Author Topic: Line breeding and outcrossing -a paper  (Read 7948 times)

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Offline Eceni

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Line breeding and outcrossing -a paper
« on: May 27, 2008, 10:06:08 AM »
Seemed to me like the Optigen thread was becoming full so I'd start a new one

this paper was just brought to my attention.  If followed, it could revolutionise (for the better) dog breeding:

http://www.siriusdog.com/genetic-health-dogs-bragg.htm

happy reading  ;)

e
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Offline djangonut

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Re: Line breeding and outcrossing -a paper
« Reply #1 on: May 27, 2008, 02:29:45 PM »
Wow!  Someone as revolutionary as me,  but having the genetic background to be authoritative, and the discursive skills to make new ideas accessible.

Two sentences stood out in this long, brilliantly argued paper.

"A breed's gene pool may be likened to a bank account; one cannot go on making withdrawls without the occasional deposit."

And

"Deep structural change cannot occur without widespread debate among fanciers."

Forums (fora?) like Cockers on Line are brilliant for introducing different ideas and debate.  And many COLers are new to the breed,  and can be influenced before the old 19th Century rules of thumb like "two generations of breeding in,  then one out" can take hold.  With modern genetics we understand so much more!

I am sure serious breeders on this list will have much food for thought if they can find the time to read it.  Thank you Eceni for sharing.

John


Offline Jane S

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Re: Line breeding and outcrossing -a paper
« Reply #2 on: May 28, 2008, 09:40:32 AM »
I've seen this article before and found it incredibly heavy going and certainly not that accessible for the average breeder. Yes there's food for thought there although this constant blaming of all that's wrong in dog breeding on the show ring seems to miss the point that (in the popular breeds anyway), most puppies do not come from show breeders (meaning breeders who actually show). Maybe things are different in Canada (or they were when this article was first written back in the 1990s) but you only have to look at the quarterly breed record supplements to see that genuine show litters make up a relatively small percentage of all Cocker litters registered in the UK. So many puppies are now coming from commercial breeders or BYBs who have no interest or knowledge of the things discussed in this article & who are far more likely to breed more closely than the average show breeder (either through ignorance or because they're trying to get currently popular colours like liver/chocolate). I looked up a pedigree recently of a dog who's currently in rescue and he's the result of a BYB mating a half brother and half sister together :o This sort of breeder couldn't care less about genetic health and diversity but he's also the type of breeder many (perhaps most) owners end up getting their Cockers from.

The small kernel of breeders who do care about these issues will already be thinking along some of the lines discussed in the article (and other articles) which is why some are importing from overseas or are using AI to bring in different lines but these kind of serious breeders are in the minority - there's a whole different world out there away from the relatively small world of the dedicated "fancier".

Jane

Offline KellyS

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Re: Line breeding and outcrossing -a paper
« Reply #3 on: May 28, 2008, 12:43:32 PM »
I printed this off, for a bit of bed time reading but found it very heavy going... ;) It does give food for thought but agree with Jane - commercial breeders & BYB have more to answer to.
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Offline Colin

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Re: Line breeding and outcrossing -a paper
« Reply #4 on: May 28, 2008, 01:02:51 PM »
I printed this off, for a bit of bed time reading but found it very heavy going... ;)

A good cure for insomnia though.  :lol2: The aim seemed to be to impress his peers with his intellectual prowess rather than state his points in a clear and concise manner for the average reader to understand - which is never a good thing. By the time I'd waded my way through to the end I was too busy sighing in relief to care what he had to say.  ph34r  :lol2:

Offline djangonut

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Re: Line breeding and outcrossing -a paper
« Reply #5 on: May 28, 2008, 02:40:08 PM »
It's good to know that Jane thinks that a kernel of thoughtful breeders are beginning to think along these lines.

I don't think that anyone is blaming or even suggesting that show breeders deliberately caused genetic disease like PRA or FN,  although some breeders fought for a long time, denying that their dogs were responsible,  sometimes blaming vaccination for inherited kidney disease. But now that greater genetic knowledge is available,  breeders cannot continue inbreeding with heads in the sand.  Jane has stated before that responsible breeders are Optigen screening,  eye testing,  and hip scoring to ensure stock is free from genetic disease.  This is great for the disease that we already know,  but not great for the next lethal mutation which will rear its head if the old breeding practices are continued.

Show breeders are not always whiter than white though.  I am aware of a "fancier",  a breeder/exhibitor and judge,  who supplies a commercial kennel with surplus stock.  And I was recently benched near a dog which lunged and snapped at other dogs passing its cage.  The dog has recently won a high show award and will possibly become a champion and be offered at stud.  No doubt it will be screened, tested and scored,  but may still pass on its poor temperament to its puppies most of whom will go into pet homes, some possibly with children.

I have had three different back-yards in my breeding career.  I have known many   caring breeders of quality show stock who have reared puppies under the sink,  in front of the fire,  or in the garden shed.  Most people probably start as back-yard breeders.

I agree with Jane that there is a problem with commercial breeding establishments.  Perhaps the Kennel Club must address the problem before registering puppies from such places.  The Kennel Club's own geneticist,  Jeff Sampson,  has only recently contributed to a paper on the problems arising from inbreeding.  Here's the introduction:

Population Structure and Inbreeding From Pedigree Analysis of Purebred Dogs

Federico C. F. Calboli, Jeff Sampson, Neale Fretwell and David J. Balding

Genetics, Vol. 179, 593-601, May 2008, Copyright © 2008

Dogs are of increasing interest as models for human diseases, and many
canine population-association studies are beginning to emerge. The choice of
breeds for such studies should be informed by a knowledge of factors such as
inbreeding, genetic diversity, and population structure, which are likely to
depend on breed-specific selective breeding patterns. To address the lack of
such studies we have exploited one of the world's most extensive resources
for canine population-genetics studies: the United Kingdom (UK) Kennel Club
registration database. We chose 10 representative breeds and analyzed their
pedigrees since electronic records were established around 1970,
corresponding to about eight generations before present. We find extremely
inbred dogs in each breed except the greyhound and estimate an inbreeding
effective population size between 40 and 80 for all but 2 breeds. For all
but 3 breeds, >90% of unique genetic variants are lost over six generations,
indicating a dramatic effect of breeding patterns on genetic diversity. We
introduce a novel index for measuring population structure directly from
the pedigree and use it to identify subpopulations in several breeds. As
well as informing the design of canine population genetics studies, our
results have implications for breeding practices to enhance canine welfare.


Dr. Sampson will surely be influencing Kennel Club policy about breeding practices over time.  With computer records and co-efficients of inbreeding it should not be beyond the bounds of fancy for a Kennel Club to refuse to register puppies from commercial kennels which indulge in thoughtless breeding practices from unscreened stock.

Finally I think the whole paper by Jeffrey Bragg neatly summarises and brings together a lot of threads that have been affecting my thinking about dog breeding.  And he offers a way forward for dog breeds to progress,  instead of to regress, in this present century.   Some people obviously found the article too long or too contentious,  just as I found Peggy Grayson's "History of the Cocker Spaniel" too dense, and too much like a list. Other people on this forum think of Peggy's book as cocker holy writ. It takes all sorts ......

John

Offline Jane S

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Re: Line breeding and outcrossing -a paper
« Reply #6 on: May 28, 2008, 05:23:21 PM »
I didn't find the article particularly contentious - it doesn't really contain anything I haven't read before. It's just too long and not written in a way that it will be widely read and understood by most breeders which should surely be the aim of any article aimed at changing the way breeders think.

Show breeders are not always whiter than white though. 

I have not claimed that all show breeders are whiter than white. The article clearly lays the blame for poor breeding practices on the show ring and my point was that show breeders form a minority of breeders out there and therefore their influence cannot possibly be as great as stated in the article. You also might have misunderstood what a backyard breeder is - I was not referring to breeders who breed litters in the home or in "front of the fire" and I can definitely guarantee that none of the breeders I respect ever started out as BYBs in the way this term is used these days.

Perhaps the Kennel Club must address the problem before registering puppies from such places.

I'm sure most good breeders would like to see the KC taking a stronger line and refusing to accept registrations from puppy farmers/commercial breeders but while they rely on the income they get from such breeders, it's never going to happen.

Jane

Offline Eceni

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Re: Line breeding and outcrossing -a paper
« Reply #7 on: May 28, 2008, 08:03:49 PM »
To be honest, if you're going to write something which is a) less than the size of a telephone directory and yet b) details the nature and causes of the current crisis in dog breeding, I don't think you can get any less dense than this paper.  I doubt very much if this author was trying to impress anyone, what he was doing, in my opinion, was bringing together in one place - in a way that accessible to professional and amateur breeders - the current (at the time of writing) science of population genetics.  It was concise, thorough and yet covered all the major bases.

and yes, most dogs are not bred by 'professional kennels' but almost everyone I've ever spoken to who breeds has got their ideas of what's 'A Good Plan' from speaking to the professional breeders in their chosen breed - and almost all have been encouraged to line breed. 

A recent letter in 'Dogs Today' - which is about as generic as you can get - was from a woman who wanted to breed her Cavalier King Charles Spaniel (we could ask why, when the world is hardly short of Cavaliers, but that's a separate thread, and not for here).  I think she could safely be characterised as a conscientious backyard breeder because she went back to the professional who had bred her bitch and asked for advice on which dog to use.  She was advised to use the bitch's own grandfather. 

In reply to her query of whether his was wise (sane woman :)) - Malcolm Willis, the KC's geneticist said that it wasn't wise at all and that in choosing a stud, she should make sure she didn't have an in-breeding co-efficient of greater than 10%.  He went on to say that most KC breeds kept their coefficients under 10 which is wild wishful thinking, but interesting that he wants people to believe it.

I have looked at a number of breeds now, and trying to find a coefficient under 10 is challenging in the extreme.  There are some working cockers, but not a huge number, and it does rather depend on how far back you go in your calculations - the original gene pool was small.  (but there are some, which is why I'm here.  If I find another breed as diverse, that has minimal inherited defects, I'll let you all know.)


So someone, somewhere has to convince the professionals who are certain that their Victorian breeding methods (which were fine then, truly) are no longer applicable in the 21st century - and these people have to start educating down the line or 20/30 years from now, the next generation of breeders are going to be very unhappy people, with even more unhappy dogs.   

that was the gist of his paper.  I think it bears reading and understanding - only with solid science have we any chance at all of convincing the vested interest that it's in their greater interests to learn and change.

every breeder practices genetic science at each mating. I'd say there's a moral and professional obligation to understand the latest science, or if not, to listen to those who do.

what we need also, is to achieve this without creating the backlash of people who feel as if they're being personally insulated and assaulted.  What he's saying, clearly, is that the 19th Century techniques were right at the time and were the peak of understanding. It's just that understanding has moved on, and dog breeding has moved on and we're in a different situation now, which we need to approach with different ideas. 

It's not that hard, I think?

e
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Offline Jane S

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Re: Line breeding and outcrossing -a paper
« Reply #8 on: May 28, 2008, 09:30:43 PM »
It's not that hard, I think?

You're not taking into account the fact that breeders come from all sorts of backgrounds - very few have the sort of training you've had and many will struggle with the concepts you're discussing here. Others will have no difficulty in understanding and will happily research & read widely into genetic issues but they're not necessarily going to accept things are as black & white as some make out - they'll make up their own minds which is as it should be. Many sensible, intelligent breeders do see the merits of a wider gene pool and will be looking at ways of achieving this and still have the kind of dogs they want to live with but they won't like being told what to do, especially in a way which comes across as patronising or hectoring - not saying this is applies to you at all but it certainly does apply to some writers I've come across (in dog magazines and online).

PS Malcolm Willis is not the KC's geneticist - this position is held by Dr Jeff Sampson. Malcolm Willis is no particular fan of the KC (having fallen out with them quite publicly a few years ago) so I would presume he must believe his statement that most KC breeds keep their coefficients below 10 (whether this belief is mistaken or not).

Jane

Offline Eceni

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Re: Line breeding and outcrossing -a paper
« Reply #9 on: May 28, 2008, 09:56:43 PM »

PS Malcolm Willis is not the KC's geneticist - this position is held by Dr Jeff Sampson. Malcolm Willis is no particular fan of the KC (having fallen out with them quite publicly a few years ago) so I would presume he must believe his statement that most KC breeds keep their coefficients below 10 (whether this belief is mistaken or not).



Heck... that must've been when I was looking the other way... apologies...

e
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Offline Eceni

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Re: Line breeding and outcrossing -a paper
« Reply #10 on: May 29, 2008, 11:42:50 AM »
For those who find the original paper too dense, this is written by a geneticist who came late to the dog world, but understood the need for change. It's more or less the same information, but written in metaphor and so might be more digestible? (the tribute to the author from his daughter on the main page, is very touching)

the article is called 'The Poodle and the Chocolate Cake' - if you can do a mental search and replace switching 'poodle' for 'cocker spaniel' (or other breed of your choice) it'll be even better   ;)

http://www.canine-genetics.com/cake.htm

m

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Offline Jane S

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Re: Line breeding and outcrossing -a paper
« Reply #11 on: May 29, 2008, 02:52:41 PM »
Yes that article is much more accessible. I also like this one on Popular Sires from the same site :-

http://www.canine-genetics.com/Popular_sires.htm
Jane

Offline spanielcrazy

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Re: Line breeding and outcrossing -a paper
« Reply #12 on: May 29, 2008, 04:35:12 PM »
"New and revolutionary ideas"? Hardly. This is at the heart of the debate that has been going on for a very long time in many many breeds. And yes, even show going folk are upset at the exaggerations and loss of working ability, among many problems and genetic defects suffered by all breeds.

The problem is so multi-faceted that it would require huge changes at all levels; the breed clubs taking a stronger stand and having more power on the directon of their breeds; a complete restructuring of the various kennel clubs functions, rules and organization; stronger judges education, including genetics as well as a general dog knowledge, in addition to breed specific education; and much much more.

At least we in cockers are in a rather unique position, having basically 3 lines running within our breed: partis, solids and working, not to mention the diversity of pedigrees afforded internationally, and as dog breeds go, ours is a very healthy, hearty breed. Having come from, and observed, many breeds who are in serious trouble, I am happy with what is available to us in cockers

Genetics is still a very inexact science (and a bit of an art). Many experienced breeders can tell you what looked good in theory didn't work in practice and vice versa, and outcrossing, either within lines, or out of the breed alltogether is not a magic bullet, and not without it's own set of problems 
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Offline workingcockers

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Re: Line breeding and outcrossing -a paper
« Reply #13 on: May 29, 2008, 11:55:26 PM »
There are some working cockers, but not a huge number, and it does rather depend on how far back you go in your calculations - the original gene pool was small.

Not too sure what you mean by this - the root gene pool was the same but by selective breeding for differents traits we are where we are with our 2 types...

The genetic conditions we inherited - nobody caused them. Dr Sampson thinks the gene mutation predates the 'land spaniel' and Optigen have said to me that the same pra mutation is found in many other breeds (cant remember the number without finding the paperwork). All we can do is now use the genetic tests but not ignore other breeding criteria. The fact is that most people on the forum are here out of a genuine love of the breed/want to learn more etc and are probably the most likely to use these tests as breeders/future breeders.

In breeding co efficients are something I keep an interested eye on

Many experienced breeders can tell you what looked good in theory didn't work in practice and vice versa, and outcrossing, either within lines, or out of the breed alltogether is not a magic bullet, and not without it's own set of problems 
I agree totally with this.
Kirsten Strachan
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Offline djangonut

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Re: Line breeding and outcrossing -a paper
« Reply #14 on: May 30, 2008, 07:08:34 AM »
PRA occurs in other breeds of course, but isn't FN a cocker confined mutation?

You can look up FN pedigrees and follow the lines almost to where and when the mutation occurred,  and where and when the disease crossed over from the particolour show lines into the solids.

John