An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs

Allelic frequency of 12-FGF4RG and the association between the genotype with number of calcified intervertebral discs visible on radiographs in Coton de Tuléar and French Bulldog breeds

BACKGROUND

Intervertebral disc disease (IVDD) is a major welfare issue in chondrodystrophic dogs. It is a consequence of chondroid metaplasia of the nucleus pulposus, leading to premature degeneration and calcification of the intervertebral discs (IVDs). Radiographic grading based on the number of calcified discs visible on radiograph (CDVR) between the ages of 24-48 months is an established method for selective breeding against IVDD in dogs. Premature IVD degeneration has a genetic background, and a FGF4 retrogene insertion on chromosome 12 (12-FGF4RG) has been shown to be involved. The aim of this study was to determine the 12-FGF4RG allele frequency and genotype proportions, and the influence of the 12-FGF4RG genotype on number of CDVR in a study population of young adult Coton de Tuléars and French Bulldogs. In this combined prospective and retrospective analytical study, we investigated dogs radiographically screened at 24-48 months of age. The first dataset consisted of 12-FGF4RG genotyping results of 465 Coton de Tuléars and intervertebral disc calcification (IDC) grading results (no, mild, moderate, or severe) for 222 of them. The second dataset included 12-FGF4RG genotypes and IDC grading results (no or severe) of 81 French Bulldogs.

RESULTS

We observed 12-FGF4RG homozygous, heterozygous and wildtype individuals in both studied breeds. The 12-FGF4RG allele frequencies were also lower than previously reported in the studied breeds and Coton de Tuléars had lower allele frequency (0.35) than French Bulldogs (0.85). The distribution of IDC grading results were 59% no, 16% mild, 9% moderate and 16% severe in Coton de Tuléars and 59% no and 41% severe in French Bulldogs. In both breeds, every copy of the 12-FGF4RG allele significantly increased the risk for a higher number of CDVR, indicating incomplete dominance.

CONCLUSIONS

Our results confirm the significant association between the 12-FGF4RG allele and the number of CDVR and IDC grade in two different chondrodystrophic breeds in age-controlled cohorts of young adult dogs. Our results also suggest that radiographic screening of CDVR and genetic testing of 12-FGF4RG could be used to breed against IVD degeneration predisposing to IVDD.

An Evolutionary Perspective on Dog Behavioral Genetics

Dogs have played an outsized role in the field of behavioral genetics since its earliest days. Their unique evolutionary history and ubiquity in the modern world make them a potentially powerful model system for discovering how genetic changes lead to changes in behavior. Genomic technology has supercharged this potential by enabling scientists to sequence the DNA of thousands of dogs and test for correlations with behavioral traits. However, fractures in the early history of animal behavior between biological and psychological subfields may be impeding progress. In addition, canine behavioral genetics has included almost exclusively dogs from modern breeds, who represent just a small fraction of all dog diversity. By expanding the scope of dog behavior studies, and incorporating an evolutionary perspective on canine behavioral genetics, we can move beyond associations to understanding the complex interactions between genes and environment that lead to dog behavior.

Case report: FGF4L1 retrogene insertion is lacking in the tall dachshund phenotype

Two retrogene insertions, FGF4L1 (formerly 18-FGF4, colloquially CDPA) and FGF4L2 (formerly 12-FGF4, colloquially CDDY), have recently been discovered as determinants of short leg phenotype in dogs. This case study is comprised of a family of standard wirehaired dachshunds in which the dogs lacking the FGF4L1 gene exhibit a tall phenotype. The tall phenotype in the dachshunds of this report precludes the dog's working function of den work. The data presented in this report provide information as to how FGF4L1 status could be used in making breeding decisions in dachshunds to maintain working ability without compromising animal health.

Identification of Retrocopies in Lepidoptera and Impact on Domestication of Silkworm

BACKGROUND

During the domestication of silkworm, an economic insect, its physiological characteristics have changed greatly. RNA-based gene duplication, known as retrocopy, plays an important role in the formation of new genes and genome evolution, but the retrocopies of lepidopteran insects have not been fully identified and analyzed, which not only severely limits researchers from exploring the effects of retrocopies on lepidopteran insects but also affects the studies on the domestication of silkworm.

METHODS

We compared the genomes and proteomes of eight lepidopteran insects and used a series of screening criteria for auxiliary screening to obtain the retrocopies in lepidopteran insects and explored their characteristics. In addition, based on the silkworm transcriptome data from the SilkDB3.0 website, we explored the functions of the retrocopies on the domestication of the silkworm.

RESULTS

A total of 1993 retrocopies and 1208 parental genes in lepidopteran insects were obtained. We revealed that the retrocopies in Lepidoptera do not conform to the "out of X" hypothesis but fit the "out of testis" hypothesis. These retrocopies were subject to strong functional constraints and performed important functions in growth and development. Transcriptome analysis revealed that the expression pattern of the retrocopies and their parental genes were irrelevant. Through the analysis of the retrocopies in silkworm generated after domestication and located in the candidate domestication regions, the possible universal connection between the retrocopies and the domestication of silkworm were found.

CONCLUSIONS

Our study pioneered the exploration of retrocopies in multiple Lepidoptera species and found the potential association between the retrocopies and the domestication of silkworm.

Genetic Testing: practical dos and don'ts for cats

PRACTICAL RELEVANCE

A significant number of genetic variants are known for domestic cats and their breeds. Several DNA variants are causal for inherited diseases and most of the variants for phenotypic traits have been discovered. Genetic testing for these variants can support breeding decisions for both health and aesthetics. Genetic testing can also be used to monitor for the health of, or provide targeted therapy for, an individual cat and, more widely, can progress scientific discovery. Technological improvements have led to the development of large panel genetic testing, which can provide many DNA results for a low cost.

CLINICAL CHALLENGES

With the development of large panel genetic testing has come companies that can carry out this service, but which company is best to use may not always be clear - more tests are not necessarily better. Usage and interpretation of genetic data and how the results are presented by commercial laboratories may also be confusing for veterinary practitioners and owners, leading to misinterpretations for healthcare, improper genetic counseling, and poor breed and population management.

EVIDENCE BASE

The information provided in this review draws on scientific articles reporting the discovery, and discussing the meaning and implications, of DNA variants, as well as information from the Online Mendelian Inheritance in Animals (OMIA) website, which documents all the DNA variant discoveries. The author also provides suggestions and recommendations based on her personal experience and expertise in feline genetics.

AUDIENCE

This review is aimed at general practitioners and discusses the genetic tests that can be performed, what to consider when choosing a testing laboratory and provides genetic testing counseling advice. Practitioners with a high proportion of cat breeder clientele will especially benefit from this review and all veterinarians should realize that genetic testing and genomic medicine should be part of diagnostic plans and healthcare for their cat clients.

Genotypic and phenotypic consequences of domestication in dogs

Runs of homozygosity (ROH) are genomic regions that arise when two copies of identical haplotypes are inherited from a shared common ancestor. In this study, we leverage ROH to identify associations between genetic diversity and non-disease phenotypes in Canis lupus familiaris (dogs). We find significant association between the ROH inbreeding coefficient (FROH) and several phenotypic traits. These traits include height, weight, lifespan, muscled, white coloring of the head and chest, furnishings, and fur length. After correcting for population structure, we identified more than 45 genes across the examined quantitative traits that exceed the threshold for suggestive significance. We observe distinct distributions of inbreeding and elevated levels of long ROH in modern breed dogs compared to more ancient breeds, which aligns with breeding practices during Victorian era breed establishment. Our results highlight the impact of non-additive variation and of polygenicity on complex quantitative phenotypes in dogs due to domestication and the breed formation bottleneck.

Extensive Epidural Hemorrhage Associated with Thoracolumbar Disc Extrusion in French Bulldogs

(1) Background: Intervertebral disc extrusion may be accompanied by extensive epidural hemorrhage (EEH) and result in spinal cord compression. EEH is more commonly seen in French Bulldogs compared to other breeds. The majority of French Bulldogs have lumbar intervertebral disc extrusion, but it is unclear if there is an association between the site of thoracolumbar disc extrusion and EEH. This retrospective study's aim was to investigate the association and prevalence between the site of thoracolumbar intervertebral disc extrusion and EEH in French Bulldogs. (2) Methods: Thoracolumbar MRI of French Bulldogs was examined for the site of intervertebral disc extrusion and the presence, distribution, and extent of EEH. (3) Results: In 148 French Bulldogs with thoracolumbar intervertebral disc extrusion, the most common location was L4/L5 (22%), followed by L3/L4 (20%) and T13/L1 (15%), and 70.3% had EEH. The highest incidence of EEH across all thoracolumbar sites was seen at L1/L2 (84.2%), followed by L5/L6 (81.3%) and L2/L3 (72.2%). The incidence of EEH was 70.5% across all lumbar sites and 66.9% for all thoracic sites. (4) Conclusion: In this population of French Bulldogs, the prevalence of lumbar disc extrusion was high, and 70.3% had EEH. There was no significant difference between the site of thoracolumbar intervertebral disc extrusion and EEH.

Prevalence of presumed endplate junction failure at the lumbosacral intervertebral junction in dogs on computed tomography

Lumbosacral intervertebral disc herniation (IVDH) is a common cause of lower back pain in dogs and humans. In humans, the vertebral endplate to annulus fibrosus (AF) attachment was implicated as an alternative failure site besides rupture through the dorsal AF (AFF). Endplate junction failure (EPJF) is characterized by IVDH, accompanied by endplate irregularities (type A), rim avulsions (type B), or larger bony avulsions on one (type C) or both endplates (type D), associated with an adjacent endplate defect. This retrospective study reports the CT prevalence of presumed EPJF in dogs and its associations with signalment and other lumbosacral CT abnormalities. CT scans, including the lumbosacral spine of dogs obtained at two institutions, were assessed, yielding 324 scans. Presumed EPJF was found in 69 dogs (21%) and AFF in 68 dogs (21%), commonly at the caudal endplate of the last lumbar vertebra (71%). The remaining 187 dogs did not show presumed EPJF or AFF. Presumed EPJF type A occurred in 49/69, type B in 19/69, and type C in 1/69 dogs. Univariable logistic regression showed that presumed EPJF was associated with significantly higher IVDH grades than AFF. In the multiple regression model, presumed EPJF and AFF remained associated with increasing age and spondylosis deformans. Presumed EPJF was associated with vertebral endplate sclerosis and AFF with zygapophyseal joint osteoarthritis. In conclusion, presumed EPJF was observed on CT in 21% of dogs with lumbosacral IVDH. Prospective studies correlating EPJF on CT with clinical, surgical, and histopathological findings are needed for a better understanding of the underlying pathology and clinical relevance.

Canine hyper-sociability structural variants associated with altered three-dimensional chromatin state

Strong selection on complex traits can lead to skewed trait means and reduced trait variability in populations. An example of this phenomenon can be evidenced in allele frequency changes and skewed trait distributions driven by persistent human-directed selective pressures in domesticated species. Dog domestication is linked to several genomic variants; however, the functional impacts of these variants may not always be straightforward when found in non-coding regions of the genome. Four polymorphic transposable elements (TE) found within non-coding sites along a 5 Mb region on canine CFA6 have evolved due to directional selection associated with heightened human-directed hyper-sociability in domesticated dogs. We found that the polymorphic TE in intron 17 of the canine GTF2I gene, which was previously reported to be negatively correlated with canid human-directed hyper-sociability, is associated with altered chromatin looping and hence distinct cis-regulatory landscapes. We reported supporting evidence of an E2F1-DNA binding peak concordant with the altered loop and higher expression of GTF2I exon 18, indicative of alternative splicing. Globally, we discovered differences in pathways regulating the extra-cellular matrix with respect to TE copy number. Overall, we reported evidence suggesting an intriguing molecular convergence between the emergence of hypersocial behaviors in dogs and the same genes that, when hemizygous, produce human Williams Beuren Syndrome characterized by cranio-facial defects and heightened social behaviors. Our results additionally emphasize the often-overlooked potential role of chromatin architecture in social evolution.

Evolution of retrocopies in the context of HUSH silencing

Retrotransposition is one of the main factors responsible for gene duplication and thus genome evolution. However, the sequences that undergo this process are not only an excellent source of biological diversity, but in certain cases also pose a threat to the integrity of the DNA. One of the mechanisms that protects against the incorporation of mobile elements is the HUSH complex, which is responsible for silencing long, intronless, transcriptionally active transposed sequences that are rich in adenine on the sense strand. In this study, broad sets of human and porcine retrocopies were analysed with respect to the above factors, taking into account evolution of these molecules. Analysis of expression pattern, genomic structure, transcript length, and nucleotide substitution frequency showed the strong relationship between the expression level and exon length as well as the protective nature of introns. The results of the studies also showed that there is no direct correlation between the expression level and adenine content. However, protein-coding retrocopies, which have a lower adenine content, have a significantly higher expression level than the adenine-rich non-coding but expressed retrocopies. Therefore, although the mechanism of HUSH silencing may be an important part of the regulation of retrocopy expression, it is one component of a more complex molecular network that remains to be elucidated.

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.

Dogs and their genes: what ever will they think of next?

The Edward Novitski Prize recognizes creativity and intellectual ingenuity in the solution of problems in genetics research. The prize honors scientific experimental work-either a single experimental accomplishment or a body of work. Ostrander is recognized for work developing the domestic dog as an experimental system for solving fundamental biological problems and identifying genetic sequences of relevance to human health and disease. Including work on disease and behavioral health, Ostrander has shown a dedication to creative methods for understanding canine genetics and the value of translating research organisms to human genetics.

Island demographics and trait associations in white-tailed deer

When a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force and results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs including LAMTOR2 which has links to pigmentation changes, and NPVF which is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number (~50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.

Multi-Allelic Mitochondrial DNA Deletions in an Adult Dog with Chronic Weakness, Exercise Intolerance and Lactic Acidemia

(1) Background: An adult dog was presented to a board-certified veterinary neurologist for evaluation of chronic weakness, exercise intolerance and lactic acidemia. (2) Methods: A mitochondrial myopathy was diagnosed based on the histological and histochemical phenotype of numerous COX-negative muscle fibers. Whole-genome sequencing established the presence of multiple extended deletions in the mitochondrial DNA (mtDNA), with the highest prevalence between the 1-11 kb positions of the approximately 16 kb mitochondrial chromosome. Such findings are typically suggestive of an underlying nuclear genome variant affecting mitochondrial replication, repair, or metabolism. (3) Results: Numerous variants in the nuclear genome unique to the case were identified in the whole-genome sequence data, and one, the insertion of a DYNLT1 retrogene, whose parent gene is a regulator of the mitochondrial voltage-dependent anion channel (VDAC), was considered a plausible causal variant. (4) Conclusions: Here, we add mitochondrial deletion disorders to the spectrum of myopathies affecting adult dogs.

A naturally occurring canine model of syndromic congenital microphthalmia

In humans, the prevalence of congenital microphthalmia is estimated to be 0.2-3.0 for every 10,000 individuals, with nonocular involvement reported in ∼80% of cases. Inherited eye diseases have been widely and descriptively characterized in dogs, and canine models of ocular diseases have played an essential role in unraveling the pathophysiology and development of new therapies. A naturally occurring canine model of a syndromic disorder characterized by microphthalmia was discovered in the Portuguese water dog. As nonocular findings included tooth enamel malformations, stunted growth, anemia, and thrombocytopenia, we hence termed this disorder Canine Congenital Microphthalmos with Hematopoietic Defects. Genome-wide association study and homozygosity mapping detected a 2 Mb candidate region on canine chromosome 4. Whole-genome sequencing and mapping against the Canfam4 reference revealed a Short interspersed element insertion in exon 2 of the DNAJC1 gene (g.74,274,883ins[T70]TGCTGCTTGGATT). Subsequent real-time PCR-based mass genotyping of a larger Portuguese water dog population found that the homozygous mutant genotype was perfectly associated with the Canine Congenital Microphthalmos with Hematopoietic Defects phenotype. Biallelic variants in DNAJC21 are mostly found to be associated with bone marrow failure syndrome type 3, with a phenotype that has a certain degree of overlap with Fanconi anemia, dyskeratosis congenita, Shwachman-Diamond syndrome, Diamond-Blackfan anemia, and reports of individuals showing thrombocytopenia, microdontia, and microphthalmia. We, therefore, propose Canine Congenital Microphthalmos with Hematopoietic Defects as a naturally occurring model for DNAJC21-associated syndromes.

Association of FGF4L1 Retrogene Insertion with Prolapsed Gland of the Nictitans (Cherry Eye) in Dogs

Cherry eye is the common name for prolapse of the nictitans gland, a tear-producing gland situated under the third eyelid of dogs. Cherry eye is characterized by a red fleshy protuberance in the corner of the eye, resembling a cherry. This protrusion is a displacement of the normal gland of the third eyelid, thought to be caused by a defect in the connective tissue that secures the gland in place. Options for treatment may include anti-inflammatory medications in mild cases, but surgical replacement of the gland is usually indicated. Cherry eye is most often seen in dogs under the age of two years, with certain breeds having a higher incidence, suggesting a potential genetic association. Integration of panel genetic testing into routine clinical practice allows for the generation of large numbers of genotyped individuals paired with clinical records and enables the investigation of common disorders using a genome-wide association study (GWAS) approach at scale. In this investigation, several thousand cases and controls for cherry eye in both purebred dogs and mixed breeds are used for a large-scale GWAS, revealing a single peak of genome-wide significance on canine chromosome 18, directly at the location of the previously identified FGF4 insertion known to cause chondrodysplasia in several breeds.

Incidence and clinical characterisation of thoracolumbar intervertebral disc extrusions in Basset Hounds compared with Dachshunds

BACKGROUND

The Basset Hound is the largest chondrodystrophic breed predisposed to thoracolumbar intervertebral disc extrusion (TL-IVDE). However, literature describing this particular breed in terms of incidence, signalment, anatomical location, clinical severity and short-term outcome of TL-IVDE is lacking.

METHODS

The medical histories of Dachshunds and Basset Hounds presenting to three neurology departments were retrospectively assessed. Information collected for each dog included signalment, whether it had received a diagnosis of TL-IVDE, duration of clinical signs, affected discs and anatomical region and neurological grading at presentation and discharge.

RESULTS

A total of 270 Dachshunds and 188 Basset Hounds were included for incidence analysis. Of these, 154 Dachshunds and 68 Basset Hounds with confirmed TL-IVDE were included for signalment, anatomical location, clinical severity and short-term outcome analysis. Statistical analysis indicated a significantly higher incidence of TL-IVDE in Dachshunds than in Basset Hounds (77.4% vs. 36.2%, p < 0.05). Basset Hounds presenting to a neurology department were older (median 87.5 months vs. 66.5 months), had a greater proportion of midlumbar IVDE (L2-L5) and were more frequently ambulatory at discharge than Dachshunds. Only one Basset Hound presented as paraplegic without nociception, compared with 16 Dachshunds (1.5% vs. 10.4%).

LIMITATIONS

The study had a retrospective design and included multicentric non-standardised cases.

CONCLUSION

TL-IVDE incidence was higher in Dachshunds than in Basset Hounds. Basset Hounds were older at presentation, frequently affected more caudally in the vertebral column and more frequently ambulatory at discharge than Dachshunds. The differences found in this study could aid in the development of preventive strategies.

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.

Evaluation of intervertebral disc degeneration in young adult asymptomatic Dachshunds with magnetic resonance imaging and radiography

BACKGROUND

Dachshunds have a high prevalence of intervertebral disc disease (IVDD) to which they are predisposed due to early intervertebral disc (IVD) degeneration and calcification. Moreover, the recently found 12-FGF4 retrogene (RG) is associated with calcified discs visible on radiographs (CDVR) and IVDD. Earlier studies suggest that all IVDs of one-year-old Dachshunds show signs of degeneration. This prospective, analytical, blinded study aimed to investigate the extent and distribution of IVD degeneration in young adult (24-31 months) asymptomatic Dachshunds (n = 21) hypothesizing that not all IVDs of two-year-old Dachshunds are degenerated. Another aim was to explore the correlations between IVD degeneration evaluated with magnetic resonance imaging (MRI), the number of CDVR, and the dog's 12-FGF4RG status. The study protocol included grading the CDVR on spinal radiographs, grading the IVD degeneration on T2-weighted sagittal and transverse high-field MR images of all IVDs (n = 546), and 12-FGF4RG variant genotyping.

RESULTS

Of all IVDs evaluated, 2% (n = 11) were normal based on MRI grading. Despite the study population having moderately degenerated IVDs (median MRI grade 3), there was also variation in the degree of IVD degeneration between individuals and in the distribution of IVD degeneration between different vertebral regions. The number of CDVR correlated significantly with the magnitude of IVD degeneration based on MRI evaluation and with the 12-FGF4RG genotype. The odds for being 12-FGF4RG homozygous were higher for Dachshunds with CDVR. However, the 12-FGF4RG variant did not alone explain the phenotypic variation in IVD degeneration.

CONCLUSIONS

The number of CDVR is a valid indicator of overall IVD degeneration, as it correlates with MRI-based IVD grading. Also, as the extent and distribution of IVD degeneration varies between individual Dachshunds, selective breeding against IVDD using radiographic screening and 12-FGF4RG variant genotyping is possible.

Retro-miRs: novel and functional miRNAs originating from mRNA retrotransposition

BACKGROUND

Reverse-transcribed gene copies (retrocopies) have emerged as major sources of evolutionary novelty. MicroRNAs (miRNAs) are small and highly conserved RNA molecules that serve as key post-transcriptional regulators of gene expression. The origin and subsequent evolution of miRNAs have been addressed but not fully elucidated.

RESULTS

In this study, we performed a comprehensive investigation of miRNA origination through retroduplicated mRNA sequences (retro-miRs). We identified 17 retro-miRs that emerged from the mRNA retrocopies. Four of these retro-miRs had de novo origins within retrocopied sequences, while 13 retro-miRNAs were located within exon regions and duplicated along with their host mRNAs. We found that retro-miRs were primate-specific, including five retro-miRs conserved among all primates and two human-specific retro-miRs. All retro-miRs were expressed, with predicted and experimentally validated target genes except miR-10527. Notably, the target genes of retro-miRs are involved in key biological processes such as metabolic processes, cell signaling, and regulation of neurotransmitters in the central nervous system. Additionally, we found that these retro-miRs play a potential oncogenic role in cancer by targeting key cancer genes and are overexpressed in several cancer types, including liver hepatocellular carcinoma and stomach adenocarcinoma.

CONCLUSIONS

Our findings demonstrated that mRNA retrotransposition is a key mechanism for the generation of novel miRNAs (retro-miRs) in primates. These retro-miRs are expressed, conserved, have target genes with important cellular functions, and play important roles in cancer.

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.

The power of "controllers": Transposon-mediated duplicated genes evolve towards neofunctionalization

Since the discovery of the first transposon by Dr. Barbara McClintock, the prevalence and diversity of transposable elements (TEs) have been gradually recognized. As fundamental genetic components, TEs drive organismal evolution not only by contributing functional sequences (e.g., regulatory elements or "controllers" as phrased by Dr. McClintock) but also by shuffling genomic sequences. In the latter respect, TE-mediated gene duplications have contributed to the origination of new genes and attracted extensive interest. In response to the development of this field, we herein attempt to provide an overview of TE-mediated duplication by focusing on common rules emerging across duplications generated by different TE types. Specifically, despite the huge divergence of transposition machinery across TEs, we identify three common features of various TE-mediated duplication mechanisms, including end bypass, template switching, and recurrent transposition. These three features lead to one common functional outcome, namely, TE-mediated duplicates tend to be subjected to exon shuffling and neofunctionalization. Therefore, the intrinsic properties of the mutational mechanism constrain the evolutionary trajectories of these duplicates. We finally discuss the future of this field including an in-depth characterization of both the duplication mechanisms and functions of TE-mediated duplicates.

Ancient segmentally duplicated LCORL retrocopies in equids

LINE-1 is an active transposable element encoding proteins capable of inserting host gene retrocopies, resulting in retro-copy number variants (retroCNVs) between individuals. Here, we performed retroCNV discovery using 86 equids and identified 437 retrocopy insertions. Only 5 retroCNVs were shared between horses and other equids, indicating that the majority of retroCNVs inserted after the species diverged. A large number (17-35 copies) of segmentally duplicated Ligand Dependent Nuclear Receptor Corepressor Like (LCORL) retrocopies were present in all equids but absent from other extant perissodactyls. The majority of LCORL transcripts in horses and donkeys originate from the retrocopies. The initial LCORL retrotransposition occurred 18 million years ago (17-19 95% CI), which is coincident with the increase in body size, reduction in digit number, and changes in dentition that characterized equid evolution. Evolutionary conservation of the LCORL retrocopy segmental amplification in the Equidae family, high expression levels and the ancient timeline for LCORL retrotransposition support a functional role for this structural variant.

The LASSIE MPS panel: Predicting externally visible traits in dogs for forensic purposes

Predicting the outward appearance of dogs via their DNA, also known as Canine DNA Phenotyping, is a young, emerging field of research in forensic genetics. The few previous studies published in this respect were restricted to the consecutive analysis of single DNA markers, a process that is time- and sample-consuming and therefore not a viable option for limited forensic specimens. Here, we report on the development and evaluation of a Massively Parallel Sequencing (MPS) based molecular genetic assay, the LASSIE MPS Panel. This panel aims to predict externally visible as well as skeletal traits, which include coat color, coat pattern, coat structure, tail morphology, skull shape, ear shape, eye color and body size from DNA using 44 genetic markers in a single molecular genetic assay. A biostatistical naïve Bayes classification approach was applied to identify the most informative marker combinations for predicting phenotypes. Overall, the predictive performance was characterized by a very high classification success for some of the trait categories, and high to moderate success for others. The performance of the developed predictive framework was further evaluated using blind samples from three randomly selected dog individuals, whose appearance was well predicted.

Cervical intervertebral disc disease in 60 Yorkshire terriers

Intervertebral disc extrusion (IVDE) is a common neurological condition in many dog breeds. This study aimed to describe this condition in Yorkshire terriers (YT) and calculate the prevalence of this condition amongst the YTs with neurological diseases. This is a double-centre retrospective study which was conducted in two arms. The first part of the study, describing the clinical features and prognosis of cervical (C) IVDE in YTs, is based on data from 2005 to 2021. The second part of the study calculated the prevalence of C IVDE amongst the YTs with neurological diseases based on data from 2016 to 2021. A retrospective search through the medical records was conducted. YTs with C IVDE diagnosed with MRI and confirmed surgically were eligible for inclusion in this study. Sixty YTs were included in the first part of the study. There were 48 (80%) dogs with acute onset and 12 (20%) with chronic onset with acute deterioration. Ambulation was preserved in 31 (51.7%) dogs on admission, and the remaining 29 (48.3%) dogs were non-ambulatory. No significant association was found between ambulation on admission and recovery status (p = 0.547). Seventy-three intervertebral spaces were treated during the surgical intervention. Relapses were seen in seven (11.7%) dogs. Forty-nine (81.7%) dogs were ambulatory at discharge. A complete recovery was observed in 46 (76.7%) dogs; the remaining dogs (14, 23.3%) were classified as incomplete recovery. A significant difference was found in time to ambulation (p = 0.0238) and time to discharge (p = 0.0139) between the on-admission ambulatory and non-ambulatory dogs. Three hundred and eight YTs were diagnosed with neurological diseases between 2016 and 2021 in one referral centre. C IVDE was diagnosed in 31 (10.06%) dogs. This is the first study explicitly describing the C IVDE in YTs and establishing the prevalence of this condition amongst YTs with other neurological disorders.

Novel functions of a retroposed gene

Retroposed protein-coding genes are commonly considered to be nonfunctional duplicates. However, they often gain transcriptional capability and have important roles. Amici et al. recently identified novel functions of a retroposed gene. HAPSTR2, a retrocopy of HAPSTR1, encodes a protein that stabilizes the HAPSTR1 protein and functionally buffers its loss.

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.

Identification of Genetic Risk Factors for Monogenic and Complex Canine Diseases

Advances in DNA sequencing and other technologies have greatly facilitated the identification of genetic risk factors for inherited diseases in dogs. We review recent technological developments based on selected examples from canine disease genetics. The identification of disease-causing variants in dogs with monogenic diseases may become a widely employed diagnostic approach in clinical veterinary medicine in the not-too-distant future. Diseases with complex modes of inheritance continue to pose challenges to researchers but have also become much more tangible than in the past. In addition to strategies for identifying genetic risk factors, we provide some thoughts on the interpretation of sequence variants that are largely inspired by developments in human clinical genetics.

Genetic prevalence and clinical relevance of canine Mendelian disease variants in over one million dogs

Hundreds of genetic variants implicated in Mendelian disease have been characterized in dogs and commercial screening is being offered for most of them worldwide. There is typically limited information available regarding the broader population frequency of variants and uncertainty regarding their functional and clinical impact in ancestry backgrounds beyond the discovery breed. Genetic panel screening of disease-associated variants, commercially offered directly to the consumer or via a veterinary clinician, provides an opportunity to establish large-scale cohorts with phenotype data available to address open questions related to variant prevalence and relevance. We screened the largest canine cohort examined in a single study to date (1,054,293 representative dogs from our existing cohort of 3.5 million; a total of 811,628 mixed breed dogs and 242,665 purebreds from more than 150 countries) to examine the prevalence and distribution of a total of 250 genetic disease-associated variants in the general population. Electronic medical records from veterinary clinics were available for 43.5% of the genotyped dogs, enabling the clinical impact of variants to be investigated. We provide detailed frequencies for all tested variants across breeds and find that 57% of dogs carry at least one copy of a studied Mendelian disease-associated variant. Focusing on a subset of variants, we provide evidence of full penetrance for 10 variants, and plausible evidence for clinical significance of 22 variants, on diverse breed backgrounds. Specifically, we report that inherited hypocatalasia is a notable oral health condition, confirm that factor VII deficiency presents as subclinical bleeding propensity and verify two genetic causes of reduced leg length. We further assess genome-wide heterozygosity levels in over 100 breeds, and show that a reduction in genome-wide heterozygosity is associated with an increased Mendelian disease variant load. The accumulated knowledge represents a resource to guide discussions on genetic test relevance by breed.

That brachycephalic look: Infant-like facial appearance in short-muzzled dog breeds

Brachycephalic dog breeds are highly popular, yet their conformation-related disorders represent a major welfare concern. It has been suggested that the current popularity of such breeds can be explained by their cute, infant-like facial appearances. The concept of 'kindchenschema' refers to the observation that certain physical features of infant humans and other animals can automatically stimulate positive and nurturant feelings in adult observers. But the proposal that brachycephalic dogs possess heightened 'kindchenschema' facial features, even into adulthood, has never been formally investigated. Here, we hypothesised that relative muzzle shortening across a range of breeds would be associated with known 'kindchenschema' facial features, including a relatively larger forehead, larger eyes and smaller nose. Relative fronto-facial feature sizes in exemplar photographs of adult dogs from 42 popular breeds were measured and associated with existing data on the relative muzzle length and height-at-withers of the same breeds. Our results show that, in adulthood, shorter-muzzled breeds have relatively larger (taller) foreheads and relatively larger eyes (i.e. area of exposed eyeball relative to overall face area) than longer-muzzled breeds, and that this effect is independent of breed size. In sum, brachycephalic dog breeds do show exaggeration of some, but not all, known fronto-facial 'kindchenschema' features, and this may well contribute to their apparently cute appearance and to their current popularity as companion animals. We conclude that the challenge of addressing conformation-related disorders in companion dogs needs to take account of the cute, 'kindchenschema' looks that many owners are likely to be attracted to.

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.

Follow-up MRI appearance of the surgical site in dogs treated for thoracolumbar intervertebral disc herniation and showing ongoing or recurrent neurological symptoms

Reherniation and reoperation rates of 4.5%-36% are reported in canine patients treated for intervertebral disc herniation (IVDH). Decision-making for surgical reintervention can prove challenging, especially since common postoperative changes are poorly described on MRI. The purpose of this single-center, retrospective, descriptive study was to describe the MRI characteristics of the surgical site in dogs treated for thoracolumbar IVDH and presenting for ongoing or recurrent neurological signs. Twenty-one patients were included for a total of 42 MRI studies. Chondrodystrophic breeds, specifically Dachshunds, were overrepresented. Mean number of days between surgery and second MRI was 335 (range 2-1367). Metallic susceptibility artifacts were seen in seven of 21 cases (33%), but these were limited in extent, spanning on average 1.3 vertebral bodies. In 11 cases, spinal cord compression suspected to be clinically significant was found at the surgical site; the extradural compressive material consisted of intervertebral disc material only, or a combination of intervertebral disc material and hematoma or inflammatory changes in 10 cases, and a displaced articular process and fibrous tissue in one case. The latter is a newly described complication of mini-hemilaminectomies. Paravertebral soft tissue changes and vertebral new bone formation varied according to the postoperative stage at which the patients were imaged. The results of this study supported the use of MRI as a diagnostic modality for spinal imaging following IVDH surgery, and showed that the presence of extradural disc material at a spinal surgical site is common along with various vertebral and paravertebral changes.

The cellular basis of cartilage growth and shape change in larval and metamorphosing Xenopus frogs

As the first and sometimes only skeletal tissue to appear, cartilage plays a fundamental role in the development and evolution of vertebrate body shapes. This is especially true for amphibians whose largely cartilaginous feeding skeleton exhibits unparalleled ontogenetic and phylogenetic diversification as a consequence of metamorphosis. Fully understanding the evolutionary history, evolvability and regenerative potential of cartilage requires in-depth analysis of how chondrocytes drive growth and shape change. This study is a cell-level description of the larval growth and postembryonic shape change of major cartilages of the feeding skeleton of a metamorphosing amphibian. Histology and immunohistochemistry are used to describe and quantify patterns and trends in chondrocyte size, shape, division, death, and arrangement, and in percent matrix from hatchling to froglet for the lower jaw, hyoid and branchial arch cartilages of Xenopus laevis. The results are interpreted and integrated into programs of cell behaviors that account for the larval growth and histology, and metamorphic remodeling of each element. These programs provide a baseline for investigating hormone-mediated remodeling, cartilage regeneration, and intrinsic shape regulating mechanisms. These programs also contain four features not previously described in vertebrates: hypertrophied chondrocytes being rejuvenated by rapid cell cycling to a prechondrogenic size and shape; chondrocytes dividing and rearranging to reshape a cartilage; cartilage that lacks a perichondrium and grows at single-cell dimensions; and an adult cartilage forming de novo in the center of a resorbing larval one. Also, the unexpected superimposition of cell behaviors for shape change onto ones for larval growth and the unprecedented exploitation of very large and small cell sizes provide new directions for investigating the development and evolution of skeletal shape and metamorphic ontogenies.

Effect of acupuncture on the energy metabolism of dogs with intervertebral disk disease and cervical disk herniation: A pilot study

Thirteen dogs with intervertebral disk disease (IVDD) and 3 dogs with cervical disk herniation (CVDH) were examined to determine the effects of acupuncture on energy metabolism. Acupuncture points GV14, GV20-1, BL18, BL23, BL26, GB30, and ST36 were selected for IVDD, while GV14, GV20-1, GB20, and BL23 were selected for CVDH. All dogs except no.13 did not receive medication during acupuncture treatment. Acupuncture effects were evaluated based on the IVDD/CVDH evaluation scales in Oji 2015 and Tanaka and Nakayama 2015. Blood samples were taken before and 30 min after acupuncture treatment. Pyruvate and lactate concentrations, lactate dehydrogenase (LDH) and malate dehydrogenase (MDH) activity, the MDH/LDH ratio (M/L ratio), and LDH isozyme electrophoretic patterns served as energy metabolism markers. In IVDD/CVDH dogs that showed improvements, plasma pyruvate concentrations significantly decreased, the M/L ratio increased, and the plasma LDH isozyme pattern changed from predominantly LDH5 to predominantly LDH1. These data suggest that local redox potential is improved and energy metabolism is increased in dogs with IVDD/CVDH after acupuncture treatment. Acupuncture treatments may activate the citric acid cycle and increase ATP production, followed by improvement of the disease. Future studies with a large sample size are needed to clarify this hypothesis.

PCYT1A Missense Variant in Vizslas with Disproportionate Dwarfism

Disproportionate dwarfism phenotypes represent a heterogeneous subset of skeletal dysplasias and have been described in many species including humans and dogs. In this study, we investigated Vizsla dogs that were affected by disproportionate dwarfism that we propose to designate as skeletal dysplasia 3 (SD3). The most striking skeletal changes comprised a marked shortening and deformation of the humerus and femur. An extended pedigree with six affected dogs suggested autosomal recessive inheritance. Combined linkage and homozygosity mapping localized a potential genetic defect to a ~4 Mb interval on chromosome 33. We sequenced the genome of an affected dog, and comparison with 926 control genomes revealed a single, private protein-changing variant in the critical interval, PCYT1A:XM_038583131.1:c.673T>C, predicted to cause an exchange of a highly conserved amino acid, XP_038439059.1:p.(Y225H). We observed perfect co-segregation of the genotypes with the phenotype in the studied family. When genotyping additional Vizslas, we encountered a single dog with disproportionate dwarfism that did not carry the mutant PCYT1A allele, which we hypothesize was due to heterogeneity. In the remaining 130 dogs, we observed perfect genotype-phenotype association, and none of the unaffected dogs were homozygous for the mutant PCYT1A allele. PCYT1A loss-of-function variants cause spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD) in humans. The skeletal changes in Vizslas were comparable to human patients. So far, no ocular phenotype has been recognized in dwarf Vizslas. We propose the PCYT1A missense variant as a candidate causative variant for SD3. Our data facilitate genetic testing of Vizslas to prevent the unintentional breeding of further affected puppies.

Across-breed genetic investigation of canine hip dysplasia, elbow dysplasia, and anterior cruciate ligament rupture using whole-genome sequencing

Here, we report the use of genome-wide association study (GWAS) for the analysis of canine whole-genome sequencing (WGS) repository data using breed phenotypes. Single-nucleotide polymorphisms (SNPs) were called from WGS data from 648 dogs that included 119 breeds from the Dog10K Genomes Project. Next, we assigned breed phenotypes for hip dysplasia (Orthopedic Foundation for Animals (OFA) HD, n = 230 dogs from 27 breeds; hospital HD, n = 279 dogs from 38 breeds), elbow dysplasia (ED, n = 230 dogs from 27 breeds), and anterior cruciate ligament rupture (ACL rupture, n = 279 dogs from 38 breeds), the three most important canine spontaneous complex orthopedic diseases. Substantial morbidity is common with these diseases. Previous within- and between-breed GWAS for HD, ED, and ACL rupture using array SNPs have identified disease-associated loci. Individual disease phenotypes are lacking in repository data. There is a critical knowledge gap regarding the optimal approach to undertake categorical GWAS without individual phenotypes. We considered four GWAS approaches: a classical linear mixed model, a haplotype-based model, a binary case-control model, and a weighted least squares model using SNP average allelic frequency. We found that categorical GWAS was able to validate HD candidate loci. Additionally, we discovered novel candidate loci and genes for all three diseases, including FBX025, IL1A, IL1B, COL27A1, SPRED2 (HD), UGDH, FAF1 (ED), TGIF2 (ED & ACL rupture), and IL22, IL26, CSMD1, LDHA, and TNS1 (ACL rupture). Therefore, categorical GWAS of ancestral dog populations may contribute to the understanding of any disease for which breed epidemiological risk data are available, including diseases for which GWAS has not been performed and candidate loci remain elusive.

Functional differentiation of bmp2a and bmp2b genes in zebrafish

Bone morphogenetic protein 2 plays an important role in the regulation of osteoblast proliferation and differentiation. Phylogenetic analysis showed that the bmp2 ortholog evolved from the same ancestral gene family in vertebrates and was duplicated in teleost, which were named bmp2a and bmp2b. The results of whole-mount in situ hybridization showed that the expression locations of bmp2a and bmp2b in zebrafish were different in different periods (24 hpf, 48 hpf, 72 hpf), which revealed potential functional differentiation between bmp2a and bmp2b. Phenotypic analysis showed that bmp2a mutations caused partial rib and vertebral deformities in zebrafish, while bmp2b^-/- embryos died massively after 12 hpf due to abnormal somite formation. We further explored the expression pattern changes of genes (bmp2a, bmp2b, smad1, fgf4, runx2b, alp) related to skeletal development at different developmental stages (20 dpf, 60 dpf, 90 dpf) in wild-type and bmp2a^-/- zebrafish. The results showed that the expression of runx2b in bmp2a^-/- was significantly downregulated at three stages and the expression of other genes were significantly downregulated at 90 dpf compared with wild-type zebrafish. The study revealed functional differentiation of bmp2a and bmp2b in zebrafish embryonic and skeletal development.

An SNN retrocopy insertion upstream of GPR22 is associated with dark red coat color in Poodles

Pigment production and distribution is controlled through multiple genes, resulting in a wide range of coat color phenotypes in dogs. Dogs that produce only the pheomelanin pigment vary in intensity from white to deep red. The Poodle breed has a wide range of officially recognized coat colors, including the pheomelanin-based white, cream, apricot, and red coat colors, which are not fully explained by the previously identified genetic variants involved in pigment intensity. Here, a genome-wide association study for pheomelanin intensity was performed in Poodles which identified an association on canine chromosome 18. Whole-genome sequencing data revealed an SNN retrocopy insertion (SNNL1) in apricot and red Poodles within the associated region on chromosome 18. While equal numbers of melanocytes were observed in all Poodle skin hair bulbs, higher melanin content was observed in the darker Poodles. Several genes involved in melanogenesis were also identified as highly overexpressed in red Poodle skin. The most differentially expressed gene however was GPR22, which was highly expressed in red Poodle skin while unexpressed in white Poodle skin (log2 fold change in expression 6.1, P < 0.001). GPR22 is an orphan G-protein-coupled receptor normally expressed exclusively in the brain and heart. The SNNL1 retrocopy inserted 2.8 kb upstream of GPR22 and is likely disrupting regulation of the gene, resulting in atypical expression in the skin. Thus, we identify the SNNL1 insertion as a candidate variant for the CFA18 pheomelanin intensity locus in red Poodles.

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.

Recent, full-length gene retrocopies are common in canids

Gene retrocopies arise from the reverse transcription and insertion into the genome of processed mRNA transcripts. Although many retrocopies have acquired mutations that render them functionally inactive, most mammals retain active LINE-1 sequences capable of producing new retrocopies. New retrocopies, referred to as retro copy number variants (retroCNVs), may not be identified by standard variant calling techniques in high-throughput sequencing data. Although multiple functional FGF4 retroCNVs have been associated with skeletal dysplasias in dogs, the full landscape of canid retroCNVs has not been characterized. Here, retroCNV discovery was performed on a whole-genome sequencing data set of 293 canids from 76 breeds. We identified retroCNV parent genes via the presence of mRNA-specific 30-mers, and then identified retroCNV insertion sites through discordant read analysis. In total, we resolved insertion sites for 1911 retroCNVs from 1179 parent genes, 1236 of which appeared identical to their parent genes. Dogs had on average 54.1 total retroCNVs and 1.4 private retroCNVs. We found evidence of expression in testes for 12% (14/113) of the retroCNVs identified in six Golden Retrievers, including four chimeric transcripts, and 97 retroCNVs also had significantly elevated F ST across dog breeds, possibly indicating selection. We applied our approach to a subset of human genomes and detected an average of 4.2 retroCNVs per sample, highlighting a 13-fold relative increase of retroCNV frequency in dogs. Particularly in canids, retroCNVs are a largely unexplored source of genetic variation that can contribute to genome plasticity and that should be considered when investigating traits and diseases.

Molecular genetic variation of animals and plants under domestication

Domesticated plants and animals played crucial roles as models for evolutionary change by means of natural selection and for establishing the rules of inheritance, originally proposed by Charles Darwin and Gregor Mendel, respectively. Here, we review progress that has been made during the last 35 y in unraveling the molecular genetic variation underlying the stunning phenotypic diversity in crops and domesticated animals that inspired Mendel and Darwin. We notice that numerous domestication genes, crucial for the domestication process, have been identified in plants, whereas animal domestication appears to have a polygenic background with no obvious "domestication genes" involved. Although model organisms, such as Drosophila and Arabidopsis, have replaced domesticated species as models for basic research, the latter are still outstanding models for evolutionary research because phenotypic change in these species represents an evolutionary process over thousands of years. A consequence of this is that some alleles contributing to phenotypic diversity have evolved by accumulating multiple changes in the same gene. The continued molecular characterization of crops and farm animals with ever sharper tools is essential for future food security.

Prevalence, clinical features, and outcome of intervertebral disc extrusion associated with extensive epidural hemorrhage in a population of French Bulldogs compared to Dachshunds

Intervertebral disc extrusion associated with extensive epidural hemorrhage (DEEH) is a well-documented pathological condition in veterinary medicine. This retrospective study aimed to evaluate the prevalence and clinical features of DEEH in a population of French Bulldogs affected by intervertebral disc extrusion (n=75), compare the findings with those from a group of Dachshunds (n=98) and identify possible predictive factors of DEEH and outcomes in surgically treated patients. The study showed that the prevalence of DEEH observed in Dachshunds (11.2% [95% confidence interval [CI]: 5.7–19.2%]) was significantly lower than that observed in French Bulldogs (41.3% [95% CI: 30.1–53.3%]). The multiple logistic regression model highlighted that the patients presenting with an acute onset of clinical signs (>24 hr) (odds ratio [OR]: 13.08; 95% CI: 4.63–37.03, P=0.00), presence of clinical signs progression (OR: 5.04; P=0.01), and French Bulldogs (OR: 5.15; 95% CI: 1.71–15.54, P=0.00) were at increased risk of developing DEEH. Secondary analysis showed that patients with DEEH were at an increased risk of being non-ambulatory at discharge (OR: 3.43; P=0.017). Overall, the surgically treated patients had favorable outcomes.

New developments in the biology of fibroblast growth factors

The fibroblast growth factor (FGF) family is composed of 18 secreted signaling proteins consisting of canonical FGFs and endocrine FGFs that activate four receptor tyrosine kinases (FGFRs 1-4) and four intracellular proteins (intracellular FGFs or iFGFs) that primarily function to regulate the activity of voltage-gated sodium channels and other molecules. The canonical FGFs, endocrine FGFs, and iFGFs have been reviewed extensively by us and others. In this review, we briefly summarize past reviews and then focus on new developments in the FGF field since our last review in 2015. Some of the highlights in the past 6 years include the use of optogenetic tools, viral vectors, and inducible transgenes to experimentally modulate FGF signaling, the clinical use of small molecule FGFR inhibitors, an expanded understanding of endocrine FGF signaling, functions for FGF signaling in stem cell pluripotency and differentiation, roles for FGF signaling in tissue homeostasis and regeneration, a continuing elaboration of mechanisms of FGF signaling in development, and an expanding appreciation of roles for FGF signaling in neuropsychiatric diseases. This article is categorized under: Cardiovascular Diseases > Molecular and Cellular Physiology Neurological Diseases > Molecular and Cellular Physiology Congenital Diseases > Stem Cells and Development Cancer > Stem Cells and Development.

Canine DUXC: implications for DUX4 retrotransposition and preclinical models of FSHD

Mis-expression of DUX4 in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). Human DUX4 and mouse Dux are retrogenes derived from retrotransposition of the mRNA from the parental DUXC gene. Primates and rodents have lost the parental DUXC gene, and it is unknown whether DUXC had a similar role in driving an early pluripotent transcriptional program. Dogs and other Laurasiatherians have retained DUXC, providing an opportunity to determine the functional similarity to the retrotransposed DUX4 and Dux. Here, we identify the expression of two isoforms of DUXC mRNA in canine testis tissues: one encoding the canonical double homeodomain protein (DUXC), similar to DUX4/Dux, and a second that includes an in-frame alternative exon that disrupts the conserved amino acid sequence of the first homeodomain (DUXC-ALT). The expression of DUXC in canine cells induces a pluripotent program similar to DUX4 and Dux and induces the expression of a similar set of retrotransposons of the ERV/MaLR and LINE-1 families, as well as pericentromeric satellite repeats; whereas DUXC-ALT did not robustly activate gene expression in these assays. Important for preclinical models of FSHD, human DUX4 and canine DUXC show higher conservation of their homeodomains and corresponding binding motifs compared with the conservation between human DUX4 and mouse Dux, and human DUX4 activates a highly similar transcriptional program in canine cells. Together, these findings show that retrotransposition resulted in the loss of an alternatively spliced isoform and that DUXC containing mammals might be good candidates for certain preclinical models ofFSHD.

Ancestry-inclusive dog genomics challenges popular breed stereotypes

Behavioral genetics in dogs has focused on modern breeds, which are isolated subgroups with distinctive physical and, purportedly, behavioral characteristics. We interrogated breed stereotypes by surveying owners of 18,385 purebred and mixed-breed dogs and genotyping 2155 dogs. Most behavioral traits are heritable [heritability (h²) > 25%], and admixture patterns in mixed-breed dogs reveal breed propensities. Breed explains just 9% of behavioral variation in individuals. Genome-wide association analyses identify 11 loci that are significantly associated with behavior, and characteristic breed behaviors exhibit genetic complexity. Behavioral loci are not unusually differentiated in breeds, but breed propensities align, albeit weakly, with ancestral function. We propose that behaviors perceived as characteristic of modern breeds derive from thousands of years of polygenic adaptation that predates breed formation, with modern breeds distinguished primarily by aesthetic traits.

mRNA Vaccines: Why Is the Biology of Retroposition Ignored?

The major advantage of mRNA vaccines over more conventional approaches is their potential for rapid development and large-scale deployment in pandemic situations. In the current COVID-19 crisis, two mRNA COVID-19 vaccines have been conditionally approved and broadly applied, while others are still in clinical trials. However, there is no previous experience with the use of mRNA vaccines on a large scale in the general population. This warrants a careful evaluation of mRNA vaccine safety properties by considering all available knowledge about mRNA molecular biology and evolution. Here, I discuss the pervasive claim that mRNA-based vaccines cannot alter genomes. Surprisingly, this notion is widely stated in the mRNA vaccine literature but never supported by referencing any primary scientific papers that would specifically address this question. This discrepancy becomes even more puzzling if one considers previous work on the molecular and evolutionary aspects of retroposition in murine and human populations that clearly documents the frequent integration of mRNA molecules into genomes, including clinical contexts. By performing basic comparisons, I show that the sequence features of mRNA vaccines meet all known requirements for retroposition using L1 elements-the most abundant autonomously active retrotransposons in the human genome. In fact, many factors associated with mRNA vaccines increase the possibility of their L1-mediated retroposition. I conclude that is unfounded to a priori assume that mRNA-based therapeutics do not impact genomes and that the route to genome integration of vaccine mRNAs via endogenous L1 retroelements is easily conceivable. This implies that we urgently need experimental studies that would rigorously test for the potential retroposition of vaccine mRNAs. At present, the insertional mutagenesis safety of mRNA-based vaccines should be considered unresolved.

The Effects of FGF4 Retrogenes on Canine Morphology

Two FGF4 retrogenes (FGF4L1 on chromosome 18 and FGF4L2 on chromosome 12) have been identified to cause dwarfism across many dog breeds. Some breeds are nearly homozygous for both retrogenes (e.g., Dachshunds) and others are homozygous for just one (e.g., Beagles and Scottish Terriers). Since most breeds do not segregate both of these retrogenes, it is challenging to evaluate their individual effects on long bone length and body size. We identified two dog breeds selected for hunting ability, the Alpine Dachsbracke and the Schweizer Niederlaufhund, that segregate both of these retrogenes. Using individual measurements of height at the shoulder, back length, head width, thorax depth and width, and thoracic limb measurements, we evaluated the combined effects of FGF4 retrogenes within these breeds. We applied multivariable linear regression analysis to determine the effects of retrogene copy numbers on the measurements. Copy numbers of both retrogenes had significant effects reducing height at the shoulders and antebrachial length, with FGF4L1 having a much greater effect than FGF4L2. FGF4L1 alone influenced the degree of carpal valgus and FGF4L2 alone increased head width. Neither retrogene had an effect on thorax width or depth. Selectively breeding dogs with FGF4L1 and without FGF4L2 would likely lead to a reduction in the FGF4L2-related risk of intervertebral disc herniation while maintaining the reduction in leg length resulting from FGF4L1.

Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas

Despite the great diversity of vertebrate limb proportion and our deep understanding of the genetic mechanisms that drive skeletal elongation, little is known about how individual bones reach different lengths in any species. Here, we directly compare the transcriptomes of homologous growth cartilages of the mouse (Mus musculus) and bipedal jerboa (Jaculus jaculus), the latter of which has "mouse-like" arms but extremely long metatarsals of the feet. Intersecting gene-expression differences in metatarsals and forearms of the two species revealed that about 10% of orthologous genes are associated with the disproportionately rapid elongation of neonatal jerboa feet. These include genes and enriched pathways not previously associated with endochondral elongation as well as those that might diversify skeletal proportion in addition to their known requirements for bone growth throughout the skeleton. We also identified transcription regulators that might act as "nodes" for sweeping differences in genome expression between species. Among these, Shox2, which is necessary for proximal limb elongation, has gained expression in jerboa metatarsals where it has not been detected in other vertebrates. We show that Shox2 is sufficient to increase mouse distal limb length, and a nearby putative cis-regulatory region is preferentially accessible in jerboa metatarsals. In addition to mechanisms that might directly promote growth, we found evidence that jerboa foot elongation may occur in part by de-repressing latent growth potential. The genes and pathways that we identified here provide a framework to understand the modular genetic control of skeletal growth and the remarkable malleability of vertebrate limb proportion.

Evaluation of the Radial Procurvatum Using the Center of Rotation of Angulation Methodology in Chondrodystrophic Dogs

The radial joint orientation angles were calculated using the center of rotation of angulation (CORA) methodology within the frontal and sagittal planes in chondrodystrophic dog breeds, including Welsh Corgi, Dachshund, Pekinese, Poodle, Beagle and Maltese, and it was compared whether there is a statistically significant difference between the breeds. Radial joint orientation angles were obtained in eighty-eight dogs, including 23 Welsh Corgis, 16 Dachshunds, 14 Pekinese, 13 Maltese, 12 Poodles and 10 Beagles. Using the CORA methodology, the cranial proximal radial angle (CrPRA) and caudal distal radial angle (CdDRA) in the sagittal plane and medial proximal radial angle (MPRA) and lateral distal radial angle (LDRA) in the frontal plane were measured for the six breeds studied. The mean values of joint angles for each breed were compared statistically were observed. The CrPRA, CdDRA, and LDRA mean values of Dachshund and Welsh Corgi breeds were significantly smaller than other breeds, and in MPRA, Pekingese showed significantly smaller values than other breeds. This study confirms that the mean values of radial joint orientation angles can be significantly different among chondrodystrophic breeds. To accurately evaluate the degree of angular deformity of the radius, it may be helpful to refer to the average value for each breed with chondrodystrophy.

Forensic DNA phenotyping: Canis familiaris breed classification and skeletal phenotype prediction using functionally significant skeletal SNPs and indels

This review highlights a novel application of breed identification and prediction of skeletal traits in forensic investigations using canine DNA evidence. Currently, genotyping methods used for canine breed classification involve the application of highly polymorphic short tandem repeats in addition to larger commercially available SNP arrays. Both applications face technical challenges. An additional approach to breed identification could be through genotyping SNPs and indels that characterise the array of skeletal differences displayed across domestic dog populations. Research has shown that a small number of genetic variants of large effect drive differences in skeletal phenotypes among domestic dog breeds. This feature makes functionally significant canine skeletal variants a cost-effective target for forensic investigators to classify individuals according to their breed. Further analysis of these skeletal variants would enable the prediction of external appearance. To date, functionally significant genes with genetic variants associated with differences in size, bulk, skull shape, ear shape, limb length, digit type, and tail morphology have been uncovered. Recommendations of a cost-effective genotyping method that can be readily designed and applied by forensic investigators have been given. Further advances to improve the field of canine skeletal forensic DNA phenotyping include the refinement of phenotyping methods, further biological validation of the skeletal genetic variants and establishing a publicly available database for storage of allele frequencies of the skeletal genetic variants in the wider domestic dog population.