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. 2019 Jul;6(4):810-824.
doi: 10.1093/nsr/nwz049. Epub 2019 Apr 10.

Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health

Elaine A Ostrander  1 , Guo-Dong Wang  2   3 , Greger Larson  4 , Bridgett M vonHoldt  5 , Brian W Davis  6 , Vidhya Jagannathan  7 , Christophe Hitte  8 , Robert K Wayne  9 , Ya-Ping Zhang  2 ; Dog10K Consortium
Collaborators, Affiliations

Collaborators

Affiliations

  • 1 National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
  • 2 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
  • 3 Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
  • 4 Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford OX1 3TG, UK.
  • 5 Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-1014, USA.
  • 6 College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA.
  • 7 Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland.
  • 8 IGDR, CNRS, University of Rennes, Rennes F-3500, France.
  • 9 Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.

Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health

Elaine A Ostrander et al. Natl Sci Rev. 2019 Jul.
. 2019 Jul;6(4):810-824.
doi: 10.1093/nsr/nwz049. Epub 2019 Apr 10.

Authors

Elaine A Ostrander  1 , Guo-Dong Wang  2   3 , Greger Larson  4 , Bridgett M vonHoldt  5 , Brian W Davis  6 , Vidhya Jagannathan  7 , Christophe Hitte  8 , Robert K Wayne  9 , Ya-Ping Zhang  2 ; Dog10K Consortium

Collaborators

Affiliations

  • 1 National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
  • 2 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
  • 3 Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
  • 4 Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford OX1 3TG, UK.
  • 5 Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-1014, USA.
  • 6 College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA.
  • 7 Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland.
  • 8 IGDR, CNRS, University of Rennes, Rennes F-3500, France.
  • 9 Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.

Abstract

Dogs are the most phenotypically diverse mammalian species, and they possess more known heritable disorders than any other non-human mammal. Efforts to catalog and characterize genetic variation across well-chosen populations of canines are necessary to advance our understanding of their evolutionary history and genetic architecture. To date, no organized effort has been undertaken to sequence the world's canid populations. The Dog10K Consortium (http://www.dog10kgenomes.org) is an international collaboration of researchers from across the globe who will generate 20× whole genomes from 10 000 canids in 5 years. This effort will capture the genetic diversity that underlies the phenotypic and geographical variability of modern canids worldwide. Breeds, village dogs, niche populations and extended pedigrees are currently being sequenced, and de novo assemblies of multiple canids are being constructed. This unprecedented dataset will address the genetic underpinnings of domestication, breed formation, aging, behavior and morphological variation. More generally, this effort will advance our understanding of human and canine health.

Keywords: breed; evolution; genome-wide association studies (GWAS); genomics; selection; variation.

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Figures

Figure 1.

Figure 1.

Morphological variation among established breeds.…

Figure 1.

Morphological variation among established breeds. Dog breeds show extraordinary amounts of variation in…

Figure 1.
Morphological variation among established breeds. Dog breeds show extraordinary amounts of variation in size, coat color, skull shape, etc. Within a breed there are high levels of uniformity, but between breeds variation is common. Beginning at upper left and going clockwise are pictures of the following breeds: Brussels Griffon, Afghan Hound, Bull Terrier, Chinese Crested Dog, Skye Terrier, Basenji, Gordon Setter and Bernese Mountain dog, and in the center is a Cocker Spaniel.
Figure 2.

Figure 2.

Phylogenetic tree shown is based…

Figure 2.

Phylogenetic tree shown is based on 15 kb of exon and intron sequence.…

Figure 2.
Phylogenetic tree shown is based on 15 kb of exon and intron sequence. Branch colors identify the red fox-like clade (red), South American clade (green), wolf-like clade (blue), and the gray and island fox clade (orange). Tree was constructed using maximum parsimony. Bootstrap values and Bayesian posterior probability values are listed above and below the internodes. Dashes indicate bootstrap values <50% or posterior probability values <95%. Species names are represented with the matching illustrations to the right. The figure is used with permission from Lindblad-Toh et al. [3].
Figure 3.

Figure 3.

Multiple bottlenecks have shaped the…

Figure 3.

Multiple bottlenecks have shaped the structure of haplotypes and LD observed in modern…

Figure 3.
Multiple bottlenecks have shaped the structure of haplotypes and LD observed in modern breeds. Schematic indicates two bottlenecks that defined modern breeds. The first is believed to have occurred more than 11 000 years ago during domestication. The second encompasses many individual bottlenecks that occurred during primary breed formation about 200 years ago, producing the founders of the breeds observed today.
Figure 4.

Figure 4.

Neighbor-joining tree of 161 dog…

Figure 4.

Neighbor-joining tree of 161 dog breeds. Cladogram showing relationships among 161 dog breeds…

Figure 4.
Neighbor-joining tree of 161 dog breeds. Cladogram showing relationships among 161 dog breeds that divide into 23 clades. Breeds that form unique clades are supported by 100% bootstraps and are combined into triangles. For all other branches, bootstrap values are ≥90% (gold star), 70%–89% (black star) and 50%–69% (silver star). The figure is used with permission from Parker et al. [63].
Figure 5.

Figure 5.

Shared regions of homozygosity (RoH)…

Figure 5.

Shared regions of homozygosity (RoH) and length of homozygosity (LnH) data derived from…

Figure 5.
Shared regions of homozygosity (RoH) and length of homozygosity (LnH) data derived from SNP chip analyses. (A) represents each of 80 individual dog breeds, and displays the overall pattern of loss of private homozygosity beginning with one dog and expanding to 10 unrelated individuals. (B) illustrate homozygosity decay curves for a small subset of breeds at high levels of RoH and a low rate of decay [Bull Terrier (BULT) and Collie (COLL)], and a low level of RoH and a high rate of decay [Chihuahua (CHIH) and Australian Shepherd (AUSS)]. The figure is used with permission from Dreger et al. [71].
Figure 6.

Figure 6.

Multiple measures define dog breeds.…

Figure 6.

Multiple measures define dog breeds. In mapping traits such as body size, height…

Figure 6.
Multiple measures define dog breeds. In mapping traits such as body size, height or mass, measures of legs, skull, back, etc. need to be considered. The most accurate results will be derived from the most precise and greatest number of appropriate well-measured features. Because recognized breeds have well-established standards that encompass the above, breed standard data can often substitute for individual measures.
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References

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