The English bulldog's limited genetic diversity could minimise the ability of breeders to recreate healthy phenotypes from the existing genetic stock, which were created by human-directed selection for specific desired physical traits.
Many large regions of the bulldog's genome have been altered to attain the extreme changes in its outward appearance.
This includes significant loss of genetic diversity in the region of the genome that contains many of the genes that regulate normal immune responses.
"The English bulldog has reached the point where popularity can no longer excuse the health problems that the average bulldog endures in its often brief lifetime," said lead author, Niels Pedersen from University of California in the US.
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"More people seemed to be enamoured with its appearance than concerned about its health," said Pedersen.
Improving health through genetic manipulations presumes that enough diversity still exists to improve the breed from within, and if not, to add diversity by outcrossing to other breeds.
"Breeders are managing the little diversity that still exists in the best possible manner, but there are still many individuals sired from highly inbred parents.
"Unfortunately eliminating all the mutations may not solve the problem as this would further reduce genetic diversity," said Pedersen.
This is the first broad-based assessment of genetic diversity in the English bulldog using DNA analysis rather than pedigrees.
The researchers examined 102 English bulldogs, 87 dogs from the US and 15 dogs from other countries.
These were genetically compared with an additional 37 English bulldogs presented to the US Davis Veterinary Clinical Services for health problems, to determine that the genetic problems of the English bulldogs were not the fault of commercial breeders or puppy mills.
The findings appear in the journal Canine Genetics and Epidemiology.