Scientists have mapped the genome of the German shepherd, one of the world’smost popular canine breeds, after using a blood sample from ‘Nala,’ a healthyfive-year-old German shepherd living in Sydney.

In a paper published today in respected ‘big data’ journal GigaScience, aglobal team of researchers from institutions including UNSW Sydney detailedthe mammoth task of unravelling the 38 pairs of dog chromosomes to decode the19,000 genes and 2.8 billion base pairs of DNA, using advanced geneticsequencing technology.

The new genome not only provides science with a more complete biologicalsnapshot of the dog species ( Canis lupus familiaris ) in general, but alsooffers a reference for future studies of the typical diseases that afflictthis much-loved breed.

Popular choice

UNSW Science’s Professor Bill Ballard, an evolutionary biologist who sequencedthe genome of the Australian dingo in 2017, says German shepherds are popularchoices in the home and the workplace because of their natural intelligence,balanced temperament and protective nature. But after more than a century ofbreeding for desired physical characteristics, they are particularlyvulnerable to genetic diseases.

“One of the most common health problems affecting German shepherds is caninehip dysplasia, which is a painful condition that can restrict their mobility,”says Professor Ballard.

“Because German shepherds make such good working dogs, there has been a lot ofmoney spent looking into the causes and predictors of this problem. Whenworking dogs – such as those trained to work with police or to help peoplewith disabilities – end up getting hip dysplasia, then that’s a lot of losttime and money that has gone into the training of that dog.

“Now that we have the genome, we can determine much earlier in life whetherthe dog is likely to develop the condition. And over time, it will enable usto develop a breeding program to reduce hip dysplasia in future generations.”

Top dog

Nala, who was described in the paper as “an easy going and approachable 5.5year old,” was selected because she was free of all known genetic diseases,including no sign of hip dysplasia. She was located by well-known TV and radiovet Dr Robert Zammit – credited as an author of this paper – who ProfessorBallard says has amassed X-rays and blood samples of more than 600 Germanshepherds.

“Now we’ll be able to look at those hip x-rays and all the DNA of those dogsand compare them back to this healthy reference female,” Professor Ballardsays.

Nala isn’t the first domestic dog to provide a sample for the mapping of thedog genome. In 2003 a poodle called Shadow provided a sample that resulted ina genome that was 80 per cent complete, followed two years later by the firstcomplete mapping of the genome of ‘Tasha’ the Boxer.

Gene machines

But in the decade and a half since, technology has vastly improved to thepoint that the number of gaps – or regions of DNA bases that are unreadable –has fallen dramatically, making the mapping of Nala’s genes the most completeyet.

“The biggest difference between the mapping today and in 2005 is that we nowuse long read sequencing,” says Professor Ballard.

“The Boxer’s genome was put together with ‘Sanger’ sequencing, which can readabout 1000 bases in length at a time, while the technology that is availabletoday – Next Generation sequencing – can read up to 15,000 bases.

“What this means is if you’ve got a region of genes that is duplicated andrunning more than 1000 bases, Sanger sequencing will not be able to tell youwhich part of the genes that particular sequence comes from. So whereas therewere about 23,000 gaps in Sanger’s Boxer genome, the Next Gen sequencer hadjust over 300.”

Bred for success

The German shepherd genome is also an advance on 2005’s Boxer genome becauseof the breed itself. As Boxers are more specialised, with more inbreeding intheir genetic history, the German shepherd’s genome is therefore more generic.The authors believe that this will provide better understanding of theevolution of dog breeds in general.

Professor Ballard reckons this will not be the last time a domestic dogbreed’s genome is sequenced.

“I would expect that as the costs come down, all the major breeds will have agenome mapped within 10 years, because this will help identify specificdiseases, and lots of breeds have known specific diseases.”

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