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

Genome Wide Association Study with Imputed Whole Genome Sequence Data Identifies a 431 kb Risk Haplotype on CFA18 for Congenital Laryngeal Paralysis in Alaskan Sled Dogs

Congenital laryngeal paralysis (CLP) is an inherited disorder that affects the ability of the dog to exercise and precludes it from functioning as a working sled dog. Though CLP is known to occur in Alaskan sled dogs (ASDs) since 1986, the genetic mutation underlying the disease has not been reported. Using a genome-wide association study (GWAS), we identified a 708 kb region on CFA 18 harboring 226 SNPs to be significantly associated with CLP. The significant SNPs explained 47.06% of the heritability of CLP. We narrowed the region to 431 kb through autozygosity mapping and found 18 of the 20 cases to be homozygous for the risk haplotype. Whole genome sequencing of two cases and a control ASD, and comparison with the genome of 657 dogs from various breeds, confirmed the homozygous status of the risk haplotype to be unique to the CLP cases. Most of the dogs that were homozygous for the risk allele had blue eyes. Gene annotation and a gene-based association study showed that the risk haplotype encompasses genes implicated in developmental and neurodegenerative disorders. Pathway analysis showed enrichment of glycoproteins and glycosaminoglycans biosynthesis, which play a key role in repairing damaged nerves. In conclusion, our results suggest an important role for the identified candidate region in CLP.

Description of breed ancestry and genetic health traits in arctic sled dog breeds

Background

This study describes the presence and frequency of health traits among three populations of dogs traditionally used for sledding and explores their ancestry and breed composition as provided by the commercially available Embark dog DNA test. The three populations include the purebred Siberian Husky and the admixed populations of Alaskan sled dogs and Polar Huskies. While the Siberian Husky represents a well-established breed with extensive historical and health data, the Alaskan sled dog is less studied but has been the subject of nutritional, physiological, and genetic studies related to ancestry and performance. In contrast, the Polar Husky is a relatively obscure and rare group of dogs used for arctic exploration with very little-known information. The three populations were compared using Embark results, providing new insight into the health traits circulating within the populations and the potential ancestral linkage of the health traits between the sledding populations. Embark results are based upon 228,588 single-nucleotide polymorphisms (SNPs) spanning the canine genome, characterized using a custom-designed Illumina beadchip array.

Results

Specifically, breed composition was summarized for the two admixed populations with most of the dogs being predominantly categorized as Alaskan husky- type dog or “Supermutt”. Mitochondrial and Y chromosome haplogroups and haplotypes were found with Alaskan sled dogs carrying most of the haplogroups and types found in Siberian and Polar Huskies. Genomic principal component analysis reflected population structure corresponding to breed and substructure within the Alaskan sled dogs related to sprint or distance competition. Genetic markers associated with Alanine Aminotransferase activity, Alaskan Husky Encephalopathy, dilated cardiomyopathy, Collie eye anomaly, degenerative myelopathy, ichthyosis, and factor VII deficiency were identified in the populations of sledding breeds.

Conclusion

These results provide a preliminary description of genetic characteristics found in sledding breeds, improving the understanding and care of working sled dogs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40575-021-00108-z.

The effect of a traditional and a stick gang-line on the body position of working sled dogs

This study aimed to investigate the effect of two different gang-lines on the pulling angle of sled dogs. It was hypothesised that dogs would run with a straighter angle of pull (in relation to the main-line) in stick gang-lines (STICK) than they would do in traditional gang-lines (TRAD). Eight sled dogs, divided into two teams, ran a 3.1 km trail twice in both types of gang-lines, pulling a quadbike on dry ground. Each dog remained in its team in the same position (side of gang line, and forward or back in the line) for both runs, using both types of lines in randomised order between the runs. Markers were placed on the dogs and on the main lines, and the runs were recorded by a video camera. The dogs’ angle of pull measured from the video recordings was compared between the two conditions. Thirteen positional measurements for each dog during each run were taken. The dogs were used to running in TRAD and were not acclimatised to STICK. Data was analysed using Wilcoxon and Spearmans rho tests. Data regarding individual dogs (n=13), teams (n=52), dogs’ placements in teams (n=4), and gang-line related pulling angles (n=104) was analysed. Overall, the position of the dogs was straighter when pulling in STICK, than when pulling in TRAD, with a median of 19° (inter quartile range (IQR) 24.75°) and 32° (IQR 25.75°), respectively (P<0.001). Between the two teams, there was no significant difference in pulling positions when running in STICK (P=0.543), but there was in TRAD (P<0.001). In individual assessment, six of the eight dogs ran in a straighter position (P=0.003 to 0.046) in STICK. Dogs running in the front of both teams pulled significantly straighter when in STICK (21°; IQR 23.75) than in TRAD (median 39°; IQR 18; P<0.001).

Local ancestry inference provides insight into Tilapia breeding programmes

Tilapia is one of the most commercially valuable species in aquaculture with over 5 million tonnes of Nile tilapia, Oreochromis niloticus, produced worldwide every year. It has become increasingly important to keep track of the inheritance of the selected traits under continuous improvement (e.g. growth rate, size at maturity or genetic gender), as selective breeding has also resulted in genes that can hitchhike as part of the process. The goal of this study was to generate a Local Ancestry Interence workflow that harnessed existing tilapia genotyping-by-sequencing studies, such as Double Digest RAD-seq derived Single-Nucleotide Polymorphism markers. We developed a workflow and implemented a suite of tools to resolve the local ancestry of each chromosomal locus based on reference panels of tilapia species of known origin. We used tilapia species, wild populations and breeding programmes to validate our methods. The precision of the pipeline was evaluated on the basis of its ability to identify the genetic makeup of samples of known ancestry. The easy and inexpensive application of local ancestry inference in breeding programmes will facilitate the monitoring of the genetic profile of individuals of interest, the tracking of the movement of genes from parents to offspring and the detection of hybrids and their origin.

Studies of modern Italian dog populations reveal multiple patterns for domestic breed evolution

Through thousands of years of breeding and strong human selection, the dog (Canis lupus familiaris) exists today within hundreds of closed populations throughout the world, each with defined phenotypes. A singular geographic region with broad diversity in dog breeds presents an interesting opportunity to observe potential mechanisms of breed formation. Italy claims 14 internationally recognized dog breeds, with numerous additional local varieties. To determine the relationship among Italian dog populations, we integrated genetic data from 263 dogs representing 23 closed dog populations from Italy, seven Apennine gray wolves, and an established dataset of 161 globally recognized dog breeds, applying multiple genetic methods to characterize the modes by which breeds are formed within a single geographic region. Our consideration of each of five genetic analyses reveals a series of development events that mirror historical modes of breed formation, but with variations unique to the codevelopment of early dog and human populations. Using 142,840 genome-wide SNPs and a dataset of 1,609 canines, representing 182 breeds and 16 wild canids, we identified breed development routes for the Italian breeds that included divergence from common populations for a specific purpose, admixture of regional stock with that from other regions, and isolated selection of local stock with specific attributes.

Genetics of canine behavior: A review

The past decade has seen rapid progress in the field of canid behavioral genetics. The recent advances are summarized in this review. The identification of the genes responsible for tameness in silver foxes is the culmination of a half century of behavioral testing and, more recently, genomic investigation. There is agreement that domestic dogs evolved from wolves, but when and from which population remains controversial. The genetic differences between wolves and dogs identified include those for neurotransmitters and digestion. Breed differences in behavior are well known, but only recently have the genetics underlying these differences been investigated. The genes responsible for flank sucking in Doberman Pinschers and for several other obsessive compulsive problems in other breeds have been identified. Aggression is the least desirable canine trait, and several laboratories have detected differences in neurotransmitters and their receptors between aggressive and non-aggressive dogs. In English Cocker Spaniels, the genes linked to aggressive behavior code for dopamine, serotonin, and glutamate receptors. A dopamine transporter gene has been associated with impulsive behavior in Malinois.

Genomic analyses of modern dog breeds

A rose may be a rose by any other name, but when you call a dog a poodle it becomes a very different animal than if you call it a bulldog. Both the poodle and the bulldog are examples of dog breeds of which there are >400 recognized worldwide. Breed creation has played a significant role in shaping the modern dog from the length of his leg to the cadence of his bark. The selection and line-breeding required to maintain a breed has also reshaped the genome of the dog, resulting in a unique genetic pattern for each breed. The breed-based population structure combined with extensive morphologic variation and shared human environments have made the dog a popular model for mapping both simple and complex traits and diseases. In order to obtain the most benefit from the dog as a genetic system, it is necessary to understand the effect structured breeding has had on the genome of the species. That is best achieved by looking at genomic analyses of the breeds, their histories, and their relationships to each other.