Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2

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.

Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration

When populations decrease in size and may become isolated, genomic erosion by loss of diversity from genetic drift and accumulation of deleterious mutations is likely an inevitable consequence. In such cases, immigration (genetic rescue) is necessary to restore levels of genetic diversity and counteract inbreeding depression. Recent work in conservation genomics has studied these processes focusing on the genetic diversity of single nucleotide polymorphisms. In contrast, our knowledge about structural genomic variation (insertions, deletions, duplications and inversions) in endangered species is limited. We analysed whole-genome, short-read sequences from 212 wolves from the inbred Scandinavian population and from neighbouring populations in Finland and Russia, and detected >35,000 structural variants (SVs) after stringent quality and genotype frequency filtering; >26,000 high-confidence variants remained after manual curation. The majority of variants were shorter than 1 kb, with a distinct peak in the length distribution of deletions at 190 bp, corresponding to insertion events of SINE/tRNA-Lys elements. The site frequency spectrum of SVs in protein-coding regions was significantly shifted towards rare alleles compared to putatively neutral variants, consistent with purifying selection. The realized genetic load of SVs in protein-coding regions increased with inbreeding levels in the Scandinavian population, but immigration provided a genetic rescue effect by lowering the load and reintroducing ancestral alleles at loci fixed for derived SVs. Our study shows that structural variation comprises a common type of in part deleterious mutations in endangered species and that establishing gene flow is necessary to mitigate the negative consequences of loss of diversity.

Skeletal Class III phenotype: Link between animal models and human genetics: A scoping review

This study aimed to identify evidence from animal studies examining genetic variants underlying maxillomandibular discrepancies resulting in a skeletal Class III (SCIII) malocclusion phenotype. Following the Manual for Evidence Synthesis of the JBI and the PRISMA extension for scoping reviews, a participant, concept, context question was formulated and systematic searches were executed in the PubMed, Scopus, WOS, Scielo, Open Gray, and Mednar databases. Of the 779 identified studies, 13 met the selection criteria and were included in the data extraction. The SCIII malocclusion phenotype was described as mandibular prognathism in the Danio rerio, Dicentrarchus labrax, and Equus africanus asinus models; and as maxillary deficiency in the Felis silvestris catus, Canis familiaris, Salmo trutta, and Mus musculus models. The identified genetic variants highlight the significance of BMP and TGF-β signaling. Their regulatory pathways and genetic interactions link them to cellular bone regulation events, particularly ossification regulation of postnatal cranial synchondroses. In conclusion, twenty genetic variants associated with the skeletal SCIII malocclusion phenotype were identified in animal models. Their interactions and regulatory pathways corroborate the role of these variants in bone growth, differentiation events, and ossification regulation of postnatal cranial synchondroses.

Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing

The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find that the Korean wolf has similar genomic diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is genetically more similar to wolves from the Tibetan Plateau; hence, Korean wolf conservation programmes might not benefit from the inclusion of this specimen.

Evolutionary mechanisms modulating the mammalian skull development

Mammals possess impressive craniofacial variation that mirrors their adaptation to diverse ecological niches, feeding behaviour, physiology and overall lifestyle. The spectrum of craniofacial geometries is established mainly during embryonic development. The formation of the head represents a sequence of events regulated on genomic, molecular, cellular and tissue level, with each step taking place under tight spatio-temporal control. Even minor variations in timing, position or concentration of the molecular drivers and the resulting events can affect the final shape, size and position of the skeletal elements and the geometry of the head. Our knowledge of craniofacial development increased substantially in the last decades, mainly due to research using conventional vertebrate model organisms. However, how developmental differences in head formation arise specifically within mammals remains largely unexplored. This review highlights three evolutionary mechanisms acknowledged to modify ontogenesis: heterochrony, heterotopy and heterometry. We present recent research that links changes in developmental timing, spatial organization or gene expression levels to the acquisition of species-specific skull morphologies. We highlight how these evolutionary modifications occur on the level of the genes, molecules and cellular processes, and alter conserved developmental programmes to generate a broad spectrum of skull shapes characteristic of the class Mammalia. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

Mutations in the CYP27B1 gene cause vitamin D dependent rickets in pugs

Rickets is a disorder of bone development and can be the result of either dietary or genetic causes. Here, related pugs from 2 litters were included. Three pugs had clinical signs including, lameness, bone deformities, and dyspnea. One other pug was found dead. Radiographs of 2 affected pugs, 5 and 6 months old, showed generalized widening, and irregular margination of the physes of both the appendicular and the axial skeleton with generalized decrease in bone opacity and bulbous swelling of the costochondral junctions. Two pugs had low serum calcium and 1,25 (OH)2 D3 concentrations. Test results further indicated secondary hyperparathyroidism with adequate concentrations of 25-hydroxyvitamin D. Necropsy revealed tongue-like projections of cartilage extending into the metaphysis consistent with rickets, loss of metaphyseal mineralization and lung pathology. Vitamin D-dependent rickets was diagnosed. A truncating mutation in the 1α-hydroxylase gene (CYP27B1) was identified by genome sequence analysis of the pugs with VDDR type 1A. Vitamin D-dependent rickets type 1A can occur in young pugs, and if left untreated is a life-threatening condition. Early medical intervention can reverse clinical signs and should be instituted as soon as possible.

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.

New genomic insights into the conformation of Lipizzan horses

Conformation traits are important selection criteria in equine breeding, as they describe the exterior aspects of the horse (height, joint angles, shape). However, the genetic architecture of conformation is not well understood, as data of these traits mainly consist of subjective evaluation scores. Here, we performed genome-wide association studies on two-dimensional shape data of Lipizzan horses. Based on this data, we identified significant quantitative trait loci (QTL) associated with cresty neck on equine chromosome (ECA)16 within the MAGI1 gene, and with type, hereby differentiating heavy from light horses on ECA5 within the POU2F1 gene. Both genes were previously described to affect growth, muscling and fatty deposits in sheep, cattle and pigs. Furthermore, we pin-pointed another suggestive QTL on ECA21, near the PTGER4 gene, associated with human ankylosing spondylitis, for shape differences in the back and pelvis (roach back vs sway back). Further differences in the shape of the back and abdomen were suggestively associated with the RYR1 gene, involved in core muscle weakness in humans. Therefore, we demonstrated that horse shape space data enhance the genomic investigations of horse conformation.

Transcriptomic Signatures of Single-Suture Craniosynostosis Phenotypes

Craniosynostosis is a birth defect where calvarial sutures close prematurely, as part of a genetic syndrome or independently, with unknown cause. This study aimed to identify differences in gene expression in primary calvarial cell lines derived from patients with four phenotypes of single-suture craniosynostosis, compared to controls. Calvarial bone samples (N = 388 cases/85 controls) were collected from clinical sites during reconstructive skull surgery. Primary cell lines were then derived from the tissue and used for RNA sequencing. Linear models were fit to estimate covariate adjusted associations between gene expression and four phenotypes of single-suture craniosynostosis (lambdoid, metopic, sagittal, and coronal), compared to controls. Sex-stratified analysis was also performed for each phenotype. Differentially expressed genes (DEGs) included 72 genes associated with coronal, 90 genes associated with sagittal, 103 genes associated with metopic, and 33 genes associated with lambdoid craniosynostosis. The sex-stratified analysis revealed more DEGs in males (98) than females (4). There were 16 DEGs that were homeobox (HOX) genes. Three TFs (SUZ12, EZH2, AR) significantly regulated expression of DEGs in one or more phenotypes. Pathway analysis identified four KEGG pathways associated with at least one phenotype of craniosynostosis. Together, this work suggests unique molecular mechanisms related to craniosynostosis phenotype and fetal sex.

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.

Bayesian mixed model analysis uncovered 21 risk loci for chronic kidney disease in boxer dogs

Chronic kidney disease (CKD) affects 10% of the human population, with only a small fraction genetically defined. CKD is also common in dogs and has been diagnosed in nearly all breeds, but its genetic basis remains unclear. Here, we performed a Bayesian mixed model genome-wide association analysis for canine CKD in a boxer population of 117 canine cases and 137 controls, and identified 21 genetic regions associated with the disease. At the top markers from each CKD region, the cases carried an average of 20.2 risk alleles, significantly higher than controls (15.6 risk alleles). An ANOVA test showed that the 21 CKD regions together explained 57% of CKD phenotypic variation in the population. Based on whole genome sequencing data of 20 boxers, we identified 5,206 variants in LD with the top 50 BayesR markers. Following comparative analysis with human regulatory data, 17 putative regulatory variants were identified and tested with electrophoretic mobility shift assays. In total four variants, three intronic variants from the MAGI2 and GALNT18 genes, and one variant in an intergenic region on chr28, showed alternative binding ability for the risk and protective alleles in kidney cell lines. Many genes from the 21 CKD regions, RELN, MAGI2, FGFR2 and others, have been implicated in human kidney development or disease. The results from this study provide new information that may enlighten the etiology of CKD in both dogs and humans.

Matricellular Protein SMOC2 Potentiates BMP9-Induced Osteogenic Differentiation in Mesenchymal Stem Cells through the Enhancement of FAK/PI3K/AKT Signaling

Mesenchymal stem cells (MSCs) can self-renew and differentiate into multiple lineages, making MSC transplantation a promising option for bone regeneration. Both matricellular proteins and growth factors play an important role in regulating stem cell fate. In this study, we investigated the effects of matricellular protein SMOC2 (secreted modular calcium-binding protein 2) on bone morphogenetic protein 9 (BMP9) in mouse embryonic fibroblasts (MEFs) and revealed a possible molecular mechanism underlying this process. We found that SMOC2 was detectable in MEFs and that exogenous SMOC2 expression potentiated BMP9-induced osteogenic markers, matrix mineralization, and ectopic bone formation, whereas SMOC2 knockdown inhibited these effects. BMP9 increased the levels of p-FAK and p-AKT, which were either enhanced or reduced by SMOC2 and FAK silencing, respectively. BMP9-induced osteogenic markers were increased by SMOC2, and this increase was partially abolished by silencing FAK or LY290042. Furthermore, we found that general transcription factor 2I (GTF2I) was enriched at the promoter region of SMOC2 and that integrin β1 interacted with SMOC2 in BMP9-treated MEFs. Our findings demonstrate that SMOC2 can promote BMP9-induced osteogenic differentiation by enhancing the FAK/PI3K/AKT pathway, which may be triggered by facilitating the interaction between SMOC2 and integrin β1.

Long-term Small Population Size, Deleterious Variation, and Altitude Adaptation in the Ethiopian Wolf, a Severely Endangered Canid

Ethiopian wolves, a canid species endemic to the Ethiopian Highlands, have been steadily declining in numbers for decades. Currently, out of 35 extant species, it is now one of the world's most endangered canids. Most conservation efforts have focused on preventing disease, monitoring movements and behavior, and assessing the geographic ranges of sub-populations. Here, we add an essential layer by determining the Ethiopian wolf's demographic and evolutionary history using high-coverage (∼40×) whole-genome sequencing from 10 Ethiopian wolves from the Bale Mountains. We observe exceptionally low diversity and enrichment of weakly deleterious variants in the Ethiopian wolves in comparison with two North American gray wolf populations and four dog breeds. These patterns are consequences of long-term small population size, rather than recent inbreeding. We infer the demographic history of the Ethiopian wolf and find it to be concordant with historic records and previous genetic analyses, suggesting Ethiopian wolves experienced a series of both ancient and recent bottlenecks, resulting in a census population size of fewer than 500 individuals and an estimated effective population size of approximately 100 individuals. Additionally, long-term small population size may have limited the accumulation of strongly deleterious recessive mutations. Finally, as the Ethiopian wolves have inhabited high-altitude areas for thousands of years, we searched for evidence of high-altitude adaptation, finding evidence of positive selection at a transcription factor in a hypoxia-response pathway [CREB-binding protein (CREBBP)]. Our findings are pertinent to continuing conservation efforts and understanding how demography influences the persistence of deleterious variation in small populations.

Virtual surgical planning and 3D printing: Methodology and applications in veterinary oromaxillofacial surgery

Virtual surgical planning is the process of planning and rehearsing a surgical procedure completely within the virtual environment on computer models. Virtual surgical planning and 3D printing is gaining popularity in veterinary oromaxillofacial surgery and are viable tools for the most basic to the most complex cases. These techniques can provide the surgeon with improved visualization and, thus, understanding of the patients' 3D anatomy. Virtual surgical planning is feasible in a clinical setting and may decrease surgical time and increase surgical accuracy. For example, pre-operative implant contouring on a 3D-printed model can save time during surgery; 3D-printed patient-specific implants and surgical guides help maintain normocclusion after mandibular reconstruction; and the presence of a haptic model in the operating room can improve surgical precision and safety. However, significant time and financial resources may need to be allocated for planning and production of surgical guides and implants. The objectives of this manuscript are to provide a description of the methods involved in virtual surgical planning and 3D printing as they apply to veterinary oromaxillofacial surgery and to highlight these concepts with the strategic use of examples. In addition, the advantages and disadvantages of the methods as well as the required software and equipment will be discussed.

SMOC2 promotes an epithelial-mesenchymal transition and a pro-metastatic phenotype in epithelial cells of renal cell carcinoma origin

Renal Cell Carcinoma (RCC) is the most common form of all renal cancer cases, and well-known for its highly aggressive metastatic behavior. SMOC2 is a recently described non-structural component of the extracellular matrix (ECM) that is highly expressed during tissue remodeling processes with emerging roles in cancers, yet its role in RCC remains elusive. Using gene expression profiles from patient samples, we identified SMOC2 as being significantly expressed in RCC tissue compared to normal renal tissue, which correlated with shorter RCC patient survival. Specifically, de novo protein synthesis of SMOC2 was shown to be much higher in the tubular epithelial cells of patients with biopsy-proven RCC. More importantly, we provide evidence of SMOC2 triggering kidney epithelial cells into an epithelial-to-mesenchymal transition (EMT), a phenotype known to promote metastasis. We found that SMOC2 induced mesenchymal-like morphology and activities in both RCC and non-RCC kidney epithelial cell lines. Mechanistically, treatment of RCC cell lines ACHN and 786-O with SMOC2 (recombinant and enforced expression) caused a significant increase in EMT-markers, -matrix production, -proliferation, and -migration, which were inhibited by targeting SMOC2 by siRNA. We further characterized SMOC2 activation of EMT to occur through the integrin β3, FAK and paxillin pathway. The proliferation and metastatic potential of SMOC2 overexpressing ACHN and 786-O cell lines were validated in vivo by their significantly higher tumor growth in kidneys and systemic dissemination into other organs when compared to their respective controls. In principle, understanding the impact that SMOC2 has on EMT may lead to more evidence-based treatments and biomarkers for RCC metastasis.

Evaluation of a Treadmill-Based Submaximal Fitness Test in Pugs, and Collecting Breed-Specific Information on Brachycephalic Obstructive Airway Syndrome

Simple Summary

In the present study, a submaximal fitness test on a treadmill was evaluated to assess its feasibility under standardised conditions. Moreover, its effectiveness in identifying pugs with clinical signs of brachycephalic obstructive airway syndrome was examined. It was apparent that respiratory symptoms can be exposed during the fitness test, and intensified with an increased duration of exercise. This method of testing improves the clinical evaluation of the dogs and helps identify restrictions due to brachycephalic obstructive airway syndrome. Since most of the dogs could be familiarised with the treadmill, it may be a feasible option for performing fitness tests in brachycephalic dogs. Major benefits, therefore, are that each dog can be closely monitored during the entire process, and that the examination can be conducted under standardised conditions.

Abstract

Despite efforts of veterinarians and breeders, brachycephalic obstructive airway syndrome (BOAS) is still a common problem in pugs, underlining the need for objective tests to identify and prevent breeding with affected dogs. In the current study, a submaximal, treadmill-based fitness test was evaluated as a tool to identify signs of airway obstruction not recognisable under rest conditions. In addition to this, different body conformation and measurements were assessed regarding their association with BOAS. A total of 62 pugs and 10 mesocephalic dogs trotted with an individual comfort speed on a treadmill for 15 min. Before and during the examination, dogs were examined for signs of respiratory distress, and a functional BOAS grading was applied. The influence of body conformation on BOAS grading was tested in a univariable and multivariable logistic regression model. During exercise, more respiratory noises were observed, and existing respiratory noises became more apparent in comparison to when at rest. In the multivariable logistic regression model, no factor had a statistically significant influence on BOAS classification. Submaximal fitness testing helped to identify signs of respiratory distress not apparent under resting conditions, and could be a valuable addition for identifying dogs with BOAS. Performing testing on a treadmill facilitates continuous observation of the patients, and enables standardisation of the test regarding the test environment, as well as provides an uninterrupted, steady workload.

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.

Biomechanical correlates of zygomaxillary-surface shape in papionin primates and the effects of hard-object feeding on mangabey facial form

Extant African papioninans are distinguished from macaques by the presence of excavated facial fossae; however, facial excavation differs among taxa. Mangabeys (Cercocebus, Rungwecebus, and Lophocebus) exhibit fossae that invade the zygomatic forming pronounced suborbital fossae (SOFs). Larger-bodied Papio, Mandrillus, and Theropithecus have lateral rostral fossae with minimal/absent suborbital fossae. Because prior studies have shown that mangabeys exhibit adaptations to anterior dental loading (e.g., palatal retraction), it is plausible that mangabey SOFs represent structural accommodation to masticatory-system shape rather than facial allometry, as commonly hypothesized. We analyzed covariation between zygomaxillary-surface shape, masticatory-system shape, and facial size in 141 adult crania of Macaca fascicularis, Papio kindae, Cercocebus, and Lophocebus. These taxa represent the range of papionin SOF expression while minimizing size variation (narrow allometry). Masticatory-system landmarks (39) registered palate shape, bite points, masticatory muscle attachments, and the temporomandibular joint. Semilandmarks (450) captured zygomaxillary-surface shape. Following Procrustes superimposition with semilandmark sliding and principal components analyses, multivariate regression was used to explore allometry, and two-block partial least-squares analyses (within-configuration and separate-blocks) were used to examine covariation patterns. Scores on principal components 1-2 and the first partial least-square (PLS1) separate mangabeys from Macaca and Papio. Both zygomaxillary-surface shape and masticatory-system shape are correlated with size within taxa and facial morphotypes; however, regression distributions indicate morphotype shape differences are non-allometric. PLS1 accounts for ∼95% of shape covariance (p < 0.0001) and shows strong linear correlations (r-PLS = ∼0.95, p < 0.0001) between blocks. Negative PLS1 scores in mangabeys reflect deep excavation of the suborbital malar surface, palatal retraction, and anterior displacement of jaw adductor muscles and the temporomandibular joint. Neither PC1 nor PLS1 scores ordinate specimens by facial size. Taken together, these results fail to support the allometric hypothesis but suggest that mangabey zygomaxillary morphology is closely linked with adaptations to hard-object feeding.

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.

Nasal hyperkeratosis in Griffon breeds: Clinical, histopathological features and the prevalence in the Swedish population compared to a control group and other brachycephalic breeds

BACKGROUND

In the Griffon breeds (GB) nasal hyperkeratosis is common and develops already in early adulthood. Breed-related features and prevalence have not previously been documented.

HYPOTHESIS/OBJECTIVES

To describe clinical and histopathological features of nasal hyperkeratosis in GB and to document the prevalence.

MATERIALS AND METHODS

Seven GB dogs with nasal hyperkeratosis were examined. Three histopathological samples were analysed. Owners of 107 GB and 493 control dogs completed a questionnaire distributed via social media.

RESULTS

Typical features of nasal hyperkeratosis in GB included varying degrees of dry, firm, excessive proliferation of keratin, affecting the dorsal or dorsolateral aspect of the planum nasale. Histopathology was characterized by severe, lamellar orthokeratotic and focal parakeratotic hyperkeratosis and multiple small serum lakes. Thirty-four of 107 GB dogs (31.8%) and 65 of 493 (13.2%) control dogs had varying degree of nasal hyperkeratosis. No sex predisposition was noted. Median age of onset was 3 years for GB, similar to brachycephalic control dogs whereas non-brachycephalic control dogs had a significantly later age of onset (p = 0.0053).

CONCLUSIONS AND CLINICAL IMPORTANCE

Idiopathic nasal hyperkeratosis is very common in GB dogs and other brachycephalic breeds with nearly one third being affected, often already a young age.

Ophthalmic disorders in a referral population of seven breeds of brachycephalic dogs: 970 cases (2008-2017)

OBJECTIVE

To evaluate the frequency of ophthalmic disorders in 7 brachycephalic dog breeds referred to an academic veterinary ophthalmology service.

ANIMALS

970 client-owned dogs of 7 brachycephalic breeds that were evaluated by the ophthalmology service in a veterinary teaching hospital from January 2008 through December 2017.

PROCEDURES

Medical records of 7 brachycephalic breeds (ie, Boston Terriers, English Bulldogs, French Bulldogs, Lhasa Apsos, Pekingese, Pugs, and Shih Tzus) were reviewed to collect data regarding patient signalment, ophthalmic diagnoses, affected eyes, and number and dates of visits.

RESULTS

Median age at the first examination was 7 years (range, 23 days to 22 years). The number of dogs seen for a first examination increased with age. Corneal ulcers, keratoconjunctivitis sicca, corneal pigmentation, immature cataracts, and uveitis were each diagnosed in ≥ 100 dogs and represented 40.4% (1,161/2,873) of all diagnoses. On the basis of anatomic location, 66.3% (1,905/2,873) of all disorders were located in either the cornea (1,014/2,873 [35.2%]) or adnexa (891/2,873 [31%]). There was a significant difference in breed proportion in the study population; of the 7 breeds studied, Shih Tzus (34.3% [333/970]), Pugs (20.8% [202/970]), and Boston Terriers (16.6% [161/970]) were the most prevalent breeds. The frequency of some diseases within the referral population was associated with breed.

CONCLUSIONS AND CLINICAL RELEVANCE

Findings suggested that the most prevalent disorders for the brachycephalic breeds in this ophthalmic referral population were corneal ulcers, keratoconjunctivitis sicca, corneal pigmentation, immature cataracts, and uveitis. Although all dogs shared brachycephalic features, the frequency of specific ophthalmic diseases varied between breeds.

Ethics in canine reproduction - a survey among veterinarians who provide canine reproductive services

OBJECTIVE

Several dog breeds suffer from health and welfare problems due to unfavorable anatomies and high prevalence of inherited diseases. Veterinarians should care for animal health and welfare but they may also be involved in breeding management including the use of reproductive techniques.

MATERIAL AND METHODS

An online survey was conducted to find out how veterinarians who are involved in small animal reproduction regard ethical issues, which services they provide, how they discuss and handle ethical concerns and talk about them with breeders.

RESULTS

In total, 83 participants mainly from Europe completed the online survey. Opinions on which interventions are ethical or not were heterogeneous. Most respondents (79.2 %) found it ethical to perform artificial insemination (AI) in dogs which did not reproduce naturally before. However, 62.7 % of participants stated that surgical insemination is not ethical. Elective cesarean sections are considered not ethical by approximately half of the participants. A closer look at responses to the questions of whether AI is ethical under specific conse quences suggests that most veterinarians are making ethical and value judgments in terms of what is justifiable or not. However, more than 80 % feel at least sometimes compromised by ethical conflicts.

CLINICAL RELEVANCE

This research intended to foster discussion of this topic. International strategies should be developed to support solving conflicts and dilemmas related to ethical issues in dog breeding and assisted reproduction, as well as diminishing physical disabilities and heritable diseases.

Complex genetic architecture of three-dimensional craniofacial shape variation in domestic pigeons

Deciphering the genetic basis of vertebrate craniofacial variation is a longstanding biological problem with broad implications in evolution, development, and human pathology. One of the most stunning examples of craniofacial diversification is the adaptive radiation of birds, in which the beak serves essential roles in virtually every aspect of their life histories. The domestic pigeon (Columba livia) provides an exceptional opportunity to study the genetic underpinnings of craniofacial variation because of its unique balance of experimental accessibility and extraordinary phenotypic diversity within a single species. We used traditional and geometric morphometrics to quantify craniofacial variation in an F2 laboratory cross derived from the straight-beaked Pomeranian Pouter and curved-beak Scandaroon pigeon breeds. Using a combination of genome-wide quantitative trait locus scans and multi-locus modeling, we identified a set of genetic loci associated with complex shape variation in the craniofacial skeleton, including beak shape, braincase shape, and mandible shape. Some of these loci control coordinated changes between different structures, while others explain variation in the size and shape of specific skull and jaw regions. We find that in domestic pigeons, a complex blend of both independent and coupled genetic effects underlie three-dimensional craniofacial morphology.

Smoc1 and Smoc2 regulate bone formation as downstream molecules of Runx2

Runx2 is an essential transcription factor for bone formation. Although osteocalcin, osteopontin, and bone sialoprotein are well-known Runx2-regulated bone-specific genes, the skeletal phenotypes of knockout (KO) mice for these genes are marginal compared with those of Runx2 KO mice. These inconsistencies suggest that unknown Runx2-regulated genes play important roles in bone formation. To address this, we attempted to identify the Runx2 targets by performing RNA-sequencing and found Smoc1 and Smoc2 upregulation by Runx2. Smoc1 or Smoc2 knockdown inhibited osteoblastogenesis. Smoc1 KO mice displayed no fibula formation, while Smoc2 KO mice had mild craniofacial phenotypes. Surprisingly, Smoc1 and Smoc2 double KO (DKO) mice manifested no skull, shortened tibiae, and no fibulae. Endochondral bone formation was also impaired at the late stage in the DKO mice. Collectively, these results suggest that Smoc1 and Smoc2 function as novel targets for Runx2, and play important roles in intramembranous and endochondral bone formation.

Takahata et al. investigate the functional role of SMOC1/2 proteins in skeletal development. They reveal a genetic pathway that includes Bmp2 and Runx2 inducing expression of the paralogous Smoc genes, which may offer novel and effective therapeutic strategies associated with various bone and cartilage diseases.

More Than a Moggy; A Population Genetics Analysis of the United Kingdom's Non-Pedigree Cats

The domestic cat is one of the most popular pets in the world. It is estimated that 89–92% of domestic cats in the UK are non-pedigree Domestic shorthair (DSH), Domestic longhair (DLH), or Domestic semi-longhair cats (DSLH). Despite their popularity, little is known of the UK non-pedigree cats’ population structure and breeding dynamics. Using a custom designed single nucleotide variant (SNV) array, this study investigated the population genetics of 1344 UK cats. Principal components analysis (PCA) and fastSTRUCTURE analysis verified that the UK’s DSH, DLH, and DSLH cats are random-bred, rather than admixed, mix breed, or crossbred. In contrast to pedigree cats, the linkage disequilibrium of these random-bred cats was least extensive and decayed rapidly. Homozygosity by descent (HBD) analysis showed the majority of non-pedigree cats had proportionally less of their genome in HBD segments compared to pedigree cats, and that these segments were older. Together, these findings suggest that the DSH, DLH, and DSLH cats should be considered as a population of random-bred cats rather than a crossbred or pedigree-admixed cat. Unexpectedly, 19% of random-bred cat genomes displayed a higher proportion of HBD segments associated with more recent inbreeding events. Therefore, while non-pedigree cats as a whole are genetically diverse, they are not impervious to inbreeding and its health risks.

Structural Variants Selected during Yak Domestication Inferred from Long-Read Whole-Genome Sequencing

Structural variants (SVs) represent an important genetic resource for both natural and artificial selection. Here we present a chromosome-scale reference genome for domestic yak (Bos grunniens) that has longer contigs and scaffolds (N50 44.72 and 114.39 Mb, respectively) than reported for any other ruminant genome. We further obtained long-read resequencing data for 6 wild and 23 domestic yaks and constructed a genetic SV map of 372,220 SVs that covers the geographic range of the yaks. The majority of the SVs contains repetitive sequences and several are in or near genes. By comparing SVs in domestic and wild yaks, we identified genes that are predominantly related to the nervous system, behavior, immunity, and reproduction and may have been targeted by artificial selection during yak domestication. These findings provide new insights in the domestication of animals living at high altitude and highlight the importance of SVs in animal domestication.

Exceptional Changes in Skeletal Anatomy under Domestication: The Case of Brachycephaly

"Brachycephaly" is generally considered a phenotype in which the facial part of the head is pronouncedly shortened. While brachycephaly is characteristic for some domestic varieties and breeds (e.g., Bulldog, Persian cat, Niata cattle, Anglo-Nubian goat, Middle White pig), this phenotype can also be considered pathological. Despite the superficially similar appearance of "brachycephaly" in such varieties and breeds, closer examination reveals that "brachycephaly" includes a variety of different cranial modifications with likely different genetic and developmental underpinnings and related with specific breed histories. We review the various definitions and characteristics associated with brachycephaly in different domesticated species. We discern different types of brachycephaly ("bulldog-type," "katantognathic," and "allometric" brachycephaly) and discuss morphological conditions related to brachycephaly, including diseases (e.g., brachycephalic airway obstructive syndrome). Further, we examine the complex underlying genetic and developmental processes and the culturally and developmentally related reasons why brachycephalic varieties may or may not be prevalent in certain domesticated species. Knowledge on patterns and mechanisms associated with brachycephaly is relevant for domestication research, veterinary and human medicine, as well as evolutionary biology, and highlights the profound influence of artificial selection by humans on animal morphology, evolution, and welfare.

Human Adult Fibroblast-like Synoviocytes and Articular Chondrocytes Exhibit Prominent Overlap in Their Transcriptomic Signatures

Objectives

Fibroblast‐like synoviocytes (FLS) and articular chondrocytes (AC) derive from a common pool of embryonic precursor cells. They are currently believed to engage in largely distinct differentiation programs to build synovium and articular cartilage and maintain healthy tissues throughout life. We tested this hypothesis by deeply characterizing and comparing their transcriptomic attributes.

Methods

We profiled the transcriptomes of freshly isolated AC, synovium, primary FLS, and dermal fibroblasts from healthy adult humans using bulk RNA sequencing assays and downloaded published single‐cell RNA sequencing data from freshly isolated human FLS. We integrated all data to define cell‐specific signatures and validated findings with quantitative reverse transcription PCR of human samples and RNA hybridization of mouse joint sections.

Results

We identified 212 AC and 168 FLS markers on the basis of exclusive or enriched expression in either cell and 294 AC/FLS markers on the basis of similar expression in both cells. AC markers included joint‐specific and pan‐cartilaginous genes. FLS and AC/FLS markers featured 37 and 55 joint‐specific genes, respectively, and 131 and 239 pan‐fibroblastic genes, respectively. These signatures included many previously unrecognized markers with potentially important joint‐specific roles. AC/FLS markers overlapped in their expression patterns among all FLS and AC subpopulations, suggesting that they fulfill joint‐specific properties in all, rather than in discrete, AC and FLS subpopulations.

Conclusion

This study broadens knowledge and identifies a prominent overlap of the human adult AC and FLS transcriptomic signatures. It also provides data resources to help further decipher mechanisms underlying joint homeostasis and degeneration and to improve the quality control of tissues engineered for regenerative treatments.

Copy number variation underlies complex phenotypes in domestic dog breeds and other canids

Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole genome CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray technologies. We have taken advantage of this data set to perform the first CNV-based genome-wide association study (GWAS) in canids. We identify 96 loci that display copy number differences across breeds, which are statistically associated with a previously compiled set of breed-specific morphometrics and disease susceptibilities. Among these, we highlight the discovery of a long-range interaction involving a CNV near MED13L and TBX3, which could influence breed standard height. Integration of the CNVs with chromatin interactions, long noncoding RNA expression, and single nucleotide variation highlights a subset of specific loci and genes with potential functional relevance and the prospect to explain trait variation between dog breeds.

The impact of identity by descent on fitness and disease in dogs

Dogs and humans have coexisted together for thousands of years, but it was not until the Victorian Era that humans practiced selective breeding to produce the modern standards we see today. Strong artificial selection during the breed formation period has simplified the genetic architecture of complex traits and caused an enrichment of identity-by-descent (IBD) segments in the dog genome. This study demonstrates the value of IBD segments and utilizes them to infer the recent demography of canids, predict case-control status for complex traits, locate regions of the genome potentially linked to inbreeding depression, and to identify understudied breeds where there is potential to discover new disease-associated variants.

Domestic dogs have experienced population bottlenecks, recent inbreeding, and strong artificial selection. These processes have simplified the genetic architecture of complex traits, allowed deleterious variation to persist, and increased both identity-by-descent (IBD) segments and runs of homozygosity (ROH). As such, dogs provide an excellent model for examining how these evolutionary processes influence disease. We assembled a dataset containing 4,414 breed dogs, 327 village dogs, and 380 wolves genotyped at 117,288 markers and data for clinical and morphological phenotypes. Breed dogs have an enrichment of IBD and ROH, relative to both village dogs and wolves, and we use these patterns to show that breed dogs have experienced differing severities of bottlenecks in their recent past. We then found that ROH burden is associated with phenotypes in breed dogs, such as lymphoma. We next test the prediction that breeds with greater ROH have more disease alleles reported in the Online Mendelian Inheritance in Animals (OMIA). Surprisingly, the number of causal variants identified correlates with the popularity of that breed rather than the ROH or IBD burden, suggesting an ascertainment bias in OMIA. Lastly, we use the distribution of ROH across the genome to identify genes with depletions of ROH as potential hotspots for inbreeding depression and find multiple exons where ROH are never observed. Our results suggest that inbreeding has played a large role in shaping genetic and phenotypic variation in dogs and that future work on understudied breeds may reveal new disease-causing variation.

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3' end of LINE-1_Cfs (i.e., LINE-1_Cf 3'-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation.

Dog breeds and body conformations with predisposition to osteosarcoma in the UK: a case-control study

Background

Osteosarcoma is an aggressive and painful bone neoplasm in dogs. Previous studies have reported epidemiological associations suggesting that large body mass, long bone length and the genetics of certain breeds including the Rottweiler are associated with elevated osteosarcoma risk. However, these studies were often limited by selection bias and confounding factors, and have rarely offered insights into breed-associated protection for osteosarcoma. The current study includes 1756 appendicular and axial osteosarcoma cases presenting to VPG Histology (Bristol, UK) compared against a control population of 905,211 dogs without osteosarcoma from primary care electronic patient records in the VetCompass™ dataset.

Methods and study design

Retrospective, case-control study. Multivariable logistic regression analysis explored associations between demographic risk factors (including breed, chondrodystrophy, age, sex/neuter status, skull-shape, and body mass) and osteosarcoma of all anatomical sites.

Results

We identified several breeds with increased and reduced odds of osteosarcoma. At highest risk were the Rottweiler and Great Dane, with > 10 times the odds of osteosarcoma compared with crossbreds, and the Rhodesian Ridgeback, which has not featured in previous lists of at-risk breeds for osteosarcoma, and had an odds ratio of 11.31 (95% confidence interval 7.37–17.35). Breeds at lowest risk of osteosarcoma (protected breeds) included the Bichon Frise, the French Bulldog and the Cavalier King Charles Spaniel, all with odd ratios of less than 0.30 compared with crossbreds. Body mass was strongly associated with osteosarcoma risk; dogs over 40 kg exhibited osteosarcoma odds of 45.44 (95% confidence interval 33.74–61.20) compared with dogs less than 10 kg. Chondrodystrophic breeds had an osteosarcoma odds ratio of 0.13 (95% confidence interval 0.11–0.16) compared with non-chondrodystrophic breeds.

Conclusions

This study provides evidence of strong breed-associated osteosarcoma risk and protection, suggesting a genetic basis for osteosarcoma pathogenesis. It highlights that breeds selected for long legs/large body mass are generally overrepresented amongst at-risk breeds, whilst those selected for short leg length/small body mass are generally protected. These findings could inform genetic studies to identify osteosarcoma risk alleles in canines and humans; as well as increasing awareness amongst veterinarians and owners, resulting in improved breeding practices and clinical management of osteosarcoma in dogs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40575-021-00100-7.

Canine DVL2 variant contributes to brachycephalic phenotype and caudal vertebral anomalies

A frameshift deletion variant in the Wnt pathway gene dishevelled 2 (DVL2) is associated with a truncated, kinked tail (“screw tail”) in English Bulldogs, French Bulldogs and Boston Terriers. These breeds are also characterized by distinctive morphological traits, including a wide head, flat face and short-limbed dwarfism, which are characteristic of Robinow syndrome in humans, caused by defects in genes such as DVL1 and DVL3. Based on these phenotypic and genetic similarities, it has previously been hypothesized that the canine DVL2 variant results in a syndromic phenotype called the Robinow-like syndrome. In our study, we investigated the distribution of the DVL2 variant in 1954 dogs from 15 breeds, identifying breeds with allele variation and enabling the dissection of the genotype–phenotype correlation for the first time. With CT examinations in American Staffordshire Terriers, we confirmed that the DVL2 allele is associated with caudal vertebral malformations and a brachycephalic phenotype. We also hypothesize that the variant may be linked to additional health conditions, including brachycephalic obstructive airway syndrome and congenital heart defects. Altogether, our study strengthens the role of DVL2 as one of the contributors to the “bulldog type” morphology and features on the spectrum of human Robinow syndrome.

A SMOC2 variant inhibits BMP signaling by competitively binding to BMPR1B and causes growth plate defects

Endochondral ossification is the major process of long bone formation, and chondrogenesis is the final step of this process. Several studies have indicated that bone morphogenetic proteins (BMPs) are required for chondrogenesis and regulate multiple growth plate features. Abnormal BMP pathways lead to growth plate defects, resulting in osteochondrodysplasia. The SPARC-related modular calcium binding 2 (SMOC2) gene encodes an extracellular protein that is considered to be an antagonist of BMP signaling. In this study, we generated a mouse model by knocking-in the SMOC2 mutation (c.1076 T > G), which showed short-limbed dwarfism, reduced, disorganized, and hypocellular proliferative zones and expanded hypertrophic zones in tibial growth plates. To determine the underlying pathophysiological mechanism of SMOC2 mutation, we used knock-in mice to investigate the interaction between SMOC2 and the BMP-SMAD1/5/9 signaling pathway in vivo and in vitro. Eventually, we found that mutant SMOC2 could not bind to COL9A1 and HSPG. Furthermore, mutant SMOC2 inhibited BMP signaling by competitively binding to BMPR1B, which lead to defects in growth plates and short-limbed dwarfism in knock-in mice.

Staffordshire Bull Terriers in the UK: their disorder predispositions and protections

Background

The Staffordshire Bull Terrier is a popular dog breed in the UK but there is limited reliable evidence on disorder predispositions and protections within the breed. Using anonymised veterinary clinical data from the VetCompass™ Programme, this study aimed to identify common disorders with predisposition and protection in the Staffordshire Bull Terrier. The study hypothesised that Staffordshire Bull Terriers would have higher odds of aggression compared with non-Staffordshire Bull Terriers.

Results

The clinical records of a random sample of dogs of all types were reviewed to extract the most definitive diagnoses for all disorders existing during 2016. A combined list from the 30 most common disorders in Staffordshire Bull Terriers and the 30 most common disorders in non-Staffordshire Bull Terriers was generated. Multivariable logistic regression was used to report the odds of each of these disorders in 1304 (5.8%) Staffordshire Bull Terriers compared with 21,029 (94.2%) non-Staffordshire Bull Terriers. After accounting for confounding, Staffordshire Bull Terriers had significantly increased odds of 4/36 (11.1%) disorders compared to non-Staffordshire Bull Terriers with highest odds for seizure disorder (OR 2.06; 95% CI 1.24 to 3.40; p = 0.005). Conversely, Staffordshire Bull Terriers had reduced odds of 5/36 (13.9%) disorders, with lowest odds for patellar luxation (OR 0.15; 95% CI 0.04 to 0.61; p = 0.008). There was no significant difference in the odds of aggression between Staffordshire Bull Terriers compared with non-Staffordshire Bull Terriers (OR 1.09; 95% CI 0.75 to 1.58; p = 0.644).

Conclusions

This study provides a reliable evidence base of breed-specific disorder predispositions and protections that can be used by breeders to optimise breeding decisions. The findings can assist prospective owners of Staffordshire Bull Terriers to make informed decisions when acquiring a dog. From the relative number of predispositions to protections identified, there is no evidence that Staffordshire Bull Terriers have higher overall health problems than non-Staffordshire Bull Terriers.

Deficiency of the SMOC2 matricellular protein impairs bone healing and produces age-dependent bone loss

Secreted extracellular matrix components which regulate craniofacial development could be reactivated and play roles in adult wound healing. We report a patient with a loss-of-function of the secreted matricellular protein SMOC2 (SPARC related modular calcium binding 2) presenting severe oligodontia, microdontia, tooth root deficiencies, alveolar bone hypoplasia, and a range of skeletal malformations. Turning to a mouse model, Smoc2-GFP reporter expression indicates SMOC2 dynamically marks a range of dental and bone progenitors. While germline Smoc2 homozygous mutants are viable, tooth number anomalies, reduced tooth size, altered enamel prism patterning, and spontaneous age-induced periodontal bone and root loss are observed in this mouse model. Whole-genome RNA-sequencing analysis of embryonic day (E) 14.5 cap stage molars revealed reductions in early expressed enamel matrix components (Odontogenic ameloblast-associated protein) and dentin dysplasia targets (Dentin matrix acidic phosphoprotein 1). We tested if like other matricellular proteins SMOC2 was required for regenerative repair. We found that the Smoc2-GFP reporter was reactivated in adjacent periodontal tissues 4 days after tooth avulsion injury. Following maxillary tooth injury, Smoc2^−/− mutants had increased osteoclast activity and bone resorption surrounding the extracted molar. Interestingly, a 10-day treatment with the cyclooxygenase 2 (COX2) inhibitor ibuprofen (30 mg/kg body weight) blocked tooth injury-induced bone loss in Smoc2^−/− mutants, reducing matrix metalloprotease (Mmp)9. Collectively, our results indicate that endogenous SMOC2 blocks injury-induced jaw bone osteonecrosis and offsets age-induced periodontal decay.

Deciphering the puzzles of dog domestication

The domestic dog, as a highly successful domestication model, is well known as a favored human companion. Exploring its domestication history should provide great insight into our understanding of the prehistoric development of human culture and productivity. Furthermore, investigation on the mechanisms underpinning the morphological and behavioral traits associated with canid domestication syndrome is of significance not only for scientific study but also for human medical research. Current development of a multidisciplinary canine genome database, which includes enormous omics data, has substantially improved our understanding of the genetic makeup of dogs. Here, we reviewed recent advances associated with the original history and genetic basis underlying environmental adaptations and phenotypic diversities in domestic dogs, which should provide perspectives on improving the communicative relationship between dogs and humans.

From head to hind: Elucidating function through contrasting morphometrics of ancient and modern pedigree dogs

Used together, caliper- and geometric-based morphometric analyses provide complimentary approaches to classifying form and function of archaeozoological remains. Here we apply these analytical tools to the skeletal remains of an ancient male dog unearthed from a rural farm settlement of Roman date near present day Warmington, United Kingdom. Our comparisons of the Warmington Roman dog against the morphological characteristics of modern dog breeds enabled us to establish the former's size and shape. It was of medium stature. Analysis of viscerocrania and neurocrania indicate it falls within the meso- to dolichocephalic rankings of modern dogs. The neurocranium shape and the dimensions of its long bones strongly suggest that the Warmington dog shares similarities to modern sight hounds. Historically sight hounds were bred for speed, as necessitated of a hunter that runs down small prey. Our analysis suggests that the Warmington dog was likely bred for, or derived from, Roman hunting stock. By revealing the Warmington Roman dog's form from cranial and postcranial analyses, we shed light on Roman life in one of the furthest outposts of the Roman Empire.

Genetic Variants Affecting Skeletal Morphology in Domestic Dogs

Purebred dog breeds provide a powerful resource for the discovery of genetic variants affecting skeletal morphology. Domesticated and subsequently purebred dogs have undergone strong artificial selection for a broad range of skeletal variation, which include both the size and shapes of their bones. While the phenotypic variation between breeds is high, within-breed morphological variation is typically low. Approaches for defining genetic variants associated with canine morphology include quantitative within-breed analyses, as well as across-breed analyses, using breed standards as proxies for individual measurements. The ability to identify variants across the genomes of individual dogs can now be paired with precise measures of morphological variation to define the genetic interactions and the phenotypic effect of variants on skeletal morphology.

A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia)

Rock pigeons (Columba livia) display an extraordinary array of pigment pattern variation. One such pattern, Almond, is characterized by a variegated patchwork of plumage colors that are distributed in an apparently random manner. Almond is a sex-linked, semi-dominant trait controlled by the classical Stipper (St) locus. Heterozygous males (Z^StZ⁺ sex chromosomes) and hemizygous Almond females (Z^StW) are favored by breeders for their attractive plumage. In contrast, homozygous Almond males (Z^StZ^St) develop severe eye defects and often lack plumage pigmentation, suggesting that higher dosage of the mutant allele is deleterious. To determine the molecular basis of Almond, we compared the genomes of Almond pigeons to non-Almond pigeons and identified a candidate St locus on the Z chromosome. We found a copy number variant (CNV) within the differentiated region that captures complete or partial coding sequences of four genes, including the melanosome maturation gene Mlana. We did not find fixed coding changes in genes within the CNV, but all genes are misexpressed in regenerating feather bud collar cells of Almond birds. Notably, six other alleles at the St locus are associated with depigmentation phenotypes, and all exhibit expansion of the same CNV. Structural variation at St is linked to diversity in plumage pigmentation and gene expression, and thus provides a potential mode of rapid phenotypic evolution in pigeons.

The genetic changes responsible for different animal color patterns are poorly understood, due in part to a paucity of research organisms that are both genetically tractable and phenotypically diverse. Domestic pigeons (Columba livia) have been artificially selected for many traits, including an enormous variety of color patterns that are variable both within and among different breeds of this single species. We investigated the genetic basis of a sex-linked color pattern in pigeons called Almond that is characterized by a sprinkled pattern of plumage pigmentation. Pigeons with one copy of the Almond allele have desirable color pattern; however, male pigeons with two copies of the Almond mutation have severely depleted pigmentation and congenital eye defects. By comparing the genomes of Almond and non-Almond pigeons, we discovered that Almond pigeons have extra copies of a chromosome region that contains a gene that is critical for the formation of pigment granules. We also found that different numbers of copies of this region are associated with varying degrees of pigment reduction. The Almond phenotype in pigeons bears a remarkable resemblance to Merle coat color mutants in dogs, and our new results from pigeons suggest that similar genetic mechanisms underlie these traits in both species. Our work highlights the role of gene copy number variation as a potential driver of rapid phenotypic evolution.

Cytological and microbiological characteristics of middle ear effusions in brachycephalic dogs

Background

Middle ear effusion is common in brachycephalic dogs with similarities to otitis media with effusion in children. Association with the cranial and eustachian tube morphology and bacterial infection is suspected in both species.

Hypothesis/objectives

To determine cytological and bacteriological features of middle ear effusions in dogs, provide information on histological features, and further assess the dog as a model of the human disease.

Animals

Sixteen live dogs, 3 postmortem cases of middle ear effusion, and 2 postmortem controls.

Methods

Prospective; clinical investigation using computed tomography, magnetic resonance imaging, video‐otoscopy, myringotomy; cytological assessment of 30 and bacteriology of 28 effusions; histology and immunohistochemistry (CD3 for T‐lymphocytes, Pax5 for B lymphocytes and MAC387 for macrophages) of 10 middle ear sections.

Results

Effusions were associated with neurological deficits in 6/16 (38%) and concurrent atopic dermatitis and otitis externa in 9/16 (56%) of live cases. Neutrophils and macrophages predominated on cytology (median 60 [range 2%‐95.5%] and 27 [2%‐96.5%]) whether culture of effusions was positive or not. In histology sections, the mucosa was thickened in affected dogs but submucosal gland dilatation occurred in affected and unaffected dogs. There was no bacterial growth from 22/28 (79%) of effusions. Bacteria isolated from the other 6 (21%) were predominantly Staphylococcus pseudintermedius (4/6, 67%).

Conclusions and Clinical Importance

Clinical, morphological, and cytological findings in middle ear effusions of dogs and people suggest similar pathogeneses. Middle ear effusion of dogs could be a useful model of human otitis media with effusion. Such comparisons can improve understanding and management across species.

Impact of gene therapy for canine monogenic diseases on the progress of preclinical studies

Rapid progress in knowledge of the organization of the dog genome has facilitated the identification of the mutations responsible for numerous monogenic diseases, which usually present a breed-specific distribution. The majority of these diseases have clinical and molecular counterparts in humans. The affected dogs have thus become valuable models for preclinical studies of gene therapy for problems such as eye diseases, immunodeficiency, lysosomal storage diseases, hemophilia, and muscular dystrophy. Successful gene therapies in dogs have significantly contributed to decisions to run clinical trials for several human diseases, such as Leber's congenital amaurosis 2-LCA2 (caused by a mutation of RPE65), X-linked retinitis pigmentosa-XLRP (caused by mutation RPGR), and achromatopsia (caused by mutation of CNGB3). Promising results were also obtained for canine as follows: hemophilia (A and B), mucopolysaccharidoses (MPS I, MPS IIIB, MPS VII), leukocyte adhesion deficiency (CLAD), and muscular dystrophy (a counterpart of human Duchenne dystrophy). Present knowledge on molecular background of canine monogenic diseases and their successful gene therapies prove that dogs have an important contribution to preclinical studies.

Secreted modular calcium-binding proteins in pathophysiological processes and embryonic development

Objective:

Secreted modular calcium-binding proteins (SMOCs) are extracellular glycoproteins of the secreted protein, acidic, and rich in cysteine-related modular calcium-binding protein family and include two isoforms, SMOC1 and SMOC2, in humans. Functionally, SMOCs bind to calcium for various cell functions. In this review, we provided a summary of the most recent advancements in and findings of SMOC1 and SMOC2 in development, homeostasis, and disease states.

Data sources:

All publications in the PubMed database were searched and retrieved (up to July 24, 2019) using various combinations of keywords searching, including SMOC1, SMOC2, and diseases.

Study selection:

All original studies and review articles of SMOCs in human diseases and embryo development written in English were retrieved and included.

Results:

SMOC1 and SMOC2 regulate embryonic development, cell homeostasis, and disease pathophysiology. They play an important role in the regulation of cell cycle progression, cell attachment to the extracellular matrix, tissue fibrosis, calcification, angiogenesis, birth defects, and cancer development.

Conclusions:

SMOC1 and SMOC2 are critical regulators of many cell biological processes and potential therapeutic targets for the control of human cancers and birth defects.

Canine Brachycephaly: Anatomy, Pathology, Genetics and Welfare

Brachycephalic dog breeds have experienced a marked rise in popularity in recent years. While numerous people clearly desire this phenotype in their pets, many of these dogs unfortunately experience several concomitant sequelae, including major problems with respiration and thermoregulation, as well as gastrointestinal, ophthalmological, dermatological, reproductive and even dental problems. This mini review focuses on the anatomical and pathological changes associated with brachycephalic skull shape, including brachycephalic obstructive airway syndrome and other co-existent disorders. It then details the known genetic contributors to brachycephaly, and concludes with a brief discourse on the welfare of these animals.

A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves

The domestic dog serves as an excellent model to investigate the genetic basis of disease. More than 400 heritable traits analogous to human diseases have been described in dogs. To further canine medical genetics research, we established the Dog Biomedical Variant Database Consortium (DBVDC) and present a comprehensive list of functionally annotated genome variants that were identified with whole genome sequencing of 582 dogs from 126 breeds and eight wolves. The genomes used in the study have a minimum coverage of 10× and an average coverage of ~24×. In total, we identified 23 133 692 single-nucleotide variants (SNVs) and 10 048 038 short indels, including 93% undescribed variants. On average, each individual dog genome carried ∼4.1 million single-nucleotide and ~1.4 million short-indel variants with respect to the reference genome assembly. About 2% of the variants were located in coding regions of annotated genes and loci. Variant effect classification showed 247 141 SNVs and 99 562 short indels having moderate or high impact on 11 267 protein-coding genes. On average, each genome contained heterozygous loss-of-function variants in 30 potentially embryonic lethal genes and 97 genes associated with developmental disorders. More than 50 inherited disorders and traits have been unravelled using the DBVDC variant catalogue, enabling genetic testing for breeding and diagnostics. This resource of annotated variants and their corresponding genotype frequencies constitutes a highly useful tool for the identification of potential variants causative for rare inherited disorders in dogs.

Association of a P2RX7 gene missense variant with brachycephalic dog breeds

Missense variants are associated with various phenotypic traits and disorders in dogs. The canine P2RX7 gene, coding the ATP-gated P2X7 receptor ion channel, contains four known missense variants. The current study aimed to examine the presence of these variants in a random sample of pedigree and mixed-pedigree dogs. Exons 3, 8, 11 and 13 of the P2RX7 gene, encoding these four respective variants, in 65 dogs were assessed by Sanger sequencing and combined with existing sequencing data from another 69 dogs. The distribution of these variants was then evaluated in all 134 dogs combined and separately within individual breeds including 35 different pure breeds. The rs23314713 (p.Phe103Leu) and rs23315462 (p.Pro452Ser) variants were present in 47 and 40% of all dogs studied respectively, with the rs23314713 variant associated with brachycephalic breeds. Among pedigree dogs, the rs23314713 and rs23315462 variants were associated with brachycephalic and non-brachycephalic breeds respectively. The rs851148233 (p.Arg270Cys) and rs850760787 (p.Arg365Gln) variants were present only in dogs of Cocker Spaniel and Labrador Retriever pedigrees respectively. No other missense variants were found in exons 3, 8, 11 and 13 of the P2RX7 gene within the dogs. In conclusion, the rs23314713 and rs23315462 missense variants of the P2RX7 gene are present in a large proportion of dogs, with the rs23314713 variant associated with a number of brachycephalic breeds. However, the association of this variant with dogs of bulldog ancestry, not brachycephaly per se, cannot be excluded.

Genome-wide association analysis for lethal brachycephalic-like facial dysmorphia in Labrador Retrievers

A GWAS was performed for inborn X-linked facial dysmorphia with severe growth retardation in Labrador Retrievers. This lethal condition was mapped on the X chromosome at 17-21 Mb and supported by eight SNPs in complete LD. Dams of affected male puppies were heterozygous for the significantly associated SNPs and male affected puppies carried the associated alleles hemizygously. In the near vicinity to the associated region, RPS6KA3 was identified as a candidate gene causing facial dysmorphia in humans and mice known as Coffin-Lowry syndrome. Haplotype analysis showed significant association with the phenotypes of all 18 animals under study. This haplotype was validated through normal male progeny from a dam with the not-associated haplotype on both X chromosomes but male affected full-sibs with the associated haplotype.

True Colors: Commercially-acquired morphological genotypes reveal hidden allele variation among dog breeds, informing both trait ancestry and breed potential

Direct-to-consumer canine genetic testing is becoming increasingly popular among dog owners. The data collected therein provides intriguing insight into the current status of morphological variation present within purebred populations. Mars WISDOM PANELTM data from 11,790 anonymized dogs, representing 212 breeds and 4 wild canine species, were evaluated at genes associated with 7 coat color traits and 5 physical characteristics. Frequencies for all tested alleles at these 12 genes were determined by breed and by phylogenetic grouping. A sub-set of the data, consisting of 30 breeds, was divided into separate same-breed populations based on country of collection, body size, coat variation, or lineages selected for working or conformation traits. Significantly different (p ≤ 0.00167) allele frequencies were observed between populations for at least one of the tested genes in 26 of the 30 breeds. Next, standard breed descriptions from major American and international registries were used to determine colors and tail lengths (e.g. genetic bobtail) accepted within each breed. Alleles capable of producing traits incongruous with breed descriptions were observed in 143 breeds, such that random mating within breeds has probabilities of between 4.9e-7 and 0.25 of creating undesirable phenotypes. Finally, the presence of rare alleles within breeds, such as those for the recessive black coloration and natural bobtail, was combined with previously published identity-by-decent haplotype sharing levels to propose pathways by which the alleles may have spread throughout dog breeds. Taken together, this work demonstrates that: 1) the occurrence of low frequency alleles within breeds can reveal the influence of regional or functional selection practices; 2) it is possible to visualize the potential historic connections between breeds that share rare alleles; and 3) the necessity of addressing conflicting ideals in breed descriptions relative to actual genetic potential is crucial.