Ok, I have an unusual problem with one of the bloodlines I'm breeding. Not 100% sure it's genetic, but have a pretty good idea that it is.
The 5yo foundation male of this line has a limp in his left rear leg, has had it since he was 7 months. Two factors brought on this limp. First, he was eating puppy food @ the time and also stealing high protein feed from one of my adults. At the same time, he was a very active pup, and played very VERY rough. There was one incident where he was chasing my Shepherd and she accidentally crashed into him, and he hit the fence 
The limp followed soon after. Was originally diagnosed as Pano, we were told to get him on a senior food, which we did, and that exasperated the problem. We bred him, thinking the problem was a combination of Pano and trauma. He still limps constantly, but can flat out run on that leg and pull on lead without showing signs of a limp?!
We've had two litters out of him, a total of 11 pups and NO limping. One male we kept back to stud out. He is 3yrs now and has a few litters on the ground. We have one very small female pup (btw, the foundation male is small, too, maybe 15lbs) who was eating homecooked until 7 months, then was switched to a 26/16 adult food and immediately developed a limp. Our Vet said Pano again (different Vet, if it matters) and doubted any genetic link since it was directly after a food change.
However, we now have 3 pups from two other litters out of the stud directly out of the foundation male. One is 7 months, the other two are 5 months. The 7 month old pup has, the past week or so, been very slightly limping on either rear leg. It's hardly noticable, comes and goes, but it's there. I had her on Wellness pup supplemented with raw. It seems to be gone when on raw for more than a few days, but returns when she's on kibble. I noticed the same thing with a male pup out of the other litter. It's practically not noticable, but every so often, his gait goes "off".
I am PULLING MY HAIR OUT. Save for the 3 pups, our sires/dams are hunting dogs that have OFA hip certs (from good to fair). Their knees have been palpated by my Vet and found to have no luxation. More importantly, my puppy buyers that own littermates and pups directly out of the affected ones have reported NOTHING. No pano, growth problems, nothing. And I do keep in close contact with most of them and ask lots of ?'s so I think I'd know if we had a pattern of this ...
It seems to me like it's a polygenic problem if it is genetic, because it's skipping generations and also seems to require other factors to come out. Also seems like it's a kennel/husbandry problem, something I'm doing wrong here. I know feed has a huge impact on growth, I know a breeder who had pups with bowed legs that went oversize constantly when she fed Ol Roy. Same breedign pairs previously produced normal pups.
I have been wondering about legg perthes but they have no real pain in the leg, I can touch it, press down on the hip - hard. They run and are active. Never move stifflly or seem in any way to be arthritic. No atrophy of the muscle, in fact, these two affected dogs have powerfully muscled rear legs.
So I am puzzled to say the least. Raw feeding and keeping them very slim seems to prevent it altogether. No puppy buyers are reporting any growth related orthopedic problems. Legg perthes is practically unheard of in Beagles and they eventually grow out of Pano. No fever or anorexia in affected dogs. Skips generations. Hips are OFA cert'd on my breeding animals.
Anyone have the slightest clue as to what this could be?
