With the publication of a new study, the accepted wisdom surrounding dog domestication has been turned on its head. It shows that a gene mutation that helped breed tiny dogs — like the Spitz and Miniature Poodle — is actually an ancient part of the canine genome, which was also found in the DNA of a 53,000-year-old Siberian wolf.
Determinants for large dogs
Human height is what is known as a “continuous trait,” where the incredible variation between individuals is due to an immensely complex combination of genes. “In man, if you look for the difference between one five foot three and six foot five […]if you look at human height, human skeletal size, and body mass, there are hundreds of genes involved,” says Dr. Elaine Ostrander, a distinguished senior researcher at the National Human Genome Research Institute of the National Institutes of Health (NIH).
When it comes to body size in dogs and other canids, the picture is a little less complicated, but there’s still no magical gene that controls whether a newborn dog is the size of a towering St. Bernard or an ankle. annoying chihuahua. However, a gene insulin-like growth factor 1 (IGF1), plays an important role in the process. The gene is thought to confer about 15% of the total variability in canine height – a far greater contribution than any height gene in humans.
While IGF1The role of the canine in canine body size has long been known, but researchers have not been able to identify a mutation in the gene that could produce the effects. “How could we not find the mutation? That can not be that hard. But it turns out we just had to look at DNA differently; backwards instead of forwards,” says Ostrander.
“Genetic Back Pocket”
A postdoc in Ostrander’s lab, Jocelyn Plassais, found the mutation in what Ostrander calls a “genetic back pocket,” hidden away on the strand of DNA that codes for the IGF1 gene, but lurk on the other strand, called the “antisense” strand, in a region that codes for a type of transcript called long non-coding RNAs (lncRNA). LncRNAs, as their name suggests, do not encode proteins, but their ability to regulate coding regions of the genome is beginning to be recognized – Ostrander points out that a similar effect has already been found on the size of dog-ears.
Plassais had searched for the gene in a catalog of 1,431 canine genomes, some generated from archives such as the Sequence Read Archive and others newly generated at the NIH’s Intramural Sequencing Center. After identifying the mutation, a single nucleotide polymorphism called rs22397284, Plassais, Ostrander and colleagues mapped three genotype variants, called alleles. Some dogs had two cytosine nucleotides (genotype CC), some had two tyrosine nucleotides (TT), and others had a heterozygous combination of both (CT).
The team then mapped these three genotypes based on body size in a sample of more than 50 dogs. The results indicated that rs22397284 was the influential point mutation they were looking for. Virtually all Miniature Schnauzers, weighing 5 to 20 pounds, had the CC allele, while a significant proportion of Standard Schnauzers (slightly stockier at 30 to 50 pounds) had a heterozygous CT genotype. Giant Schnauzers, who live up to their name at up to 85 kilos, were practically all TT in polymorphism.
The team did not discontinue its analysis in domestic dogs. They also studied other animals in the canid family, such as coyotes and jackals, the genomes of wolves and even the closely related Andean fox. This analysis showed a strong geographic association, with canids in the Global South tending to have a CC genotype associated with smaller body size. “In the southern hemisphere,” says Ostrander, “there seems to be an advantage to being smaller.”
A Tale of Little Dogs
In collaboration with evolutionary biologists Professor Greger Larson from the University of Oxford and Dr. Laurent Franz of Queen Mary University of London/Ludwig-Maximilians-Universität, the team then took a look back in time to try to determine the origin of the “little” dog allele. Their findings turned paradigms surrounding dog domestication on their head. Since wolves are large and domestic dogs are smaller, conventional wisdom would suggest that the domestication of dogs, which began around 20,000 to 40,000 years ago, would have been accompanied by a chance mutation that reduced their body size. “Then people picked on it because we wanted little dogs for our companions,” says Ostrander. The new findings, she says, suggest that “only the last part of it is true.”
Instead, the team’s analysis showed that CT-heterozygous wolves with one copy of the “large” allele and one copy of the “small” allele roamed the Siberian tundra over 50,000 years ago. “That was so exciting and so surprising,” says Ostrander, “because it didn’t fit into our naive worldview.”
While the exact path that IGF1 has taken over over the last 50 millennia is yet to be recorded, it appears that it has almost become extinct among wolf populations. However, it was reawakened by the genetic forces of selective breeding during domestication, illustrated in Ostrander’s article by the emergence of many ancient genomes with CC alleles in the Middle East around 10,000 years ago.
A genetic continuum
In the next steps of Ostrander’s team, the researchers will approach this surprising finding from different angles. Plassais is striving to figure out exactly how a mutation in an lncRNA can lead to such dramatic changes in body size, and aims to do functional work to map the pathway. Ostrander has targeted other genes – her analysis shows that another gene, LCORLprobably has a similar effect on height as IGF1. “I want to know how all these proteins work together and affect body size,” says Ostrander.
There is incredible complexity in the genetic and proteomic pathways. But, Ostrander reminds me, there is also incredible phenotypic variation among man’s best friends that we’ve only just begun to scratch the surface of. “We always talk about the little things: the toy poodles and the miniature spitz and the Chihuahuas, and the big things, the Newfoundlands and the Saint Bernards and the Great Danes,” Ostrander concludes. “But there’s a whole continuum in the middle. Where all those genes are so important. And I also want to understand this continuum.”
reference: Plassais, J., vonHoldt, BM, Parker, HG, et al. Natural and human-directed selection of a single non-coding body size variant in ancient and modern canids. act. organic 2022;32:1-9 doi:10.1016/j.cub.2021.12.036.