Genetic mapping of principal components of canine pelvic morphology

The Role of Femoral Head Size and Femoral Head Coverage in Dogs with and without Hip Dysplasia

The subject of hip dysplasia in dogs is still current and preoccupies both animal owners and veterinarians. Major factors affecting the development of the disorder are hip laxity and incongruent joints. Many studies on etiology, pathogenesis, and early diagnosis have been performed to reduce prevalence and select healthy dogs for breeding. The purpose of the present study was to investigate a possible relationship between dysplasia and femoral head area (FHA), femoral coverage by the acetabulum (CFH) and cranio-caudal distance of the dorsal acetabular rim (CrCdAR). Radiographs of a total of 264 skeletally mature dogs with similar physical characteristics (German wirehaired pointers (GWP), German shepherd dogs (GSD) and Labrador retrievers (LAB)) presented for routine hip dysplasia screening were recruited for the study. FHA, CFH and CrCdAR were measured and related to dysplasia status. Evaluations of FHA (p = 0.011), CFH (p < 0.001) and CrCdAR length (p = 0.003) measurements revealed significant interactions between breed, sex and FCI scores, so they had to be assessed separately. The results revealed that FHA tends to decrease as the hip dysplasia score worsens. There was no significant relationship between FHA and dysplasia assessment. FHA is breed-specific and is larger in normal and near-normal male (p = 0.001, p = 0.020) and female (p = 0.001, p = 0.013) GWP compared to GSD, respectively. FHA is greater in normal male GWP (p = 0.011) and GSD (p = 0.040) compared to females. There was a significant and strong positive correlation between FHA and CrCdAR in all breeds and sexes. Additionally, FCI scoring had a medium (GWP, GSD) to strong (LAB) negative correlation with CFH.

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

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

The effect of inbreeding, body size and morphology on health in dog breeds

Background

Dog breeds are known for their distinctive body shape, size, coat color, head type and behaviors, features that are relatively similar across members of a breed. Unfortunately, dog breeds are also characterized by distinct predispositions to disease. We explored the relationships between inbreeding, morphology and health using genotype based inbreeding estimates, body weight and insurance data for morbidity.

Results

The average inbreeding based on genotype across 227 breeds was F_adj = 0.249 (95% CI 0.235–0.263). There were significant differences in morbidity between breeds with low and high inbreeding (H = 16.49, P = 0.0004). There was also a significant difference in morbidity between brachycephalic breeds and non-brachycephalic breeds (P = 0.0048) and between functionally distinct groups of breeds (H = 14.95 P < 0.0001). Morbidity was modeled using robust regression analysis and both body weight (P < 0.0001) and inbreeding (P = 0.013) were significant (r² = 0.77). Smaller less inbred breeds were healthier than larger more inbred breeds.

Conclusions

In this study, body size and inbreeding along with deleterious morphologies contributed to increases in necessary health care in dogs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40575-021-00111-4.

Evolution of Lactase Persistence: Turbo-Charging Adaptation in Growth Under the Selective Pressure of Maternal Mortality?

The emergence of the capacity to digest milk in some populations represents a landmark in human evolution, linking genetic change with a component of niche construction, namely dairying. Alleles promoting continued activity of the enzyme lactase through the life-course (lactase persistence) evolved in several global regions within the last 7,000 years. In some European regions, these alleles underwent rapid selection and must have profoundly affected fertility or mortality. Elsewhere, alleles spread more locally. However, the functional benefits underlying the rapid spread of lactase persistence remain unclear. Here, we set out the hypothesis that lactase persistence promoted skeletal growth, thereby offering a generic rapid solution to childbirth complications arising from exposure to ecological change, or to new environments through migration. Since reduced maternal growth and greater neonatal size both increase the risk of obstructed labour, any ecological exposure impacting these traits may increase maternal mortality risk. Over many generations, maternal skeletal dimensions could adapt to new ecological conditions through genetic change. However, this adaptive strategy would fail if ecological change was rapid, including through migration into new niches. We propose that the combination of consuming milk and lactase persistence could have reduced maternal mortality by promoting growth of the pelvis after weaning, while high calcium intake would reduce risk of pelvic deformities. Our conceptual framework provides locally relevant hypotheses to explain selection for lactase persistence in different global regions. For any given diet and individual genotype, the combination of lactase persistence and milk consumption would divert more energy to skeletal growth, either increasing pelvic dimensions or buffering them from worsening ecological conditions. The emergence of lactase persistence among dairying populations could have helped early European farmers adapt rapidly to northern latitudes, East African pastoralists adapt to sudden climate shifts to drier environments, and Near Eastern populations counteract secular declines in height associated with early agriculture. In each case, we assume that lactase persistence accelerated the timescale over which maternal skeletal dimensions could change, thus promoting both maternal and offspring survival. Where lactase persistence did not emerge, birth weight was constrained at lower levels, and this contributes to contemporary variability in diabetes risk.

The slope of the pelvis is variable in dogs but does not show correlation with femoral subluxation

The aim of this study was to investigate the variability of the slope of the pelvis in different dog breeds and the correlation between pelvic slope and femoral subluxation. The sacrum-pelvis angle (SPA), the angulation between the sacrum and the axis of the ilium was created to represent the differences in the slope of the pelvis on lateral pelvic radiographs. The Norberg angle (NA) was used to quantify the femoral subluxation on hip-extended radiographs. Archived standard ventrodorsal hip radiographs and lateral lumbosacral radiographs of the same dogs were retrieved and a single observer measured the SPA and the NA in each case. A total of 180 dogs from six different breeds were sampled. The SPA varied between 40° and 71.5° and the NA between 71.2° and 113.9°. The findings indicated that there are significant individual and interbreed variations in the slope of the pelvis. However, no significant relationship between the slope of the pelvis and femoral subluxation could be identified.

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.

Genetic mapping of distal femoral, stifle, and tibial radiographic morphology in dogs with cranial cruciate ligament disease

Cranial cruciate ligament disease (CCLD) is a complex trait. Ten measurements were made on orthogonal distal pelvic limb radiographs of 161 pure and mixed breed dogs with, and 55 without, cranial cruciate partial or complete ligament rupture. Dogs with CCLD had significantly smaller infrapatellar fat pad width, higher average tibial plateau angle, and were heavier than control dogs. The first PC weightings captured the overall size of the dog’s stifle and PC2 weightings reflected an increasing tibial plateau angle coupled with a smaller fat pad width. Of these dogs, 175 were genotyped, and 144,509 polymorphisms were used in a genome-wide association study with both a mixed linear and a multi-locus model. For both models, significant (p_genome <3.46×10⁻⁷ for the mixed and< 6.9x10^-8 for the multilocus model) associations were found for PC1, tibial diaphyseal length and width, fat pad base length, and femoral and tibial condyle width at LCORL, a known body size-regulating locus. Other body size loci with significant associations were growth hormone 1 (GH1), which was associated with the length of the fat pad base and the width of the tibial diaphysis, and a region on CFAX near IRS4 and ACSL4 in the multilocus model. The tibial plateau angle was associated significantly with a locus on CFA10 in the linear mixed model with nearest candidate genes BET1 and MYH9 and on CFA08 near candidate genes WDHD1 and GCH1. MYH9 has a major role in osteoclastogenesis. Our study indicated that tibial plateau slope is associated with CCLD and a compressed infrapatellar fat pad, a surrogate for stifle osteoarthritis. Because of the association between tibial plateau slope and CCLD, and pending independent validation, these candidate genes for tibial plateau slope may be tested in breeds susceptible to CCLD before they develop disease or are bred.