Breed-specific ancestry studies and genome-wide association analysis highlight an association between the MYH9 gene and heat tolerance in Alaskan sprint racing sled dogs

Abstract

Alaskan sled dogs are a genetically distinct population shaped by generations of selective interbreeding with purebred dogs to create a group of high-performance athletes. As a result of selective breeding strategies, sled dogs present a unique opportunity to employ admixture-mapping techniques to investigate how breed composition and trait selection impact genomic structure. We used admixture mapping to investigate genetic ancestry across the genomes of two classes of sled dogs, sprint and long-distance racers, and combined that with genome-wide association studies (GWAS) to identify regions that correlate with performance-enhancing traits. The sled dog genome is enhanced by differential contributions from four non-admixed breeds (Alaskan Malamute, Siberian Husky, German Shorthaired Pointer, and Borzoi). A principal components analysis (PCA) of 115,000 genome-wide SNPs clearly resolved the sprint and distance populations as distinct genetic groups, with longer blocks of linkage disequilibrium (LD) observed in the distance versus sprint dogs (7.5-10 and 2.5-3.75 kb, respectively). Furthermore, we identified eight regions with the genomic signal from either a selective sweep or an association analysis, corroborated by an excess of ancestry when comparing sprint and distance dogs. A comparison of elite and poor-performing sled dogs identified a single region significantly associated with heat tolerance. Within the region we identified seven SNPs within the myosin heavy chain 9 gene (MYH9) that were significantly associated with heat tolerance in sprint dogs, two of which correspond to conserved promoter and enhancer regions in the human ortholog.

Figure 1

Alaskan sled dogs are a mixed breed dog, bred strictly for performance attributes. A) Left column: distance racing dogs. B) Right column: sprint racing dogs.

Figure 2

Principle component analysis plots of Alaskan sled dogs (A and B) and four ancestry reference breeds (B) using a panel of 7K highly (F_ST >0.35) informative SNPs. A) Alaskan sled dogs from either distance (DIST-blue) or sprint (SPRT-red) racing kennels. B) Four ancestry reference breeds including AMAL, BORZ, GSHP, and HUSK as well as Alaskan sled dogs divided into their two populations of distance and sprint.

Figure 3

The estimated decay of linkage disequilibrium and degree of autozygosity among Alaskan sled dogs and their four ancestral component breeds. Alaskan sled dogs are divided into distance and sprint racing styles, and compared with their four ancestral reference populations. A) The decay of linkage disequilibrium (LD) is estimated from the distance at which the genotypic association, r², reaches a threshold of 0.5. B) The degree of autozygosity is determined through the cumulative number of runs of homozygosity (ROH) of various length (Mb).

Figure 4

Genome-wide association results of elite versus poorly performing sprint dogs for the heat tolerance attribute. Two genomic loci located on CFA2 and 10 were identified in a comparison of 21 elite and 17 poor performing sprint dogs with regard to the heat tolerance attribute. A panel of 115,425 SNPs, spanning all autosomes and the X chromosome was tested. The x-axis denotes SNP positions in increasing genomic order from CFA 1 through 38 and the X chromosome. The y-axis indicates the –log₁₀ p-value as determined in an association analysis using the program EMMAX.

Figure 5

A comparison of the most prevalent diploid state ancestry blocks across the genome of sprint and distance sled dogs. Individual chromosomes are indicated on the x-axis denoting genomic position (Mb). The most common diploid ancestry blocks across the genome are visualized using the following color scheme with the diploid states (homozygous or heterozygous) defined in the figure legend.

Figure 6

A comparison of the genome-wide frequency of four ancestral reference breeds within the distance and sprint sled dog populations. A) The genome-wide proportion of the individual ancestral reference breeds of AMAL, BORZ, GSHP, and HUSK within the distance and sprint populations. B) The genome-wide proportion of diploid ancestry states within the distance and sprint populations.

Figure 7

Chromosome 16 SNP frequency differences for the four ancestral breeds when comparing distance and sprint populations. The difference in frequency scores (y-axis) between distance and sprint dogs for each ancestral breed was plotted in relation to chromosome 16 SNPs (x-axis). A more positive frequency difference corresponds to a higher selection of the ancestral breed within the distance population while the more negative frequency difference corresponds to a greater selection of the ancestral breed within the sprint population. The region within the red circle denotes an area highlighted as being in the top 5% of genomic regions demonstrating the greatest degree of ancestry selection between sprint and distance dogs, as well as corresponding to a region of selective sweep within distance dogs.