The Effects of FGF4 Retrogenes on Canine Morphology

Large-scale genomic analysis of the domestic dog informs biological discovery

Recent advances in genomics, coupled with a unique population structure and remarkable levels of variation, have propelled the domestic dog to new levels as a system for understanding fundamental principles in mammalian biology. Central to this advance are more than 350 recognized breeds, each a closed population that has undergone selection for unique features. Genetic variation in the domestic dog is particularly well characterized compared with other domestic mammals, with almost 3000 high-coverage genomes publicly available. Importantly, as the number of sequenced genomes increases, new avenues for analysis are becoming available. Herein, we discuss recent discoveries in canine genomics regarding behavior, morphology, and disease susceptibility. We explore the limitations of current data sets for variant interpretation, tradeoffs between sequencing strategies, and the burgeoning role of long-read genomes for capturing structural variants. In addition, we consider how large-scale collections of whole-genome sequence data drive rare variant discovery and assess the geographic distribution of canine diversity, which identifies Asia as a major source of missing variation. Finally, we review recent comparative genomic analyses that will facilitate annotation of the noncoding genome in dogs.

Use of a free proximal ulnar autograft for ipsilateral radial lengthening in a dog with a short radius and subsequent elbow incongruity

OBJECTIVE

To report the technique and outcome of proximal ulnar autograft transplantation to achieve ipsilateral radial lengthening in a dog with premature closure of both proximal and distal radial physes.

STUDY DESIGN

Case report.

ANIMALS

An 8-month-old female spayed Border Collie.

METHODS

The dog was presented for a grade III/IV left thoracic limb lameness localized to the elbow. Orthogonal radiographs of both forelimbs revealed a 7% length deficit of the left radius and elbow subluxation indices indicative of left elbow incongruity due to suspect premature closure of both radial physes. Radial lengthening consisted of a proximal ulnar ostectomy, a radial osteotomy, and transplantation of the ulnar autograft into the radial osteotomy site secured with an eight-hole dynamic compression plate. Orthopedic examinations were conducted at 2 weeks, 4 weeks, and 3 years postoperatively. Radiographic examinations were completed preoperatively, immediately postoperatively, and at 4 weeks and 3 years postoperatively.

RESULTS

Lameness improved with a grade II/IV lameness at 4 weeks postoperatively and complete resolution at 3 years postoperatively. Radiographic examination at 4 weeks showed persistent radial lengthening of 1 cm, and a decreased humeroradial index (HRI), humeroulnar index (HUI), and radioulnar index (RUI) compared with preoperative values. At the 3 year examination, the HRI and HUI had increased indicating progression of elbow incongruity. The patient remained clinically unaffected.

CONCLUSION

In dogs with radial shortening and elbow incongruity, use of an ipsilateral proximal ulnar autograft with rigid internal fixation can be an effective treatment for radial lengthening to improve elbow congruity and resolve lameness.

Association of the FGF4L2 retrogene with fibrocartilaginous embolic myelopathy in dogs

BACKGROUND

Fibrocartilaginous embolic myelopathy (FCE) is a well-documented condition in dogs although rarely reported in chondrodystrophic breeds. Genetic associations have not been defined.

OBJECTIVES

Define the association of the chondrodystrophy-associated FGF4L2 retrogene with histopathologically confirmed cases of FCE.

ANIMALS

Ninety-eight dogs with a histopathologic diagnosis of FCE.

METHODS

Retrospective multicenter study. Dogs were genotyped for the FGF4L2 and FGF4L1 retrogenes using DNA extracted from formalin-fixed, paraffin-embedded tissue. Associations between breed, FCE and retrogene status were investigated with reference to a hospital population and known breed and general population allele frequencies.

RESULTS

FGF4L2 genotype was defined in 89 FCE cases. Fibrocartilaginous embolic myelopathy was present in 22 dogs from FGF4L2-segregating breeds with allele frequencies of ≥5%; however, all dogs were wild type. Two Labrador retrievers with FCE carried FGF4L2 alleles. Frequency of the FGF4L2 allele was significantly (P < .001) and negatively associated with FCE relative to predicted hospital-population dogs. FCE was overrepresented in Boxer, Great Dane, Yorkshire Terrier, Bernese Mountain Dog, Miniature Schnauzer, Rottweiler, and Shetland Sheepdog breeds.

CONCLUSIONS AND CLINICAL IMPORTANCE

Study data based on genotypically and histopathologically defined cases support the historical observation that FCE is uncommon in chondrodystrophic dog breeds. FGF4 plays an important role in angiogenesis and vascular integrity; anatomical studies comparing chondrodystrophic and non-chondrodystrophic dogs might provide insight into the pathogenesis of FCE.

Special Issue: "Canine Genetics 2"

Wolves were the first animal species to become domesticated by humans, approximately 30,000-50,000 years ago. Human-directed dog breeding over thousands of generations has generated more than 350 recognized breeds displaying surprisingly different phenotypes with respect to morphology, behavior and disease predispositions. The domestication of wolves and the subsequent breeding of dogs can be viewed as one of humankind's oldest and largest genetic experiments and provides us with unique opportunities for research. Dogs have not only become human's best friend but were also described as geneticists' best friend in a past issue of Science. In recognition of the importance of canine genetics, this Special Issue, entitled "Canine Genetics 2", was compiled. It represents a sequel to the former Special Issue "Canine Genetics", which was published in 2019. During the last 15 years, the canine community has heavily relied on a reference genome derived from the female Boxer Tasha. "Canine Genetics 2" includes an article describing a greatly improved version of this important community resource. This Special Issue further contains several reports related to monogenic or complex inherited diseases in dogs. Finally, important aspects of wild canid research, genetic diversity in different populations and canine morphology were investigated.

Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

BACKGROUND

The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.

RESULTS

We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.

CONCLUSIONS

We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.

FGF4L2 retrogene copy number is associated with intervertebral disc calcification and vertebral geometry in Nova Scotia Duck Tolling Retrievers

OBJECTIVES

To evaluate the effects of the chondrodystrophy-associated FGF4L2 retrogene on intervertebral disc (IVD) calcification and vertebral geometry.

ANIMALS

22 Nova Scotia Duck Tolling Retrievers (NSDTR) with no FGF4L2 retrogene (n = 7, wild-type dogs), 1 retrogene copy (8, heterozygous dogs), or 2 retrogene copies (7, homozygous dogs).

PROCEDURES

Computed tomography (CT) scans of the vertebral column were analyzed using computer-aided design (CAD) software. IVD calcification, vertebral column length, and vertebral geometry of the third cervical (C3), 13th thoracic (T13), and first lumbar (L1) vertebrae were compared.

RESULTS

IVD calcification was not found in wild-type dogs. IVD calcification was more frequent in homozygous dogs than heterozygous (P = .008) or wild-type dogs (P < .001) and in heterozygous dogs compared to wild-type dogs (P < .001). Four IVDs were subclinically herniated in 3 dogs (2 homozygous, 1 heterozygous). Calcified IVD had a greater volume and surface area in heterozygous dogs than homozygous dogs. C3 vertebral canal height-to-width ratio was greater in homozygous dogs than heterozygous dogs (P = .044) and wild-type dogs (P = .010).

CLINICAL RELEVANCE

IVD calcification and vertebral geometry can be analyzed using CAD software. The presence of 1 or 2 FGF4L2 copies in the absence of the FGF4L1 retrogene has an additive effect on the number of calcified IVD and a minor effect on vertebral geometry in NSDTR dogs. Data support the use of FGF4L2 phenotyping to reduce clinical disease in segregating breeds and to monitor the introduction of wild-type alleles into fixed breed populations.

Breed-typical front limb angular deformity is associated with clinical findings in three chondrodysplastic dog breeds

Angular front limb deformity (ALD) refers to an excessively curved limb conformation, which is seen in some chondrodysplastic dog breeds. Common characteristics of ALD include carpal valgus (VALG), front limb rotation (ROT), elbow incongruity, and lateral radial head subluxation. These may cause lameness and discomfort in affected dogs. The clinical impact and breed-specific characteristics of front limb conformation in chondrodysplastic breeds are unknown. This prospective and cross-sectional study aimed to investigate differences in front limb conformation between three chondrodysplastic breeds. We further evaluate whether front limb conformation is associated with clinical findings and limb function. We propose novel methods to classify findings in the interosseous space and to quantify lateral radial head subluxation. Data from a total of 224 front limbs from 112 dogs of three chondrodysplastic dog breeds (30 Standard Dachshunds, 29 Skye terriers, and 53 Glen of Imaal terriers) were included in the study. Front limb VALG and ROT were measured with a goniometer. From the radiographs, the elbow joint was graded for incongruity (INC), and the humeroradial angle (HRA) was measured to assess lateral radial subluxation. The association of front limb conformation with clinical signs and limb function was investigated using orthopedic examination, goniometric and kinetic measurements, and radiography. The breeds differed significantly in their front limb conformation. The Dachshund had the least ROT and the least radial head subluxation. The Skye terrier had the most VALG, the most radial head subluxation, and the largest prevalence of moderate and severe INC. The Glen of Imaal terrier had the most ROT. In addition, INC, ROT, VALG, and HRA were found to be independent of each other and were associated with several measurable clinical abnormalities and limb function such as pain, lameness, limited range of motion, and elbow joint osteoarthritis. This implies that VALG, ROT, and HRA could be used in addition to INC grading when choosing musculoskeletal characteristics of dogs suitable for breeding.

Short term outcomes and complications of distal ulnar ostectomy in 23 juvenile dogs with carpal valgus secondary to discordant radial-ulnar physeal growth

Objective

The goal of this study was to report short term clinical and radiographic outcomes after distal ulnar ostectomy in dogs with carpal valgus due to discordant radial-ulnar growth.

Study design

Retrospective case study.

Sample group

Client owned dogs under 1 year of age with carpal valgus and open distal radial physes pre-operatively.

Methods

Medical records from four veterinary referral centers were searched from January 1, 2015 to January 1, 2022 for juvenile dogs that had been treated with distal ulnar ostectomy for carpal valgus due to premature closure of the distal ulnar physis. Patients were excluded if they were skeletally mature at the time of ostectomy; medical records were incomplete; radial physis was closed at surgery; or definitive corrective osteotomy was performed. Radiographs were evaluated pre-operatively and for short term follow up at ~8 weeks. Complications and short term clinical outcomes were evaluated also.

Results

31 limbs from 23 dogs were evaluated. Patients ranged from 4 to 10.8 months of age. All dogs presented for visible carpal valgus and varying degrees of thoracic limb lameness. Sixty-four percent of patients showed resolution of lameness while an additional 13% showed an improvement in clinical lameness without complete resolution. Complications were seen in 32% of patients with 70% percent of those being minor, bandage related complications. Radiographically, 38% of limbs showed bridging callus formation of the ostectomy at an average of 7.5 weeks post operatively and 75% percent of patients with elbow incongruity improved radiographically. There was no significant difference in radial joint angles pre-operatively and at the time of follow up.

Conclusion

Distal ulnar ostectomy ameliorates lameness in juvenile dogs with premature distal ulnar physeal closure and shows lack of progression of distal carpal valgus deformity, but does not improve joint angulation.

Clinical significance

Distal ulnar ostectomy is associated with mild bandage-related complications and halting of progressive limb deformity within the time frame evaluated, and should therefore be considered a treatment for premature closure of the distal ulnar physis. It does not lead to deformity correction at 8 weeks following surgery but is associated with improved elbow congruity.