From wild animals to perfect pets, dogs have undergone some interesting changes during their centuries-long domestication
Intent on unraveling some of the developmental secrets of the domestication process, a team of scientists from the University of New South Wales in Sydney, Australia, is doing deep dives into the genomes of a range of canine cousins along the evolutionary chain.
A desert dingo named Sandy has already provided some insight into the process after it beat out an explosive beetle, a pit viper and pink pigeon to win a grant to have its genome decoded as part of the 2017 Plant and Animal SMRT Grant. The SMRT Grant programs enable the scientific community to submit their genome or transcriptome projects for a chance to win PacBio SMRT (Single Molecule, Real-Time) sequencing, which enables the most detailed and comprehensive look at genomes by generating information about long segments of DNA.
Study leader Bill Ballard described in this presentation at the 2018 Plant and Animal Genome Conference that pure dingoes are intermediates between wild wolves and domestic dogs, with a range of domestication traits. This includes duplication of the amylase (AMY2B) locus, associated with adaptation to starch in the diet common in domestic canines, which the dingo lacked.
Being able to study structural variation was key, so Ballard was delighted to use SMRT Sequencing to generate in-depth “long read” sequencing. His team is just beginning to delve into the data they generated from sequencing Sandy’s genome, but they have already noted differences in chromosomal loci. To fully annotate the dingo genome, they are also sequencing the transcriptome of three tissues and the epigenome.
The UNSW team will then compare the dingo genome with those of the grey wolf and the German Shepherd, which they also plan to generate with long reads. This will help shed further light on the domestication process.
As Ballard described in his original SMRT Grant pitch, the team has set out to test a 150-year-old theory by Charles Darwin, which stated that domestication can be divided into two steps, which we now call unconscious and artificial selection; unconscious selection may be defined as non-intentional human selection, while artificial selection is the breeding of desirable traits.
“This is thought to be the process by which thousands of domestic animals and plants around the world have been produced and continue to be developed,” Ballard states. “We aim, for the first time and in a unique case, to test Darwin’s hypothesis and differentiate the genomic and genetic processes involved in unconscious and artificial selection.”
Blood, saliva and hip x-rays have been collected from more than 400 German shepherds.
They are hoping one dog in particular, Kira, will provide additional insight into a debilitating dog condition, hip dysplasia. The seven-year-old female has good hips, and her full DNA sequence could help identify why some dogs get the condition while others do not.
She has become the mascot of the project, and the poster dog for their Hip2Fitcrowdfunding campaign. They are aiming to collect $50,000 AUS to cover the costs of PacBio sequencing and assembly and Bionano scaffolding.
“This work is critical to help ease the pain associated with this condition and to ensure that service dogs are able to help their humans for as long as possible,” Ballard notes on the fundraising page.
Identification of DNA variations that cause hip dysplasia in German Shepherds will also help future studies in other breeds that have hip-associated problems, including golden retrievers, St Bernards, labradors and rottweilers, he adds. Like the dingo project, it will also advance our overall knowledge of canine genetics and development.
