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

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.

Fig. 1

Genetic associations with ear type and body mass among dog breeds. a Manhattan plot showing raw p-value of association with ear type (upper panel) and body mass (lower panel) among dog breeds across ~174,000 SNPs. The most significant associations with ear type are found within a region 9.5–12.5 Mb on CFA10. The most significant association with body mass is found on CFA15, close to the IGF1 gene. The CFA10 region associated with ear type is the second most strongly associated region for body mass. b Expanded view of the CFA10 region showing association with ear type (upper panel) and body mass (lower panel). c Significance of association between allele frequency and ear type (upper panel) and body mass (lower panel) at 123 candidate SNPs within a ~2 Mb region on CFA10 in 288 samples from 46 breeds. d Position of human RefSeq genes mapped onto the canFam2.0 reference. Genes are labelled +/− according to direction of transcription

Fig. 2

Patterns of SNP variation in a 3 Mb region on CFA10. The first 5 bars show variation in the sequence capture (SC) pools of single breeds and the next 6 bars show variation in the whole genome sequencing pools (WGS; see Table 2 for details). Red lines represent SNP positions that are fixed for a non-reference allele in a particular pool, grey lines represent SNP positions that cannot be confidently assessed due to low coverage. Sites that are polymorphic within a breed, or that match the reference allele are not marked. The bottom 3 bars represent SNPs that display patterns of fixation that matches phenotypic variation. Candidate SNPs for controlling variation in body mass (blue) ear type (green) and those that are fixed for alternate alleles in all dogs compared to wolves (purple) are shown. The location of protein coding genes in the region are also shown, which were identified by mapping human RefSeq genes onto the canFam2.0 dog assembly. Genes are labelled +/− according to direction of transcription. Ear and body mass candidates are concentrated in a region between the MSRB3 and HMGA2 genes, whereas a cluster of dog-wolf fixations is found within the MSRB3 gene

Figure 3

Haplotype structure inferred across 15 SNPs highly associated with ear type or body mass and patterns of linkage disequilibrium. a Locations of SNPs on the haplotype relative to the MSRB3 and HMGA2 genes. SNPs and haplotypes associated with ear type are highlighted yellow whereas those associated only with body mass are highlighted orange. Only haplotypes present >7 times in the dataset are shown. b Pairwise estimates of linkage disequilibrium measured by |D’|

Fig. 4

Patterns of genetic variation and candidate SNPs. a Variation in heterozygosity within dogs and F_ST between wolves and dogs in a 3 Mb region on CFA10 encompassing the critical interval associated with ears and body mass. Both statistics were measured in 40 kb windows. Horizontal dotted lines represent cutoff values for percentiles across the entire genome. A region with extremely high F_ST and extremely low heterozygosity (11.15–11–-25 Mb) is marked by a vertical dotted line. b Detailed view of the SNPs most associated with ear type, which are clustered downstream of the MSRB3 gene and the SNPs that are fixed for alternate alleles between wolves and dogs, including a cluster of SNPs within the MSRB3 gene. The ear type associated SNPs are located at sites that map to lincRNA transcripts in the human genome, whereas the cluster of dog-wolf fixed SNPs are found in introns of MSRB3. Also shown are the GERP conserved elements derived from a 39 eutherian mammal alignment [50]