Copy number variation underlies complex phenotypes in domestic dog breeds and other canids

Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole genome CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray technologies. We have taken advantage of this data set to perform the first CNV-based genome-wide association study (GWAS) in canids. We identify 96 loci that display copy number differences across breeds, which are statistically associated with a previously compiled set of breed-specific morphometrics and disease susceptibilities. Among these, we highlight the discovery of a long-range interaction involving a CNV near MED13L and TBX3, which could influence breed standard height. Integration of the CNVs with chromatin interactions, long noncoding RNA expression, and single nucleotide variation highlights a subset of specific loci and genes with potential functional relevance and the prospect to explain trait variation between dog breeds.

Dogs have been the subject of intense study over many decades (Vilà et al. 1999; Ostrander and Wayne 2005; Freedman et al. 2014; Ostrander et al. 2019), providing valuable insight into human history, disease, and evolution (Coelho et al. 2018; Ní Leathlobhair et al. 2018; Wang et al. 2019). Much has been learned about canines through traditional approaches, including genotype studies with microsatellites (Irion 2003), single nucleotide polymorphisms (SNPs) (Gundry et al. 2007; Boyko et al. 2010; Vaysse et al. 2011), and, finally, whole genome sequencing (WGS) (Lindblad-Toh et al. 2005; Freedman et al. 2014; Plassais et al. 2019).As a result of the extensive history of genetic studies in dogs, remarkable advances have been made toward the resolution of the canine phylogeny (vonHoldt et al. 2010; Parker et al. 2017) and the temporal, geographic, and demographic history of dog domestication (Freedman et al. 2014; Shannon et al. 2015; Skoglund et al. 2015). Studies suggest that dogs were initially domesticated from gray wolves 15,000 to 40,000 yr ago (Freedman et al. 2014; Skoglund et al. 2015; Freedman and Wayne 2017; Ostrander et al. 2019), with a rapid diversification of breeds occurring within the past few hundred years. Currently, about 400 dog breeds exist worldwide, 193 recognized by the American Kennel Club and 360 by the Fédération Cynologique Internationale. Breed classification schemes have been proposed based on occupation, morphology, and geographic origin (American Kennel Club 2007; Wucher et al. 2017). The most recent genetic analysis, encompassing nearly 200 breeds and populations, suggests a monophyletic origin for most modern breeds and provides data regarding their origins and timing (Parker et al. 2017). Clusters of genetically similar breeds were identified and assigned to clades, which often reflected occupational and geographical origins.Targeted and genome-wide genotyping approaches have led to the discovery of nearly 400 variants associated with more than 270 traits, over 220 of which correspond to possible models for human diseases (Online Mendelian Inheritance in Animals [OMIA], Sydney School of Veterinary Science, https://omia.org/). Particularly, genome-wide association studies (GWASs) involving modest size cohorts of dogs have led to the identification of variants controlling a variety of morphological, behavioral, and disease traits (Akey et al. 2010; Vaysse et al. 2011; Rimbault et al. 2013; Hayward et al. 2016; MacLean et al. 2019; Plassais et al. 2019).The recent and intense artificial selective pressure exerted on dogs has induced pronounced inter-breed phenotypic differences while preserving intra-breed homogeneity. This process makes dogs of the same breed more likely to share not only morphometric traits but also disease susceptibilities (Karlsson and Lindblad-Toh 2008; Chase et al. 2009; Akey et al. 2010; Boyko et al. 2010; Marchant et al. 2017; Mansour et al. 2018; Ostrander et al. 2019). The level of anatomic similarity among dogs of any one breed is sufficiently strong that genetic studies have been successfully executed using breed standards as phenotypes, thus unraveling the genetic bases of some complex traits such as body size or behavior (Akey et al. 2010; Boyko et al. 2010; Vaysse et al. 2011; Hayward et al. 2016; MacLean et al. 2019; Plassais et al. 2019), which remain elusive, even in humans.However, all these analyses have been performed using a subset of indicative SNPs and, more recently, SNPs from WGSs (Jagannathan et al. 2019; Plassais et al. 2019), but other forms of genomic variation have rarely been studied systematically. In fact, there is still a lack of fine-scale, genome-wide analyses of any variants other than SNPs across dog breeds, a notable exception when compared to humans and other model organisms (Yalcin et al. 2011; Brown et al. 2012; Sudmant et al. 2015). Copy number variation (CNV) has been previously studied in canines to elucidate specific phenotypes (Karyadi et al. 2013; Arendt et al. 2014; Waldo and Diaz 2015; Deane-Coe et al. 2018). However, most studies have focused on the comparison of dogs and wolves using array-based technologies, rather than undertaking a comprehensive and unbiased examination of all CNVs across the genome of distinct breeds (Berglund et al. 2012; Schoenebeck et al. 2012). Most CNV-related studies published to date only aimed to identify segmentally duplicated regions and did not aim to produce quantitative copy-number (CN) genotypes (Quilez et al. 2012; Molin et al. 2014). Knowing the exact number of copies at a locus is crucial for an accurate comparison of closely related organisms, such as distinct dog breeds and wild canids.Here, we present a fine-scale CNV map of over 300 canid samples using WGS to produce the most extensive, high-resolution CNV panel in dogs to date. We examine more than 145 individual breeds, as well as nonbreed dogs, including village dogs, dingoes, captive New Guinea singing dogs, and wild canids such as wolves. We employ this data set to determine the ability of CNVs to recreate a current dog phylogeny. Moreover, we test for breed-phenotype associations using an extensive data set of breed standards as individual phenotypes in the first CNV-based GWAS performed in dogs to date.