An International Sequencing Effort to Advance Studies
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National Science Review REVIEW 6: 810–824, 2019 doi: 10.1093/nsr/nwz049 Advance access publication 10 April 2019 1National Human MOLECULAR BIOLOGY & GENETICS Genome Research Institute, National Institutes of Health, Dog10K: an international sequencing effort to advance Bethesda, MD 20892, USA; 2State Key Laboratory of Genetic studies of canine domestication, phenotypes and health Resources and ∗ † † Evolution, Kunming Elaine A. Ostrander1, , , Guo-Dong Wang2,3, , Greger Larson4, Institute of Zoology, 5 6 7 8 Chinese Academy of Bridgett M. vonHoldt , Brian W. Davis , Vidhya Jagannathan , Christophe Hitte , Sciences, Kunming 9 2,∗ 650223, China; 3Center Robert K. Wayne , Ya-Ping Zhang and the Dog10K Consortium for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, ABSTRACT Kunming 650223, Dogs are the most phenotypically diverse mammalian species, and they possess more known heritable China; 4Palaeogenomics and disorders than any other non-human mammal. Efforts to catalog and characterize genetic variation across Bio-Archaeology well-chosen populations of canines are necessary to advance our understanding of their evolutionary history Research Network, and genetic architecture. To date, no organized effort has been undertaken to sequence the world’s canid School of Archaeology, populations. The Dog10K Consortiumhttp://www.dog10kgenomes.org ( ) is an international collaboration University of Oxford, × Oxford OX1 3TG, UK; of researchers from across the globe who will generate 20 whole genomes from 10 000 canids in 5 years. 5Department of Ecology This effort will capture the genetic diversity that underlies the phenotypic and geographical variability of and Evolutionary modern canids worldwide. Breeds, village dogs, niche populations and extended pedigrees are currently Biology, Princeton being sequenced, and de novo assemblies of multiple canids are being constructed. This unprecedented University, Princeton, NJ 08544-1014, USA; dataset will address the genetic underpinnings of domestication, breed formation, aging, behavior and 6College of Veterinary morphological variation. More generally, this effort will advance our understanding of human and canine Medicine and health. Biomedical Sciences, Texas A&M University, Keywords: genomics, genome-wide association studies (GWAS), breed, selection, variation, evolution College Station, TX 77840, USA; 7Institute of Genetics, Vetsuisse INTRODUCTION numbers of founders [24,25]. Consequently, the Faculty, University of extraordinary phenotypic variation across dog Bern, Bern CH-3001, Domestic dogs (Canis lupus familiaris)arethe Switzerland; 8IGDR, most variable mammalian species on Earth [1–3] breeds is accessible through analysis of only a CNRS, University of (Fig. 1). Strong artificial selection has produced modest number of genetic markers [3,26–29]. Rennes, Rennes approximately 450 globally recognized breeds To create dogs with specific phenotypes, breed- F-3500, France and ers often cross closely related individuals, and this 9Department of Ecology with distinct traits related to morphology [4] and Evolutionary including, but not limited to, body size [4,5], tail particularly took place during the early formative Biology, University of phenotype [6], fur type [7,8], skull shape [6,9–11] years of many breeds. One consequence of this strat- California, Los Angeles, and pigmentation [12–15]. Strong breed variation egyhasbeenanincreasedincidenceofbreed-specific Los Angeles, CA 90095, genetic disease. A growing community has taken USA also exists in behavioral traits including herding, guarding and hunting [16], as well as personality advantage of these observations to identify genes for canine maladies that recapitulate human disor- ∗Corresponding traits (e.g. hypersocial behavior) [17] including authors. E-mails: boldness [18] and aggression [19]. The adoption ders, many of which lack suitable mouse models. [email protected]; of the ‘breed barrier rule’, i.e. that no dog may Indeed, with few exceptions, dogs experience the [email protected] same common disorders as humans including can- † become a registered member of a breed unless Equally contributed to cer, heart disease, neurological disorders and di- this work. both its dam and sire are registered members, has led to the establishment of breeds with highly abetes (reviewed in: [20,21,30]). The underlying disease pathology is often similar to humans, as is Received 23 January restricted gene pools [20–22]. As a result, there is 2019; Revised 14 strong phenotypic homogeneity within all breeds the response to treatment and final outcomes (e.g. March 2019; [23]. Most breeds were established within the last [31]). One additional consequence of the restrictive Accepted 9 April 2019 200 years [23,24] and were derived from small breeding programs that produced many modern C The Author(s) 2019. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd. This is an Open Access articleder distributedun the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. REVIEW Ostrander et al. 811 dogs were derived from gray wolves [40] and that no other canine species were involved during the initial phases of domestication [40–42]. In addi- tion, the wolf population(s) that were involved in the early phases of domestication are likely extinct [42]. Despite the recent publication of numerous genetic studies of both modern and ancient dogs, there is as yet no firm consensus regarding either the timing [38,43,44] or location(s) [42,45–49]ofdo- mestication, the long-term effect of domestication on modern dog genomes [37,50], or even the num- ber of independent wolf populations that were in- volved in the process [33,39]. The interpretation of the archaeological record has also been contentious. Though canid remains potentially derived from dogs have been excavated from Mesolithic contexts dated Figure 1. Morphological variation among established to 15 000 years before present in Europe and East breeds. Dog breeds show extraordinary amounts of varia- tion in size, coat color, skull shape, etc. Within a breed there Asia, the status of these remains as dogs or wolves are high levels of uniformity, but between breeds variation is not easily resolved [33,51]. The characterization is common. Beginning at upper left and going clockwise are of genomic sequences from additional ancient and pictures of the following breeds: Brussels Griffon, Afghan modern dog populations has the potential to resolve Hound, Bull Terrier, Chinese Crested Dog, Skye Terrier, these controversies, and establish the early history of Basenji, Gordon Setter and Bernese Mountain dog, and in human–dog relationships. the center is a Cocker Spaniel. Since their domestication, dogs have both adapted to novel environments as they dispersed breeds is the observed excess of recessive diseases, across continents with their human companions many of which have the potential to significantly ad- [52–59], and been subjected to human selection for vance our understanding of human orphan disor- a diversity of occupations and aesthetic preferences. ders, a benefit of no other medical model32 [ ]. As a result, dogs are now globally dispersed, and One of the primary goals of this initiative is there- they are the most abundant carnivore species in fore to advance dogs as a model genetic species. the world with a cosmopolitan distribution. Whole- Dogs were the first domesticated species and the genome sequencing (WGS) studies of numerous only animal domesticated prior to the advent of agri- populations, breeds and wild canids are therefore culture [33]. In order to understand the range of ge- crucial to advance our basic knowledge regarding netic variability in dogs, it is crucial to investigate the genetic outcomes of canine evolution (Fig. 2). the entirety of canine evolution and domestication Generating genome sequences on this scale will history (Fig. 2), which are tightly linked to that of enable us to identify and characterize signals of humans [34–36]. As a result, strong selection on rel- selection related to domestication and dog breed atively few genes underlies many modern domes- formation at an unprecedented level of detail. Such tic phenotypes and may, in some cases, have led to studies will include not only the analysis of single genetic hitchhiking of deleterious alleles that con- nucleotide variants (SNVs), insertion deletions tribute to disease risk [37]. In order to maximize the (indels) and copy number variants (CNVs), but power of dogs as a genetic system for the study of also large structural variants, which are known for human health and biology, and to comprehend the their key roles in aiding our understanding of the genetic basis for the myriad stages of domestication, evolution of humans [28,60]. it is crucial to ascertain the timing, geographical lo- cation and number of wolf populations that were in- volved during domestication [38,39]. Admixture Following domestication, dogs have traveled along- AIMS, SCOPE AND METHODS side humans across continents, often hybridizing Aim 1: define the consequences of with local wild canids. As a result, patterns of re- domestication on existing dog genomic cent and ancient admixture among wild and domes- diversity tic canid species are complex [38,42,60–63]. Dog10K will take advantage of this introgression Domestication