Canine DNA Database Provides Unprecedented Look at Dog Evolution

A global collaboration of scientists, under the leadership of Dr. Jeff Kidd from the University of Michigan, Dr. Jennifer R. S. Meadows from Uppsala University in Sweden, and Dr. Elaine A. Ostrander from the NIH National Human Genome Research Institute, is leveraging an exceptionally extensive canine DNA database to conduct an impartial exploration into the evolutionary processes that have given rise to the diverse breeds of our canine companions.

Canine DNA Database Provides Unprecedented Look at Dog Evolution
The team analyzed more than 48 million pieces of genetic information, discovering that each breed dog has around 3 million single nucleotide polymorphism differences. Image Credit: Jacob Dwyer

A recently published paper in the journal Genome Biology unveils the findings of the Dog10K project. This initiative involved the sequencing of genomes from nearly 2,000 samples representing 321 distinct breeds of dogs, wild dogs, coyotes, and wolves, with a reference sample taken from a German Shepherd named Mischka.

By examining over 48 million genetic data points, the research revealed that each breed of dog exhibited approximately 3 million single nucleotide polymorphism differences.

These single nucleotide polymorphisms, often abbreviated as SNPs or colloquially referred to as “snips,” are primarily responsible for the genetic diversity observed among both humans and dogs.

Additionally, the study identified 26,000 deleted sequences unique to the German Shepherd, absent in the compared breed, and 14,000 sequences in the compared breed that were absent from Mischka’s DNA.

We did an analysis to see how similar the dogs were to each other, and it ended up that we could divide them into around 25 major groups that pretty much match up with what people would have expected based on breed origin, the dogs’ type, size and coloration.”

Dr. Jeff Kidd, Professor, Human Genetics and Computational Medicine and Bioinformatics, University of Michigan

He further noted that the majority of these differing genes were linked to morphology, reinforcing the notion that the distinctions among breeds were primarily shaped by the dogs’ physical appearances.

In comparison to dogs, wolves displayed approximately 14% greater genetic diversity. Interestingly, wild village dogs, which are dogs cohabiting with humans in villages or urban areas but not kept as pets, showcased a higher degree of genetic variability than purebred dogs.

Moreover, the dataset, processed using the high-performance computing cluster at the University of Michigan, unveiled an unusual prevalence of retrogenes. Retrogenes are novel genes formed when RNA is reversed into DNA and reinserted into the genome at a different location.

In the study, a total of 926 retrogenes were identified, with one of the most well-known examples being a retrogene known as FGF4. This particular gene is responsible for the short-leg characteristic observed in breeds like dachshunds and corgis.

Dogs tend to have an increased amount of retrogenes which have resulted in mutations that were selected for, that perhaps people found cute and bred more of.”

Dr. Jeff Kidd, Professor, Human Genetics and Computational Medicine and Bioinformatics, University of Michigan

Dr. Kidd’s laboratory is currently working to unravel the reasons behind the frequent occurrence of retrogenes and insertions in dogs.

One of the advantages of the Dog10K consortium lies in its extensive scale. This sizeable collaboration empowers researchers not only at the University of Michigan but also across the scientific community to investigate the genetic foundations of various canine traits and even prevalent canine illnesses, including cancer.

Source:
Journal reference:

Kidd, J. M. J, et al. (2023). Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biology. doi.org/10.1186/s13059-023-03023-7.

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