Inbreeding, Line Breeding, Out-crossing

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default Inbreeding, Line Breeding, Out-crossing

Post  FinchG on Tue Feb 01, 2011 9:16 pm

Inbreeding, Line-breeding, Out-crossing and Pedigree Analysis.
By Dave Henderson

Gregor Mendel was the founder of modern genetics. Over a hundred years ago he established a set of “rules” which still hold true today. He established the principles of dominant and recessive traits and worked out the expected ratios of these when different combinations were paired together. Mendel used plants in his studies. The traits he studied were all SINGLE GENE characteristics. Most bird breeders are familiar with colour variants. All of the colour mutations we know of in birds are single gene traits. This makes it relatively easy to predict the expected outcomes of pairings involving colour mutations in birds.

However, all of the other traits we tend to look for in exhibition birds are governed by MULTIPLE GENES all acting together in combination. These traits such as size, shape, feather quality, colour etc are known as POLYGENIC TRAITS. Although the individual genes in polygenic traits conform to Mendel’s rules, collectively they don’t. This tend to make these trait’s a lot less predictable.

Polygenes and genetic variation.

Birds and animals inherit one copy of each gene from their parents. In birds and mammals two alternate forms of each gene can exist and these are called alleles. For any one gene each parent can pass on one of it’s two alleles to it‘s offspring. Therefore, for a single gene there are four possible combinations of alleles which an individual can inherit from it’s parents. When more than one gene is involved the number of possible combinations of alleles increases. For example when two different genes are involved in a trait then there are eight alleles involved and 16 potential combinations possible. If three genes were involved then there would be 12 alleles and 64 possible combinations. If ten genes were involved(i.e. 40 alleles- 20 from each parent) then there are over a million possible combinations of the alleles involved. The study of mathematical combinations of genes is known as quantitative genetics.

Polygenic traits involve a massive element of chance. Say, for example, with greenfinches, the shape and size of the head was governed by 5 different genes then there would be over a thousand possible combinations of the alleles involved when two birds were paired together. Obviously, there will be an optimum mix of the alleles which will result in the best possible head shape obtainable from the alleles involved. On the other hand the breeder may be unlucky and breed some birds which have inherited the worst possible mix of the alleles available.

In other words, even when breeding from outstanding birds, there is a very high element of chance involved and the breeder may be unlucky and end up with youngsters at the lower end of the quality scale. Often when two very good birds have produced poor quality youngsters, the breeder has been unlucky and further matings from the same pair could still potentially produce very good chicks.

Just now and again, the breeder may hit the jackpot and breed birds which have inherited the best possible allele combinations from their parents and in inheriting double copies of some desirable genes the youngsters can turn out to be better than both parent birds.

The genetic basis for breeding from related birds.

When we breed from related birds we greatly increase the chances that the youngsters will inherit double copies of the same alleles because it’s more likely their parents share the same alleles given that they descended from common ancestors. In other words, we reduce the amount of variation.

In the example given above where 5 genes are involved in head quality, lets say that because the parent birds are closely related, the two alleles the cock has for Gene number 3 are identical and are exactly the same as the two alleles the hen has for Gene number 3. In this case were are now really only dealing with variable alleles from four genes instead of five. This would mean then that the total number of allele combinations would be reduced from over a thousand to around two hundred and fifty. In other words, by doubling up on identical alleles from one of the 5 genes involved, we’ve reduced the statistical variation of the trait by 75%.


By inbreeding, a family of birds tends to be created in which all of the birds tend to look like one another. Unfortunately, inbreeding often produces a family of uniformly mediocre birds rather than a family of uniformly excellent birds but more of this later!

What is the difference between inbreeding and line-breeding?

Inbreeding by it’s widest definition, is the breeding together of related individuals.

The term “close-breeding” is a better way of describing pairings between closely related individuals such as brother/sister, mother/son, grandfather/granddaughter, cousin/cousin etc. In these cases the common ancestor appears “close-up” in the pedigree i.e. seond generation.

“Line-breeding” is generally a milder form of inbreeding in which a deliberate attempt is made to repeat lines to a specific target ancestor. Compared to close-breeding the common ancestor in a line bred individual will typically appear further back in the pedigree often at the fourth or fifth generation. IDEALLY, THE DUPLICATED ANCESTOR(S|) SHOULD APPEAR ON BOTH SIDES OF THE PEDIGREE(i.e. behind both the sire and the dam) otherwise the breeder is only line breeding on one side of the pedigree and this lessens the chances of the offspring inheriting double copies of the target ancestors alleles. Olin Gentry (one of the great American racehorse breeders) is often quoted as saying “ breed the sire to the best blood of his dam”. Many racehorse breeders firmly believe that horses will go on breeding in kind when returned to opposite sex strains of the gene pool from which they descend.

In many forms of bloodstock e.g. thoroughbred racehorses, breeders refer to inbred animals as those with a common ancestor within the first four generations of the pedigree. They tend to consider animals with a common ancestor beyond the fourth generation as being line-bred.

The importance of selection.

When practising inbreeding you reap what you sow. It is very easy to start an inbreeding programme in which you inbreed to a really good cock bird who perhaps excels in many ways. However, lets say that despite appearing to be an outstanding specimen the cock bird happens to be very nervous in temperament. It’s almost certain that four or five generations down the line, the whole family will be acting like a complete bunch of highly strung lunatics because by being inbred they’ll all have inherited large doses of the genes which governed his temperament.

So the key here is to be really observant when selecting your foundation stock because if you aren’t it’ll come back to haunt you.

In my experience some of the most significant negative traits to watch for in native birds are (1)nervousness (2)twirling or twisting (3)dropped wings (4)dipped or hollow backs (5)narrowness of the skull (6)eyes too high up on the skull (7)infertility (8)hens which are poor feeders.

The last two are really important. If you select birds which are poor breeders the family will not be able to propagate itself in the long term.


The key to effective inbreeding is to select for “good” traits and be ruthless in weeding out birds which have “negative” traits. This requires a high degree of discipline from the breeder and you have to be the worst critic of your own birds! If a breeder of racing pigeons only selects birds for breeding based on their looks rather than their flying ability he’ll soon be breeding birds which can barely fly across the street.

The pros and cons of inbreeding.

Geneticists and breeders have known for hundreds of years that one of the quickest ways to “fix” desired characteristics or traits into a bloodline of any species is to inbreed to the most superior individuals. Inbreeding can and does produce marvels but as highlighted above it can also produce the worst of the worst. Ugly, nervous, bad tempered, infertile, unhealthy individuals.

This negative effect of pairing together related birds is known as INBREEDING DEPRESSION.

It happens because it is almost impossible to only double up on the “good” alleles. Inbreeding also concentrates the negative ones as well. The difficulty is that very often the negative traits won’t be visually obvious in the early part of the breeding programme. They are often difficult to detect for they can accumulate slowly. As the breeding programme progresses they’ll usually come to the surface.

An inbreeding experiment in America using pigs from excellent bloodlines was started in 1935. By 1940 there were only 37 left in the breeding programme. By 1953 this had dropped to 27 and by 1960, when the experiment was abandoned there were only 10 left! A perfect example of inbreeding depression.

In my experience of years of breeding greenfinches, it is very difficult to maintain size in a bloodline year in and year out. Even if you start with a lot of big birds they’ll soon, after a short number of years, be producing smaller birds unless you introduce new blood. The famous budgerigar breeder Harry Bryan maintained that if you took a pair of top class exhibition budgies and bred them and their youngsters together year after year, without introducing any new blood, you’d soon arrive back of the quality of the wild budgerigar. In fact Harry Bryan at one time bred exhibition rabbits and it was common for breeders to inbreed rabbits deliberately in order to REDUCE their size!

It is true that some bloodlines do seem to be resistant to inbreeding depression but they’re the exception to the rule.


If you spend time reading and studying about breeding animals and birds whether it is racehorses, pigeons, pigs, sheep, dogs or greenfinches one thing becomes obvious. Out-crossing has to be utilized in order to breed functional and effective animals.

It is also a fact that animals that truly possess pre-potency(the ability to produce offspring of superior quality) are hardly ever inbred individuals.

Out-crossing produces “heterosis” or hybrid vigour. Introducing hybrid vigour normally produces positive effects. Let me give some examples.

During the 1980’s my fathers’ pigeons were descended from the strain of the great John Kilpatrick.However, his birds were quite inbred so he decided to bring in some new blood. At that time one of the Belgian strains of pigeons(called Catrysse) were doing a lot of winning not only in Belgium but in England as well. One particular English fancier( Les Newman from Cambridgeshire) had the Catrysse strain from birds he’d selected directly himself from Belgium. My father bought some of these birds from Les Newman and crossed them into the Kilpatricks. He hit the jackpot. The hybrid pigeons which resulted were exceptional flyers. Among the many wins he had, my father won the Rennes race from France(over 500 miles) which was the top race in Scotland and was known as “The Blue Riband” of pigeon racing. In that one race alone he won a lot of money and a brand new car!

The largest of the big cats isn’t the lion or the tiger. It’s the liger which is a cross between a lion and a tiger. At the moment there are only 13 examples of this hybrid in the world. All of them are huge, powerful beasts which are much bigger than even the biggest lions and tigers. Some of these hybrids are twelve foot in length excluding their tail!

The Aga Khan is one of the worlds richest men and one of the most successful breeders of racehorses in Europe. During the 1950s and 1960s Marcell Boussac was one of France’s richest men and he was also a famous owner/breeder of racehorses. However, as Marcell Boussac got older, his health and business empire began to falter and he became bankrupt. In his later years his horses became quite inbred because he only used his own homebred stallions for covering his mares as he couldn’t afford the stud fees to use outside stallions. When Marcel Boussac became bankrupt, the Aga Khan bought out his horses lock stock and barrel. The Aga then sold off the poorer quality mares and bred the best ones to his own stallions. This out crossing of two exceptional bloodlines resulted in a number of fantastic racehorses being bred. Among them was Shergar, who still holds the record for winning the Derby by the widest margin in the history of the race.

Out-crossing very often produces superstars. It’s also a fact that the positive effects from out crossing are usually at their optimum effect in first crosses (F1 hybrids).

Over the years that I’ve been breeding birds, I’ve seen many exhibitors reach the top of the tree with their birds only to have their bloodline “collapse” a short number of years afterwards. I’ve seen it countless times with greenfinches in particular. Many people who start up with birds will make it their business to find out who the top breeders are and buy birds from a number of them. They then interbreed these birds from different strains and produce some very good birds, often unknowingly benefiting from the effects of hybrid vigour by using unrelated birds in the first place. As their birds improve they interbreed them and continue to improve their birds by inbreeding until they reach the stage a few years down the line where their birds get so inbred they start to go back the way.

The biggest mistake a breeder can make is to fail to recognise the early signs of inbreeding depression and worse still fail to take action to counteract it. The correct action would be to bring in some outcrosses. However, the breeder who is at the very top of the tree has the best birds in the country. Where can he go to get birds which are worthy of breeding with his own? So he ploughs on with his own birds and ends up ruining his bloodline.

So where should the breeder go for an outcross?

The outcross should come from an unrelated strain of birds which themselves have been the subject of rigorous selection over a number of years. In other words, don’t bring in any old bird just because it looks like a good specimen. It is far better to bring in an average bird from a good bloodline than a good bird from a weak family( i.e. a family in which there are only one or two good birds and the rest are mediocre). Many breeders fail to realise this and become obsessed with only bringing in exceptional birds.

It is a fact that some strains of birds and animals work well when crossed with other specific strains of their species and don’t work so well with others. My greenfinches for example may work well when paired with some of John Smith’s birds but not so well with Joe Bloggs’ line. Horse breeders call these compatible bloodlines “nicks”.

If you do bring in a bird from a really good line and it doesn’t click with yours it doesn’t mean to say your line isn’t compatible with the other guys. It may just be that that particular bird didn’t work for you.

I think the best tactic when out crossing is not to bring in just one bird but to bring in several in the same year and try all of them. That way you’ll find out which ones work. When a stud of birds has reached the stage that it’s been poisoned by inbreeding then bringing only one cock bird as an outcross is hopeless because it’s likely that every hen in the stud needs to be bred to a totally unrelated cock bird and vice versa. The other advice I would give would be to use both cocks and hens for out crossing rather than just one sex alone.

You may well end up breeding some youngsters from an outcross which turn out to be disappointing. However, if you select the best youngsters and breed them back to your own birds the following year there’s a very good chance you’ll then produce some better birds. They’ll benefit from the hybrid vigour introduced.

One last point about out-crossing. It sometimes produces birds which although very good individuals themselves, fail in turn to produce good birds when used for breeding themselves. This is due to the “hybrid” mix of their alleles which can prevent them from passing on enough “concentrated” traits themselves. It’s case of trial and error when breeding with out-crossed birds. Sometimes it works, other times it doesn’t.

What does good look like in a pedigree

In my experience very few bird British bird breeders keep pedigrees for their birds. They can usually tell you the sire and dam of most of their birds and also the grandparents but beyond that they tend to struggle. However, keeping pedigrees is a good thing because it allows you to see at a glance all the immediate ancestors of the bird and this has it benefits. So what should we look for in a pedigree?

AP Indy was a top racehorse having won 8 of his 11 races all at the very top level and is one of the top racehorse stallions in the US. He stands at a stud fee of $300,000 and he’ll typically cover up to 120 mares in a season. AP Indy has an exceptional pedigree and is a pre-potent stallion. He produces a high number of stakes winners.

In the US there are a series of three top races for 3 year old horses called the Triple Crown. Pretty much all of the top horses compete in these races. It is very hard to win one of these races. It is extremely rare for a horse to win all three. In fact only 13 horses in history have won the triple crown. AP Indy’s sire Seattle Slew won the triple crown. His dam(Weekend Surprise) was an exceptional broodmare and her sire, Secretariat, was arguably the best racehorse in the history of American racing. Secretariat was also a triple crown winner and broke the track record in two of his triple crown races. All of the other horses listed in the 3 generation pedigree were top class. Poker, Buckpasser and Bold Ruler were all fantastic runners and stallions and among the very best of their generation.

There are no duplicated ancestors in the first 3 generations of the pedigree. However, Bold Ruler was also the sire of Boldnesian. So in fact AP Indy is line bred to 4x3 to Bold Ruler. If you go further back in the pedigree AP Indy is also line bred 5x4 to Nasrullah. This latter horse was the pre-eminent stallion in America in the 1950s and had a massive influence on shaping the breed in that country.

So to sum up. The horse is bred from two outstanding parents. He has two exceptional formers in the first two generations of his pedigree and there is not a weak ancestor anywhere in his first four generations. Further back in his pedigree there are duplications of high performing, pre-potent animals. His pedigree is packed with quality and the best performers “close up” in the pedigree.

When breeding animals, if you continually breed from exceptional performers, particularly those that are also pre-potent then you are likely to breed a high number of good individuals. This holds true both for animals which compete athletically and those which compete based on their looks e.g. show birds.


Breeding winners is a numbers game

I hopefully outlined at the start of this article the complexity that exists in birds and animals as a result of polygenic traits. Many of the polygenic traits that we look for in our birds e.g. feather quality aren’t governed by 4 or 5 genes interacting together but thousands. The fact is that even with meticulous attention to detail, rigorous selection during breeding etc the breeder (even those with outstanding birds) will, every year, breed more average birds than exceptional ones. In my experience, in an average year, about 20% of the birds I breed are worth keeping back. In exceptional years it can be 50%.

In thoroughbred horse racing the races are graded based on quality. The top races are known as “stakes races” and this bracket also includes the Classics such as the 2000 Guineas, the Derby, the St. Ledger etc. The authorities publish a table each year which lists, for each stallion at stud, how many of his sons and daughters have won stakes races. Lists are also available which detail for each stallion how many of the foals he has produced in his lifetime have been stakes winners. The top commercial stallion in Britain and Ireland is a horse called Saddlers Wells. His covering fee is a whopping £250,000. With a fee like that he attracts mares which are bred in the purple, many of which are winners of top races or have already produced foals which have turned out to be exceptional performers. Yet remarkably, Saddlers Wells lifetime stakes winners to foals produced ratio is only 13%. I say remarkably, but in fact he’s the only stallion in the British Isles who’s stakes winners ratio is in double figures. The best of the rest are typically 8%-9%.


Here is a summary of some of the points made above.

- Breeding programmes should consist of a combination of inbreeding and out-crossing.
- When inbreeding make sure that the target ancestor(s) appears on both sides of the
-It is a waste of time inbreeding to poor quality birds
- You reap what you sow. Selection is the key to breeding good birds.
- Try to follow a practice of breeding together the best birds possible
- Repeated, unrelenting inbreeding is likely to lead to the collapse of the bloodline.
- When introducing an outcross ideally it should come from another top bloodline which has itself
been subjected to rigorous selection over a number of generations
- Accept that when bringing in new blood sometimes you have to go backwards to go forwards
- Breeding involves a large element of chance(luck). It’s a numbers game. The more birds you breed
the more likely you are to breed some good ones.
-Accept that even with the best planning and attention to detail you will still produce more bad birds
than good ones

FinchG Inbreeding, Line Breeding, Out-crossing Birds_zps98e5f41b Inbreeding, Line Breeding, Out-crossing Dans-fleur_zpsc53bae9e
Lots Of Societies, 11 Gouldians, 4 Orange Cheek Waxbills, 2 Orange Weavers, 3 Spice Finches,1 Quaker, 1 Conure and 2 Lineolated Parakeets


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