The Staffordshire County Showground in January is one place where good breeding really does matter. Amid the white picket fences and royal blue carpets of the Manchester Dog Show Society’s General Championship Show, a trotting Chihuahua is overtaken by a Great Dane that is 25 times her size. Long-faced Afghan hounds stick up their noses at flat-fronted pugs. Trimmed boxers yawn nonchalantly in pens while big, bouffanted breeds submit to rigorous backcombing.

Nature in its infinite variety? Not exactly. The story of how the wolf developed into the 200 breeds now recognised by the UK Kennel Club takes in Dawkins via Darwin. It arrives, at the present day, with a stand-off between a film-maker and the Kennel Club, the BBC’s refusal to broadcast Crufts, which starts next week, because of cruelty concerns and a recent report: The Independent Inquiry into Dog Breeding. All three are grappling with the same question: are dog shows the healthy pursuit of perfection, or simply genetic freak shows?

When Sir Patrick Bateson, Emeritus Professor of Ethology at the University of Cambridge and President of the Zoological Society, was asked in December 2008 to chair an inquiry into pedigree dogs, the Kennel Club was embroiled in the biggest controversy of its 137-year history, caused by a BBC film, Pedigree Dogs Exposed, shown a few months before.

Claiming to “lift the lid” on the health and welfare problems of the UK’s five million pedigree dogs — and the £10 million of vets fees spent on them every week — Jemima Harrison’s film showed spaniels writhing in pain and boxers convulsed in epileptic fits. It laid the blame squarely on the Kennel Club: the exaggerated traits encouraged in show rings — curly tails, dwarfism — were leading to horrific disability, deformity and disease. It was, the film concluded, “the greatest animal welfare scandal of our time”.

The shock was seismic. The BBC called an abrupt halt to 40 years of broadcasting Crufts. The RSPCA also deserted, taking many of the show’s sponsors with it. The Kennel Club fought back, lodging a complaint with Ofcom saying it had been treated unfairly. It also announced more tests to screen for diseases and introduced random monitoring of judges.

In December, as Professor Bateson was putting the final touches to his report, Ofcom made its ruling. The BBC film was not unfairly edited, but the Kennel Club had not been given enough time to respond to some of the accusations. Both sides claimed victory.

So January’s report was anticipated by both sides as a final vindication. Evidence had been gathered from breeders, clubs, vets, scientists, welfare groups and pet owners. When it arrived, it too trod a delicate line.

While recognising the potential of dog shows to promote better practice, Bateson outlined four areas as urgently needing improvement: the poor treatment of bitches and litters in commercial establishments known as “puppy farms”; dogs being kept in homes that stifle their instincts; inbreeding being widely practised; and the desire to produce extreme physical traits causing pain and disease in some animals.

“Take almost any breed and it will have experienced significant changes in its form over the last 100 years,” says Dr David Sargan, a geneticist and co-author of another report commissioned in the documentary’s aftermath, Pedigree Dog Breeding in the UK: a Major Welfare Concern?.

Sitting in a room at the School of Biological Sciences at the University of Cambridge, he flicks through the pages of both reports. “The bulldog’s nose has become shorter, but its soft palette hasn’t, which leads to breathing and other problems,” he says, pointing to images of a breed whose head is now so large that 86 per cent of puppies cannot be born naturally.

“Neoteny, or breeding so that adult animals retain a babyish look, is another good example. The Cavalier King Charles Spaniel is bred to have large eyes and a domed skull, like the features of a newborn puppy. But if the animal grows to adulthood with this shaped skull, it can present problems. The back part of the brain, the cerebellum, is also rather too large for the skull. This can cause syringomyelia, the painful condition shown in the BBC’s documentary.”

Sargan’s report, commissioned by the RSPCA and published last February, reached many of the same conclusions as Professor Bateson’s. It found that while the Kennel Club has been quietly working to improve the lot of pedigree dogs, progress has been too slow. Urgent changes were needed, including an independent panel of experts, the systematic collection of data on diseased dogs and a ban on mating half-siblings or grandparents and offspring.