Analyzing Genome Sequencing of 2,000 Canids by the Dog10K Consortium

More than 2,000 canine genomes have been generated and examined by an international research consortium.

Image Credit: rosemaryandpine/Shutterstock.com

Image Credit: rosemaryandpine/Shutterstock.com

The consecutive advanced genetics toolkit could currently be used to answer complex spanning dog domestication, biological questions, behavior and disease susceptibility, genetic differences in breed morphology, as well as the evolution and structure of the genome.

The study, reported in Genome Biology, explains the toolkit resource package and presents the first set of discoveries.

The publication is known to be the culmination of measures from the Dog10K consortium; 48 scientists throughout 25 institutions, contributing samples and resources to the enormous analytical effort.

The goal was to produce a resource the global community could access, and which they could use to speed the translation of their own research, be that in the study of the shared ancestors of dogs and wolves, or the clinical treatment of cancers. All these avenues are exciting, and all can benefit from the Dog10K catalog.”

Jennifer Meadows, Study Co-Lead Author and Research Scientist, Uppsala University

The power of the Dog10K analyses comes from the depth of genetic diversity that the research group was able to capture. Canine samples were drawn from over 320 of the approximately 400 identified pedigree dog breeds, and also niche populations of village wolves, dogs, and coyotes.

With this, the team developed:

  • An extensive catalog of single nucleotide variants, such as those which could disturb protein-coding genes and might impact the extremes of dog appearance and physiology. In the study, all pedigree dogs were free from disease when sampled, implying that a few of the variants that lead to a loss of protein function do not result in obvious disease in that population.
  • A catalog of structural variants. This category of variants consists of a minimum size of 50 base pairs, and so affects more space in the genome compared to a single nucleotide variant.
  • Few structural variants were discovered to affect protein-coding genes. This could imply that too much, or too little of the protein is made in that individual, but again did not result in clear disease in the pedigree population.
  • For both single nucleotide and structural variants, the Dog10K team demonstrated how such variants have been distributed inside and between pedigree dog breeds, and how these variants might impact the study of possible drug therapies.
  • Publicly available data processing pipelines. Integrating the outcomes from various studies can be made highly challenging when various settings are utilized to map sequencing data and further call variation. The pipeline utilized by the Dog10K consortium sets the stage for the community so that new or existing data could be processed and integrated easily with this set.
  • An imputation panel from the single nucleotide variants. Imputation is a process that enables scientists to infer changes at sites that they did not directly quantify.

The Dog10K group displayed that by utilizing the imputation panel, a dataset that contained 170 thousand single nucleotide sites, generally utilized in genotyping array studies, could be expanded to up to 8 million sites. This enables scientists to reuse their useful samples, and to revisit complicated questions that require more data.

We have just scratched the surface of the data’s potential. There is yet more genetic diversity left to be found in dogs, wolves and coyotes, but the Dog10K team looks forward to seeing how this first effort is applied by the canine science community.”

Jennifer Meadows, Study Co-Lead Author and Research Scientist, Uppsala University

This phase of the Dog10K consortium was financially supported by multiple grants, such as the National Institutes of Health (USA), the Chinese Academy of Sciences, the Jane and Aatos Erkko Foundation, the European Research Council, and the Swedish Research Council.

Dr Jennifer Meadows (Uppsala University) and Dr Jeffery Kidd (University of Michigan) are the study’s co-lead authors, with Dr Ya-Ping Zhang (Chinese Academy of Sciences, China) and Dr Elaine Ostrander (National Human Genome Research Institute (NIH)) as the co-senior authors.

Source:
Journal reference:

Meadows, J. R. S., 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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