Linked genetic variants on chromosome 10 control ear morphology and body mass among dog breeds

Webster et al. BMC Genomics (2015) 16:474 DOI 10.1186/s12864-015-1702-2 RESEARCH ARTICLE Open Access Linked genetic variants on chromosome 10 control ear morphology and body mass among dog breeds Matthew T. Webster1*, Nona Kamgari1, Michele Perloski2, Marc P. Hoeppner1,3, Erik Axelsson1, Åke Hedhammar4, Gerli Pielberg1 and Kerstin Lindblad-Toh1,2* Abstract Background: The domestic dog is a rich resource for mapping the genetic components of phenotypic variation due to its unique population history involving strong artificial selection. Genome-wide association studies have revealed a number of chromosomal regions where genetic variation associates with morphological characters that typify dog breeds. A region on chromosome 10 is among those with the highest levels of genetic differentiation between dog breeds and is associated with body mass and ear morphology, a common motif of animal domestication. We characterised variation in this region to uncover haplotype structure and identify candidate functional variants. Results: We first identified SNPs that strongly associate with body mass and ear type by comparing sequence variation in a 3 Mb region between 19 breeds with a variety of phenotypes. We next genotyped a subset of 123 candidate SNPs in 288 samples from 46 breeds to identify the variants most highly associated with phenotype and infer haplotype structure. A cluster of SNPs that associate strongly with the drop ear phenotype is located within a narrow interval downstream of the gene MSRB3, which is involved in human hearing. These SNPs are in strong genetic linkage with another set of variants that correlate with body mass within the gene HMGA2, which affects human height. In addition we find evidence that this region has been under selection during dog domestication, and identify a cluster of SNPs within MSRB3 that are highly differentiated between dogs and wolves. Conclusions: We characterise genetically linked variants that potentially influence ear type and body mass in dog breeds, both key traits that have been modified by selective breeding that may also be important for domestication. The finding that variants on long haplotypes have effects on more than one trait suggests that genetic linkage can be an important determinant of the phenotypic response to selection in domestic animals. Keywords: Artificial selection, Dogs, Ear morphology, Body mass, Genome-wide association study Background The huge phenotypic variation in domestic dog breeds i s the result of their unique evolutionary history, which involved two main phases. Firstly, the domestication of dogs from wolves, likely more than 15,000 years ago, involved selection for phenotypes necessary for life with humans [1–3]. Subsequently, in the last few hundred years, a huge variety of breeds were formed from the ancestral dog gene pool, a process that involved extreme * Correspondence: ; 1 Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden Full list of author information is available at the end of the article population bottlenecks and strong artificial selection. These processes have left impacts on patterns of genetic variation, including long blocks of linkage disequilibrium (LD) [4, 5], increased incidence of deleterious mutations [6, 7] and a high prevalence of inherited disease that varies specific to dog breeds. Recent studies have identified specific mutations involved in both phases of dog domestication. These studies give insight into the nature and timing of the dog domestication process and selective pressures involved [8, 9]. Scanning the genome for regions of extreme FST between dogs and wolves and reduced heterozygosity in dogs, consistent with selective sweeps, has identified © 2015 Webster et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Webster et al. BMC Genomics (2015) 16:474 genetic variants that were likely selected during the descent of modern dogs. These include genes involved in starch digestion and brain function, which may underlie adaptation to new diet and behavioural changes [10, 11]. Studies of genomic variation among dog breeds have also uncovered a catalogue of variants underlying their extreme morphological variation and also potentially behaviour and physiology [12–14]. These include shape of ears, snout and limbs, size, tails, coat type and colour. The simplified genetic basis of normal and pathological inherited traits that segregate within dog breeds coupled with long blocks of LD also makes them an outstanding resource for genetic mapping using genome wide association studies (GWAS). The genetic basis of a large number of traits has been identified by taking advantage of these features [15, 16]. Ear phenotypes are of particular interest because phenotypes of many domestic animals are floppy (drop) compared with their wild ancestors, including cattle, goats, rabbits and pigs. The presence of drop ears as a common correlate of domestication is argued to be related to pleiotropic effects of selection for tameness [17, 18]. In support of this, selective breeding experiments to produce tame foxes also resulted in the emergence of drop ears and a suite of other peadomorphic characteristics [19]. Present day dog breeds show huge variation in ear morphology, from pricked ears seen in German Shepherds to large hanging drop ears of Basset Hounds. Ear morphology is included in breed standards and has clearly been under strong artificial selection for these various divergent types. A region on CFA10 (9.8 - 11.8 Mb canFam2.0) harbours a locus with highly divergent SNP frequencies between dog breeds. FST values in this region are among the highest in the genome [12–14]. Across-breed GWAS identified a strong association with ear type in this region. There is also a weaker association with body mass. The strongest correlation with size between dog breeds has been found to be on CFA15, close to the IGF1 gene [20] and the region on CFA10 is secondary to this [12, 13]. Derived variants at six loci, including these two have been shown to account for 64.3 % of variance in weight among breeds with standard weights (<41 kg) [21]. Whereas a single locus in the CFA10 region correlates strongly with the ear phenotype of almost all drop and prick ear breeds [12, 13], body mass correlates with a variant at high frequency in a subset of small breeds [12, 21]. The strongest associations with both body mass and ear type identified from GWAS lie in a region 3′ (downstream) of the methionine sulfoxide reductas (...truncated)