Rory J. Todhunter

Complex population structure in African village dogs and its implications for inferring dog domestication history

High genetic diversity of East Asian village dogs has recently been used to argue for an East Asian origin of the domestic dog. However, global village dog genetic diversity and the extent to which semiferal village dogs represent distinct, indigenous populations instead of admixtures of various dog breeds has not been quantified. Understanding these issues is critical to properly reconstructing the timing, number, and locations of dog domestication. To address these questions, we sampled 318 village dogs from 7 regions in Egypt, Uganda, and Namibia, measuring genetic diversity >680 bp of the mitochondrial D-loop, 300 SNPs, and 89 microsatellite markers. We also analyzed breed dogs, including putatively African breeds (Afghan hounds, Basenjis, Pharaoh hounds, Rhodesian ridgebacks, and Salukis), Puerto Rican street dogs, and mixed breed dogs from the United States. Village dogs from most African regions appear genetically distinct from non-native breed and mixed-breed dogs, although some individuals cluster genetically with Puerto Rican dogs or United States breed mixes instead of with neighboring village dogs. Thus, African village dogs are a mosaic of indigenous dogs descended from early migrants to Africa, and non-native, breed-admixed individuals. Among putatively African breeds, Pharaoh hounds, and Rhodesian ridgebacks clustered with non-native rather than indigenous African dogs, suggesting they have predominantly non-African origins. Surprisingly, we find similar mtDNA haplotype diversity in African and East Asian village dogs, potentially calling into question the hypothesis of an East Asian origin for dog domestication.

Simulation Appraisal of the Adequacy of Number of Background Markers for Relationship Estimation in Association Mapping

Complex trait dissection through association mapping provides a powerful complement to traditional linkage analysis. The genetic structure of an association mapping panel can be estimated by genomewide background markers and subsequently accounted for in association analysis. Deciding the number of background markers is a common issue that needs to be addressed in many association mapping studies. We first showed that the adequacy of markers in relationship estimation influences the maximum likelihood of the model explaining phenotypic variation and demonstrated this influence with a series of computer simulations with different trait architectures. Analyses and computer simulations were then conducted using two different data sets: one from a diverse set of maize (Zea mays L.) inbred lines with a complex population structure and familial relatedness, and the other from a group of crossbred dogs. Our results showed that the likelihood‐based model‐fitting approach can be used to quantify the robustness of genetic relationships derived from molecular marker data. We also found that kinship estimation was more sensitive to the number of markers used than population structure estimation in terms of model fitting, and a robust estimate of kinship for association mapping with diverse germplasm requires a certain amount of background markers (e.g., 300–600 biallelic markers for the simulated pedigree materials, >1000 single nucleotide polymorphisms or 100 simple sequence repeats [SSRs] for the diverse maize panel, and about 100 SSRs for the canine panel). Kinship construction with subsets of the whole marker panel and subsequent model testing with multiple phenotypic traits could provide ad hoc information on whether the number of markers is sufficient to quantify genetic relationships among individuals.

Genetic structure in village dogs reveals a Central Asian domestication origin

Significance Dogs were the first domesticated species, but the precise timing and location of domestication are hotly debated. Using genomic data from 5,392 dogs, including a global set of 549 village dogs, we find strong evidence that dogs were domesticated in Central Asia, perhaps near present-day Nepal and Mongolia. Dogs in nearby regions (e.g., East Asia, India, and Southwest Asia) contain high levels of genetic diversity due to their proximity to Central Asia and large population sizes. Indigenous dog populations in the Neotropics and South Pacific have been largely replaced by European dogs, whereas those in Africa show varying degrees of European vs. indigenous African ancestry. Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations—including those of Vietnam, India, and Egypt—show minimal evidence of European admixture. These populations exhibit a clear gradient of short-range linkage disequilibrium consistent with a Central Asian domestication origin.

Quantitative trait loci for hip dysplasia in a crossbreed canine pedigree

Canine hip dysplasia is a common developmental inherited trait characterized by hip laxity, subluxation or incongruity of the femoral head and acetabulum in affected hips. The inheritance pattern is complex and the mutations contributing to trait expression are unknown. In the study reported here, 240 microsatellite markers distributed in 38 autosomes and the X chromosome were genotyped on 152 dogs from three generations of a crossbred pedigree based on trait-free Greyhound and dysplastic Labrador Retriever founders. Interval mapping was undertaken to map the QTL underlying the quantitative dysplastic traits of maximum passive hip laxity (the distraction index), the dorsolateral subluxation score, and the Norberg angle. Permutation testing was used to derive the chromosome-wide level of significance at p < 0.05 for each QTL. Chromosomes 4, 9, 10, 11 (p < 0.01), 16, 20, 22, 25, 29 (p < 0.01), 30, 35, and 37 harbor putative QTL for one or more traits. Successful detection of QTL was due to the crossbreed pedigree, multiple-trait measurements, control of environmental background, and marked advancement in canine mapping tools.

Corticosteroids alter the differentiated phenotype of articular chondrocytes

Experimental evidence suggests that recommended dosages of some corticosteroids used clinically as antiinflammatory agents for treating arthropathies damage articular cartilage, but low dosages may be chondroprotective. The purpose of this study was to evaluate how different concentrations of methylprednisolone affect chondrocyte function and viability. Articular cartilage and chondrocytes were obtained from young adult horses, 1.5–3.5 years of age. Corticosteroid‐induced changes in collagen expression were studied at the transcriptional level by Northern blot analyses and at the translational level by measuring [3H]‐proline incorporation into [3H]‐hydroxyproline. Fibronectin mRNA splicing patterns were evaluated with ribonuclease protection assays. Cytotoxicity was studied using erythrosin B dye exclusion. Steady‐state levels of type II procollagen mRNA decreased without concurrent changes in type I procollagen expression as the medium methylprednisolone concentrations were increased from 1 × 101 to 1 × 108 pg/ml, dropping below 10% of control values by 1 × 105 pg/ml. Cytotoxicity occurred as methylprednisolone levels were increased further from 1 × 108 to 1 × 109 pg/ml. Changes in total collagen (protein) synthesis were less pronounced, but also demonstrated significant suppression between 1 × 104 and 1 × 108 pg/ml. Corticosteroid‐induced changes in fibronectin isoform levels were evaluated in articular cartilage samples without in vitro culture. The cartilage‐specific (V + C)− isoform was suppressed in both normal and inflamed joints by a single intraarticular injection (0.1 mg/kg) of methylprednisolone. Combined, these data indicate that methylprednisolone suppresses matrix protein markers of chondrocytic differentiation. Decreased and altered chondrocyte expression of matrix proteins likely contributes to the pathogenesis of corticosteroid‐induced cartilage degeneration.

Linkage and Segregation Analysis of Black and Brindle Coat Color in Domestic Dogs

Mutations of pigment type switching have provided basic insight into melanocortin physiology and evolutionary adaptation. In all vertebrates that have been studied to date, two key genes, Agouti and Melanocortin 1 receptor (Mc1r), encode a ligand-receptor system that controls the switch between synthesis of red–yellow pheomelanin vs. black–brown eumelanin. However, in domestic dogs, historical studies based on pedigree and segregation analysis have suggested that the pigment type-switching system is more complicated and fundamentally different from other mammals. Using a genomewide linkage scan on a Labrador × greyhound cross segregating for black, yellow, and brindle coat colors, we demonstrate that pigment type switching is controlled by an additional gene, the K locus. Our results reveal three alleles with a dominance order of black (KB) > brindle (kbr) > yellow (ky), whose genetic map position on dog chromosome 16 is distinct from the predicted location of other pigmentation genes. Interaction studies reveal that Mc1r is epistatic to variation at Agouti or K and that the epistatic relationship between Agouti and K depends on the alleles being tested. These findings suggest a molecular model for a new component of the melanocortin signaling pathway and reveal how coat-color patterns and pigmentary diversity have been shaped by recent selection.

Complex disease and phenotype mapping in the domestic dog

The domestic dog is becoming an increasingly valuable model species in medical genetics, showing particular promise to advance our understanding of cancer and orthopaedic disease. Here we undertake the largest canine genome-wide association study to date, with a panel of over 4,200 dogs genotyped at 180,000 markers, to accelerate mapping efforts. For complex diseases, we identify loci significantly associated with hip dysplasia, elbow dysplasia, idiopathic epilepsy, lymphoma, mast cell tumour and granulomatous colitis; for morphological traits, we report three novel quantitative trait loci that influence body size and one that influences fur length and shedding. Using simulation studies, we show that modestly larger sample sizes and denser marker sets will be sufficient to identify most moderate- to large-effect complex disease loci. This proposed design will enable efficient mapping of canine complex diseases, most of which have human homologues, using far fewer samples than required in human studies.

Long-term functional outcome of tibial plateau leveling osteotomy versus extracapsular repair in a heterogeneous population of dogs.

OBJECTIVE To compare the long-term outcome of tibial plateau leveling osteotomy (TPLO) and extracapsular repair (ECR) for treatment of a ruptured cranial cruciate ligament (RCCL). STUDY DESIGN Prospective clinical trial. ANIMALS Normal adult dogs (control, n = 79); dogs with unilateral CCL disease (n = 38). METHODS Dogs had TPLO (n = 15) or ECR (n = 23) for treatment of RCCL. Force plate gait analysis was performed for the control group at one time point and for treatment groups at serial points: preoperatively, 2 weeks, 8 weeks, 6 and 12 months postoperatively. Symmetry indices (SIs) were calculated between operated and unoperated pelvic limb for ground reaction forces (GRFs), including peak vertical force (PVF), contact time (CT), and vertical impulse (VI). GRFs of the treatment groups and control group were compared using a general linear model and Kaplan-Meier survival analysis. RESULTS At 8 weeks, for PVF and VI, the TPLO group had more symmetric limb loading than the ECR group at the walk and trot. SIs of the TPLO group were not different from the control group by 6 months to 1 year postoperatively. SIs for the ECR group were less symmetrical than the control group at all time periods. Using survival analysis, median time to normal function was no different at the walk between groups, but was shorter for the TPLO group for VI and PVF. CONCLUSIONS Dogs achieved normal limb loading faster after TPLO than ECR. TPLO resulted in operated limb function that was indistinguishable from the control population by 1 year postoperatively.

Estimation of heritabilities, genetic correlations, and breeding values of four traits that collectively define hip dysplasia in dogs

OBJECTIVE-To estimate heritabilities and genetic correlations among 4 traits of hip joints (distraction index [DI], dorsolateral subluxation [DLS] score, Norberg angle [NA], and extended-hip joint radiograph [EHR] score) and to derive the breeding values for these traits in dogs. ANIMALS-2,716 dogs of 17 breeds (1,551 dogs in which at least 1 hip joint trait was measured). PROCEDURES-The NA was measured, and an EHR score was assigned. Hip joint radiographs were obtained from some dogs to allow calculation of the DI and DLS score. Heritabilities, genetic correlations, and breeding values among the DI, DLS score, NA, and EHR score were calculated by use of a set of multiple-trait, derivative-free, restricted maximum likelihood computer programs. RESULTS-Among 2,716 dogs, 1,411 (52%) had an estimated inbreeding coefficient of 0%; the remaining dogs had a mean inbreeding coefficient of 6.21%. Estimated heritabilities were 0.61, 0.54, 0.73, and 0.76 for the DI, DLS score, NA, and EHR score, respectively. The EHR score was highly genetically correlated with the NA (r = -0.89) and was moderately genetically correlated with the DI (r = 0.69) and DLS score (r = -0.70). The NA was moderately genetically correlated with the DI (r = -0.69) and DLS score (r = 0.58). Genetic correlation between the DI and DLS score was high (r = -0.91). CONCLUSIONS AND CLINICAL RELEVANCE-Establishment of a selection index that makes use of breeding values jointly estimated from the DI, DLS score, NA, and EHR score should enhance breeding programs to reduce the incidence of hip dysplasia in dogs.

Retrospective analysis for genetic improvement of hip joints of cohort labrador retrievers in the United States: 1970-2007.

Background Canine Hip Dysplasia (CHD) is a common inherited disease that affects dog wellbeing and causes a heavy financial and emotional burden to dog owners and breeders due to secondary hip osteoarthritis. The Orthopedic Foundation for Animals (OFA) initiated a program in the 1960s to radiograph hip and elbow joints and release the OFA scores to the public for breeding dogs against CHD. Over last four decades, more than one million radiographic scores have been released. Methodology/Principal Findings The pedigrees in the OFA database consisted of 258,851 Labrador retrievers, the major breed scored by the OFA (25% of total records). Of these, 154,352 dogs had an OFA hip score reported between 1970 and 2007. The rest of the dogs (104,499) were the ancestors of the 154,352 dogs to link the pedigree relationships. The OFA hip score is based on a 7-point scale with the best ranked as 1 (excellent) and the worst hip dysplasia as 7. A mixed linear model was used to estimate the effects of age, sex, and test year period and to predict the breeding value for each dog. Additive genetic and residual variances were estimated using the average information restricted maximum likelihood procedure. The analysis also provided an inbreeding coefficient for each dog. The hip scores averaged 1.93 (±SD = 0.59) and the heritability was 0.21. A steady genetic improvement has accrued over the four decades. The breeding values decreased (improved) linearly. By the end of 2005, the total genetic improvement was 0.1 units, which is equivalent to 17% of the total phenotypic standard deviation. Conclusion/Significance A steady genetic improvement has been achieved through the selection based on the raw phenotype released by the OFA. As the heritability of the hip score was on the low end (0.21) of reported ranges, we propose that selection based on breeding values will result in more rapid genetic improvement than breeding based on phenotypic selection alone.