as the power stays on, but it also does a disservice to the animals. I find that roosters and drakes that are raised by "real moms" are much more respectful of the hens/ducks and will actually perform a mating ritual. I've culled roosters I've been given that were incubator/human raised if they demonstrated behavior akin to "rape". (I have a very deep-seated internal moral objection to "rape" - I am who I am...)
 
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Bringing it back to the Farmyard, with veterinary medicine, Nature is a lot less involved with selecting which animals get to breed and don't.  

So it's up to the farmer to choose which traits they want to keep in the flock or herd.   It's very important to be aware of the ancestry and any genetic bottlenecks that might have occurred in the lines.  
 
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I find it very interesting that in mammals and birds in the wild, many species have social or other methods of preventing inbreeding, sometimes at the cost of number of offspring. This implies to me that, although not always immediately harmful, there is strong selection pressure against extensive inbreeding.

Typical social methods are either dispersal of young, avoidance of known kin, and other methods include avoidance of animals with similar phenotypes.

Wikipedia has a neat discussion on this:
https://en.m.wikipedia.org/wiki/Inbreeding_avoidance

On the farmyard- most long term farmers I know take great care to swap in "new blood" from afar. I have one friend who talks about trading barn kittens with distant farms to prevent genetic defects and the more insidious "lack of vigour".



 
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There's a pedigree program called 'Kintracks' which is inexpensive and has a handy 'coefficient of inbreeding' tool.  From an animal's page, you can click on the inbreeding tool and match them up with an animal of another gender and it will give you the percentage of inbreeding along with details on which other animals they're related to.  It's a free download and you can test out the program with the addition of quite a few animals before you need to pay for it and it's not expensive (around $20 Australian) when you do.

I've been breeding angora rabbits since 2009 starting from eight individuals and have been able to keep the levels of inbreeding below 25%.  There's been the addition of several new animals over the years, but not very many.  Just lately, I've allowed the level of inbreeding to be a bit higher and it's been interesting to see some of the changes in the offspring.  Some of them are getting extra fuzzy and some are losing the fluff on their ears.  Another has showed up in a color that I haven't a clue what it is.  Looks like a very chocolatey dark sable, but that's an impossible color from a tort x REW cross.  Well, fortunately, there's the Kintracks database so maybe the color and genetics behind it can be figured out.

Keeping good records is important for any kind of animal breeding, whether it's tracking the level of inbreeding or fertility rates or production rates.  
 
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Tom Pivac wrote: Do you care about inbreeding in your farm animals (or you do for some types but not for others) and what steps do you take to prevent inbreeding if you do? Cheers.



That is a very good question. My personal opinion is that the best animals I've ever had came from crossing purebreds from 2 different breeds. So, for example, my favorite dog was 50% Border Collie and 50% Blue Heeler. Doing this provides hybrid vigor and an outcross that greatly reduces any weaknesses caused by inbreeding in the original 2 breeds.

I did the same with horses. When I no longer bred registered Thoroughbreds (TBs) for racing, I outcrossed them to AQHA (quarter horses / QHs) so that my younger horses are 50% TB and 50% QH. In so doing, I retained the endurance and quality of the TB side, but greatly improved their feet, made them easier keepers, and gave them strength to do work around the homestead should that become useful in the future.

Many horse breeds are very inbred, but only through the best lines. TBs we typically avoid inbreeding closer than 2x4 or 3x3 because close inbreeding often results in much smaller offspring that are potentially unsound for the purpose intended. That close they tend to be dominant breeding animals and when it works, outstanding performers.

On the other hand, QH breeders often breed extremely closely. Daughter to sire (father) matings are common, especially in lines where people are trying to increase or maintain very high inbreeding co-efficients. The lines that inbreed are typically working horses rather than racing horses.

And QHs are often less inbred to start with than TBs which can trace their lineages back to the 1800s. That said, most QHs carry TB bloodlines if you go back far enough. They just don't have records because the AQHA is a young breed of horse.

When I decided to get ducks, I am doing the same thing. My drakes (males) are American Pekin aka Long Island Pekin and Buff. When I acquired more females, I bought Silver Appleyard, Buff, Rouen and Khaki Campbell -- primarily Silver Appleyard. All of these breeds were developed from the same duck lines (Ayershire and Mallard principally), but the ducks I have would not be related to each other (except 1 Pekin female).

I thought horse color genetics was complicated; duck color genetics is even more complex and the available tools aren't as useful. In case anyone is interested:

BUFF
The buff ducks are a result of a cross between Indian Runner, Rouen and Aylesbury ducks.

PEKIN (American Pekin is actually a Long Island)
original Pekins descended from mallards and were upright like runners. American Pekins were developed by crossing with Aylesbury ducks.

Silver Appleyard
Created by crossing Rouen, Pekin, and Aylesbury. Appleyards as previously mentioned are light phase restricted mallards. The restricted mallard gene (M^R) is reportedly dominant over its alleles (M+ & m^d), & was called "restricted mallard" largely due to melanin restricting action in duckling down. very young pure bred Appleyard ducklings are ususally yellow-ish with only the "mohawk" & tail showing dark pigmentation. As the ducklings age dark pigments do come through

Rouen
Also referred to as Giant Mallards, they are descendants of wild mallards  developed in France

Khaki Campbell
To begin, Campbell crossed an Indian Runner that was an exceptional layer with a Rouen of good size. Later, she bred the resulting offspring with a Mallard to develop hardiness in her breed. Next, Mrs. Campbell wanted a particular buff coloration, so she added Penciled Runners to the mix. The end result were the attractive, excellent laying Khaki Campbells that we know today.

CROSSES

Pekin over Silver Appleyard
Mallard x2 / Aylesbury x2 / Rouen / Pekin x2

Pekin over Rouen
Aylesbury / Mallardx2

Pekin over Khaki Campbell
Aylesbury / Indian Runner x2, Rouen, Mallard x3 (one from the Rouen)  

Buff over Silver Appleyard
Indian Runner, Rouen x2, Aylesbury x2

Buff over Rouen
Indian Runner, Rouen x2, Aylesbury, Mallard

Buff over Khaki Campbell
Indian Runner x2, Rouen x2, Aylesbury

If anyone is interested in inbreeding patterns, I'm happy to answer questions. In TBs, we intentionally linebreed one family, especially through the best females and then outcross from that family while simultaneously linebreeding another family in the same pedigree.

Studying how cattle ranchers brought in new sire lines can be useful. And I suspect that would work well with most livestock. They intentionally inbred to determine whether their breeding stock carried any negative recessive traits (so they could cull them). But then they typically outcrossed or linebred once they knew a line was solid.

When choosing breeding stock, the conformation / health / disposition of the offspring is more important than that of the parents themselves. Sometimes, a beautifully put-together mare will through bad foals and a mediocre mare will throw good foals when bred to a better stallion. I used to call those "pass-through" mares = mares whose own genetics were so weak that all her offspring resembled their sires.
 
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Often times I see people talk about line breeding and what not but not very many go into the logistics of how specifically they keep track of individuals and who the parents are ect.

Take chickens for example with clan breeding. Where you have 3 clans and 3 separate pens  1 rooster per ~12 hens in each.

You can use color leg bands and even put a unique ID # or something on each one. but how do people go about determining what chick came from what hen in this situation ?  especially on larger scale breeding programs.

I heard a few methods but none seem scalable or convenient I should say.  
-trap nest boxes
-breed one rooster to one hen at a time
-assume the hens are laying on their own eggs

or maybe I'm overthinking it - and just simply knowing a chick came from Clan B or w/e is good enough to trace issues back.

I like the idea of using kintraks or some other software to track lines once you have correctly established who the parents are with 100% accuracy though

 
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Having been involved in breeding dogs, horses and cattle I can tell you that willy nilly inbreeding or line breeding is disastrous.  Ask anyone who has a dog with cherry eye or hip dysplasia about how well that works out.  This has to do with recessive genes being paired up so that a problematic gene is no longer masked by its healthy counterpart.  

Line breeding can be done responsibility to fix a specific genetic trait in a  the population you are breeding.  However, it has to be done very carefully.  You must be certain that the original parents are not carrying undesirable recessive genes or you will end up with defective traits also being fixed in the line along with the trait(s) you wanted.

This generally requires breeding both parents first with partners that are known to carry defective recessive genes to see if any of the recessive traits appear in the off spring or doing extensive genetic testing on the proposed parents to look for known bad genes.  

Get with your neighbors and swap stock.  Keep records on who's stock you swapped with and cross them off the list.  It's worth driving an hour or two to keep your herd healthy and not running up the vet bills.
 
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Lisa Sampson wrote:Having been involved in breeding dogs, horses and cattle I can tell you that willy nilly inbreeding or line breeding is disastrous.  Ask anyone who has a dog with cherry eye or hip dysplasia about how well that works out.  This has to do with recessive genes being paired up so that a problematic gene is no longer masked by its healthy counterpart.  

Line breeding can be done responsibility to fix a specific genetic trait in a  the population you are breeding.  However, it has to be done very carefully.  You must be certain that the original parents are not carrying undesirable recessive genes or you will end up with defective traits also being fixed in the line along with the trait(s) you wanted.

This generally requires breeding both parents first with partners that are known to carry defective recessive genes to see if any of the recessive traits appear in the off spring or doing extensive genetic testing on the proposed parents to look for known bad genes.  

Get with your neighbors and swap stock.  Keep records on who's stock you swapped with and cross them off the list.  It's worth driving an hour or two to keep your herd healthy and not running up the vet bills.



This is a great post.  Hybrid vigor is real, and it is important.  Line breeding does work to produce offspring with desirable characteristics, but it can absolutely magnify faults.  Wild animals that have very small gene pools show the effects pretty strongly of too much inbreeding.  The dogs that are the healthiest and live longest, respective of their size, are dogs that are bred for function only.  That types of breeding ignores the breed of dog, and outcrosses of different breeds that function well are common.  Dogs that are still used for their purpose in their native regions are almost never any sort of "pure" breed.
 
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Regarding spiral breeding of chickens. Males don't stay in their mother's flock, they move to the next flock in the rotation. You don't have to keep track of individual hens, roosters, or eggs, you only have to keep track of which flock they belong to. Spiral breeding isn't about keeping pedigrees, it's about separating the birds so that you don't have to.
 
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