Variants in FtsJ RNA 2'-O-Methyltransferase 3 and Growth Hormone 1 are associated with small body size and a dental anomaly in dogs

Genomic analyses identify 15 susceptibility loci and reveal HDAC2, SOX2-OT, and IGF2BP2 in a naturally-occurring canine model of gastric cancer

Gastric cancer (GC) is the fifth most common human cancer worldwide, but the genetic etiology is largely unknown. We performed a Bayesian genome-wide association study and selection analyses in a naturally-occurring canine model of GC, the Belgian Tervuren and Sheepdog breeds, to elucidate underlying genetic risk factors. We identified 15 loci with over 90% predictive accuracy for the GC phenotype. Variant filtering revealed germline putative regulatory variants for the EPAS1 (HIF2A) and PTEN genes and a coding variant in CD101. Although closely related to Tervuren and Sheepdogs, Belgian Malinois rarely develop GC. Across-breed analyses uncovered protective haplotypes under selection in Malinois at SOX2-OT and IGF2BP2. Among Tervuren and Sheepdogs, HDAC2 putative regulatory variants were present at comparatively high frequency and were associated with GC. Here, we describe a complex genetic architecture governing GC in a dog model, including genes such as PDZRN3, that have not been associated with human GC.

Unravelling novel and pleiotropic genes for cannon bone circumference and bone mineral density in Yorkshire pigs

Leg weakness is a prevalent health condition in pig farms. The augmentation of cannon bone circumference and bone mineral density can effectively improve limb strength in pigs and alleviate leg weakness. This study measured forelimb cannon bone circumference (fCBC) and rear limb cannon bone circumference (rCBC) using an inelastic tapeline and rear limb metatarsal area bone mineral density (raBMD) using a dual-energy X-ray absorptiometry bone density scanner. The samples of Yorkshire castrated boars were genotyped using a 50K single-nucleotide polymorphism (SNP) array. The SNP-chip data were imputed to the level of whole-genome sequencing data (iWGS). This study used iWGS data to perform genome-wide association studies and identified novel significant SNPs associated with fCBC on SSC6, SSC12, and SSC13, rCBC on SSC12 and SSC14, and raBMD on SSC7. Based on the high phenotypic and genetic correlations between CBC and raBMD, multi-trait meta-analysis was performed to identify pleiotropic SNPs. A significant potential pleiotropic quantitative trait locus (QTL) regulating both CBC and raBMD was identified on SSC15. Bayes fine mapping was used to establish the confidence intervals for these novel QTLs with the most refined confidence interval narrowed down to 56 kb (15.11 to 15.17 Mb on SSC12 for fCBC). Furthermore, the confidence interval for the potential pleiotropic QTL on SSC15 in the meta-analysis was narrowed down to 7.45 kb (137.55 to137.56 Mb on SSC15). Based on the biological functions of genes, the following genes were identified as novel regulatory candidates for different phenotypes: DDX42, MYSM1, FTSJ3, and MECOM for fCBC; SMURF2, and STC1 for rCBC; RGMA for raBMD. Additionally, RAMP1, which was determined to be located 23.68 kb upstream of the confidence interval of the QTL on SSC15 in the meta-analysis, was identified as a potential pleiotropic candidate gene regulating both CBC and raBMD. These findings offered valuable insights for identifying pathogenic genes and elucidating the genetic mechanisms underlying CBC and BMD.

GWAS using low-pass whole genome sequence reveals a novel locus in canine congenital idiopathic megaesophagus

Congenital idiopathic megaesophagus (CIM) is a gastrointestinal disorder of dogs wherein the esophagus is dilated and swallowing activity is reduced, causing regurgitation of ingesta. Affected individuals experience weight loss and malnourishment and are at risk for aspiration pneumonia, intussusception, and euthanasia. Great Danes have among the highest incidences of CIM across dog breeds, suggesting a genetic predisposition. We generated low-pass sequencing data for 83 Great Danes and used variant calls to impute missing whole genome single-nucleotide variants (SNVs) for each individual based on haplotypes phased from 624 high-coverage dog genomes, including 21 Great Danes. We validated the utility of our imputed data set for genome-wide association studies (GWASs) by mapping loci known to underlie coat phenotypes with simple and complex inheritance patterns. We conducted a GWAS for CIM with 2,010,300 SNVs, identifying a novel locus on canine chromosome 1 (P-val = 2.76 × 10-10). Associated SNVs are intergenic or intronic and are found in two clusters across a 1.7-Mb region. Inspection of coding regions in high-coverage genomes from affected Great Danes did not reveal candidate causal variants, suggesting that regulatory variants underlie CIM. Further studies are necessary to assess the role of these non-coding variants.

Prevalence of Dental and Skeletal Malocclusions in Mesaticephalic and Dolichocephalic Dogs—a Retrospective Study (2015–2018)

Medical records of dogs with dolico- or mesaticephalic conformation who were presented to a private veterinary referral dental practice with malocclusion of the deciduous or permanent dentition were retrospectively reviewed from a 3-year period (2015–2018). Records were evaluated to determine the type(s) of malocclusions and 198 dogs were evaluated with permanent malocclusions. Of the dogs with deciduous malocclusions, 45 (60%) had variations of a MAL1, 28 (38%) had a MAL2, 13 (17.6%) had a MAL3, and four (5.4%) had a MAL4, with 19 (26%) having more than one type of malocclusion. Poodles, Labrador Retrievers, and Cavalier King Charles Spaniels consisted of 37 (50%) of the dogs with deciduous malocclusions. Fifty-five (74%) dogs proceeded with interceptive orthodontics. Of the dogs with permanent malocclusions, 128 (65%) had a variant of a MAL1, 60 (30%) had a MAL2, 75 (38%) had a MAL3, and 11 (5.6%) had a MAL4, with a MAL1 occurring concurrently with 49 (82%) MAL2 cases. The most common type of MAL1 was linguoversion of one or both mandibular canine teeth in 92 (72%) dogs. The five most commonly affected breeds with permanent malocclusions were Poodles, Labrador Retrievers, Chihuahuas, Pit Bull Terriers, and Cavalier King Charles Spaniels. Overall, 39 (18%) dogs presented with malocclusions observed in this study were associated with the Poodle breed and 20 (9%) dogs were associated with the Labrador Retriever breed. This trend among Poodle mixes and Labrador Retrievers supports a familial pattern to malocclusions.