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The Korean Sapsaree dog is a native breed known for its distinctive appearance and historical significance in Korean culture. The accurate estimation of breeding values is essential for the genetic improvement and conservation of such indigenous breeds. This study aimed to evaluate the accuracy of breeding values for body height, body length, chest width, hair length, and distraction index (DI) traits in Korean Sapsaree dogs. Additionally, a genome-wide association study (GWAS) was conducted to identify the genomic regions and nearby candidate genes influencing these traits. Phenotypic data were collected from 378 Korean Sapsaree dogs, and of these, 234 individuals were genotyped using the 170k Illumina CanineHD BeadChip. The accuracy of genomic predictions was evaluated using the traditional BLUP method with phenotypes only on genotyped animals (PBLUP-G), another traditional BLUP method using a pedigree-based relationship matrix (PBLUP) for all individuals, a GBLUP method based on a genomic relationship matrix, and a single-step GBLUP (ssGBLUP) method. Heritability estimates for body height, body length, chest width, hair length, and DI were 0.45, 0.39, 0.32, 0.55, and 0.50, respectively. Accuracy values varied across methods, with ranges of 0.22 to 0.31 for PBLUP-G, 0.30 to 0.57 for PBLUP, 0.31 to 0.54 for GBLUP, and 0.39 to 0.67 for ssGBLUP. Through GWAS, 194 genome-wide significant SNPs associated with studied Sapsaree traits were identified. The selection of the most promising candidate genes was based on gene ontology (GO) terms and functions previously identified to influence traits. Notable genes included CCKAR and DCAF16 for body height, PDZRN3 and CNTN1 for body length, TRIM63, KDELR2, and SUPT3H for chest width, RSPO2, EIF3E, PKHD1L1, TRPS1, and EXT1 for hair length, and DDHD1, BMP4, SEMA3C, and FOXP1 for the DI. These findings suggest that significant QTL, combined with functional candidate genes, can be leveraged to improve the genetic quality of the Sapsaree population. This study provides a foundation for more effective breeding strategies aimed at preserving and enhancing the unique traits of this Korean dog breed., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Haque et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: DNA methylation is a covalent bond modification that is observed mainly at cytosine bases in the context of CG pairs. DNA methylation patterns reflect the status of individual tissues, such as cell composition, age, and the local environment, in mammals. Genetic factors also impact DNA methylation, and the genetic diversity among various dog breeds provides a valuable platform for exploring this topic. Compared to those in the human genome, studies on the profiling of methylation in the dog genome have been less comprehensive., Results: Our study provides extensive profiling of DNA methylation in the whole blood of three dog breeds using whole-genome bisulfite sequencing. The difference in DNA methylation between breeds was moderate after removing CpGs overlapping with potential genetic variation. However, variance in methylation between individuals was common and often occurred in promoters and CpG islands (CGIs). Moreover, we adopted contextual awareness methodology to characterize DNA primary sequences using natural language processing (NLP). This method could be used to effectively separate unmethylated CGIs from highly methylated CGIs in the sequences that are identified by the conventional criteria., Conclusions: This study presents a comprehensive DNA methylation landscape in the dog blood. Our observations reveal the similar methylation patterns across dog breeds, while CGI regions showed high variations in DNA methylation level between individuals. Our study also highlights the potential of NLP approach for analyzing low-complexity DNA sequences, such as CGIs., Competing Interests: Declarations Ethics approval and consent to participate Ethical approval to conduct this study was approval by Laboratory Animal Experimentation Committee of the Graduate School of Veterinary Medicine, Hokkaido University (Approval number: 2022-012) and by The Ethics Screening Committees of Anicom Speciality Medical Institute, Inc. (Approval number: 2022-02). Consent for publication Not applicable. Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Objectives: As the public's interest in companion dogs grows, health issues in these animals are also emerging, necessitating the optimization of whole exome sequencing (WES) as a valuable method for disease prediction. While WES targeting the human genome is well established, WES targeting the canine genome is understudied, and there is a need to find effective analysis kits., Methods: We compared and analyzed the performance of three WES kits from Twist and Agilent using the canine genome as the target to perform genetic analysis of canine diseases effectively. The levels of total reads, the duplication rate, and variant calling in canine genomic DNA samples from seven healthy dogs (three beagles, one bichon fry, one maltese, one welsh corgi, and one mixed breed) without any interventions were examined through WES via Twist and Agilent kits., Results: We found that while Twist had the lowest total read number, the number of reads in the SSXT series was significantly (P<0.05) greater. Twist showed low evenness and high standard deviation, but the SSXT series showed relatively high evenness. Compared with Twist, the SSXT series from a depth of 30× presented a significantly (P<0.05) greater target ratio. Among the four kits, the significantly lowest duplicate ratio was confirmed for SSXT (O/N) (30% lower than Twist)., Conclusion: The most important performance of the kit, the number of variants detected, was 48,302 for Twist and 130,506 for SSXT (O/N). On the basis of the performance comparison results, SSXT (O/N) was found to have the best performance., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Jang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: While complex dog-human coexistence has been deeply investigated, there is a relative scarcity of similar knowledge regarding dog-dog interactions. Social learning, a fundamental synchronizing mechanism between dogs and humans, was recently found to be influenced by the functional breed selection of dogs: with the cooperative breeds being more effective learners from a human demonstrator than the independent working breeds were. Here, we investigated whether these differences would also be present when dogs had to learn from another dog and how to effectively perform a detour around a transparent V-shaped obstacle. We tested dogs from 28 independent and 19 cooperative breeds in three consecutive trials. In the control groups, all dogs had to detour on their own the obstacle. In the dog demonstration groups, in trial 1, the subjects had to detour on their own, but before the next two trials, a trained dog showed them the solution., Results: We found that the performance of the two breed groups was the same in the without demonstration groups. However, after observing the dog demonstrator, the independent dogs learned the task more successfully than the cooperative breeds did. In the case of the independent working breeds, detour latencies significantly dropped along the consecutive trials, and these dogs also showed higher rate of successful detours after observing the demonstrator dog's action than in the control group., Conclusions: This is the first study where the consequences of functional breed selection were confirmed in a scenario that involved conspecific social learning in dogs. The results fit well to the ecologically valid framework of the evolutionary past of dog breed formation, in which cooperative breeds were selected for their interactivity with humans, whereas independent breeds often had to work together with their conspecifics., (© 2024. The Author(s).)

The dog, Canis lupus familiaris, is an important model for studying human diseases. Unlike many model organisms, the dog genome has a comparatively poor functional annotation, which hampers gene discovery for development, morphology, disease, and behavior. To fill this gap, we established a comprehensive tissue biobank for both the dog and wolf samples. The biobank consists of 5485 samples representing 132 tissues from 13 dogs, 12 dog embryos, and 24 wolves. In a subset of 100 tissues from nine dogs and 12 embryos, we characterized gene expression activity for each promoter, including alternative and novel, i.e., previously not annotated, promoter regions, using the 5' targeting RNA sequencing technology STRT2-seq. We identified over 100,000 promoter region candidates in the recent canine genome assembly, CanFam4, including over 45,000 highly reproducible sites with gene expression and respective tissue enrichment levels. We provide a promoter and gene expression atlas with interactive, open data resources, including a data coordination center and genome browser track hubs. We demonstrated the applicability of Dog Genome Annotation (DoGA) data and resources using multiple examples spanning canine embryonic development, morphology and behavior, and diseases across species., (© 2024. The Author(s).)

Background: The presence of mitochondrial sequences in the nuclear genome (Numts) confounds analyses of mitochondrial sequence variation, and is a potential source of false positives in disease studies. To improve the analysis of mitochondrial variation in canines, we completed a systematic assessment of Numt content across genome assemblies, canine populations and the carnivore lineage., Results: Centering our analysis on the UU&#95;Cfam&#95;GSD&#95;1.0/canFam4/Mischka assembly, a commonly used reference in dog genetic variation studies, we found a total of 321 Numts located throughout the nuclear genome and encompassing the entire sequence of the mitochondria. A comparison with 14 canine genome assemblies identified 63 Numts with presence-absence dimorphism among dogs, wolves, and a coyote. Furthermore, a subset of Numts were maintained across carnivore evolutionary time (arctic fox, polar bear, cat), with eight sequences likely more than 10 million years old, and shared with the domestic cat. On a population level, using structural variant data from the Dog10K Consortium for 1879 dogs and wolves, we identified 11 Numts that are absent in at least one sample, as well as 53 Numts that are absent from the Mischka assembly., Conclusions: We highlight scenarios where the presence of Numts is a potentially confounding factor and provide an annotation of these sequences in canine genome assemblies. This resource will aid the identification and interpretation of polymorphisms in both somatic and germline mitochondrial studies in canines.

The Kazakh Tobet is an indigenous Kazakh dog breed that has been used to guard livestock since ancient times. To understand the genetic structure and phylogenetic relationship of the Kazakh Tobet breed with other herding and livestock guarding dog breeds, we analysed short tandem repeat data of 107 Kazakh Tobet dogs from different regions of Kazakhstan and Mongolia, as well as whole genome sequencing data from two Kazakh Tobet dogs and 43 dogs from 24 working breeds. Our results indicate a high genetic diversity of the Kazakh Tobet, with the average number of alleles per locus ranging from 6.00 to 10.22 and observed heterozygosity ranging from 76 to 78%. The breed has a complex genetic structure characterised by seven different clusters. The neighbour-joining tree constructed based on 14,668,406 autosomal and the maximum likelihood tree based on mitochondrial D-loop sequences indicate a common genetic heritage between the Kazakh Tobet, the Central Asian Shepherd Dog and the Turkish Akbash. The presence of haplotype A18 in the Kazakh Tobets supports the hypothesis of the ancient origin of the breed, which was previously suggested by archaeological finds and written sources. These results provide an important genetic basis for the ongoing efforts to improve the Kazakh Tobet breed, to ensure its preservation as an independent genetic lineage and to recognise a breed on an international level., (© 2024. The Author(s).)

Canines are an important model system for genetics and evolution. Recent advances in sequencing technologies have enabled the creation of large databases of genetic variation in canines, but analyses of allele sharing among canine groups have been limited. We applied GeoVar, an approach originally developed to study the sharing of single nucleotide polymorphisms across human populations, to assess the sharing of genetic variation among groups of wolves, village dogs, and breed dogs. Our analysis shows that wolves differ from each other at an average of approximately 2.3 million sites while dogs from the same breed differ at nearly 1 million sites. We found that 22% of the variants are common across wolves, village dogs, and breed dogs, that ~16% of variable sites are common across breed dogs, and that nearly half of the differences between two dogs of different breeds are due to sites that are common in all clades. These analyses represent a succinct summary of allele sharing across canines and illustrate the effects of canine history on the apportionment of genetic variation.

Recent evidence demonstrates genomic and morphological continuity in the Arctic ancestral lineage of dogs. Here, we use the Siberian Husky to investigate the genomic legacy of the northeast Eurasian Arctic lineage and model the deep population history using genome-wide single nucleotide polymorphisms. Utilizing ancient dog-calibrated molecular clocks, we found that at least two distinct lineages of Arctic dogs existed in ancient Eurasia at the end of the Pleistocene. This pushes back the origin of sled dogs in the northeast Siberian Arctic with humans likely intentionally selecting dogs to perform different functions and keeping breeding populations that overlap in time and space relatively reproductively isolated. In modern Siberian Huskies, we found significant population structure based on how they are used by humans, recent European breed introgression in about half of the dogs that participate in races, moderate levels of inbreeding, and fewer potentially harmful variants in populations under strong selection for form and function (show, sled show, and racing populations of Siberian Huskies). As the struggle to preserve unique evolutionary lineages while maintaining genetic health intensifies across pedigreed dogs, understanding the genomic history to guide policies and best practices for breed management is crucial to sustain these ancient lineages and their unique evolutionary identity., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Similar to that in Europe and the United States, the need for forensic DNA identification in dogs is increasing in Japan. As few studies have used commercial genotyping kits, the effectiveness of the Canine Genotypes TM Panel 2.1 Kit for individual DNA identification in dogs bred in Japan was examined. We genotyped 150 unrelated dogs (50 Golden Retrievers, 50 Miniature Dachshunds, and 50 Shiba Inu) at 18 canine short tandem repeat loci by the Kit. The allele frequency, expected heterozygosity, observed heterozygosity, p-value, power of the discriminant, and of exclusion, polymorphic information content, and random matching probability were calculated for each marker. The random matching probability was subsequently estimated to be 4.394×10 -22 in the 150 dogs of the three pure-bred groups based on 18 STR loci; 3.257 × 10 -16 in the Golden Retriever, 3.933 × 10 -18 in the Miniature Dachshund, and 2.107 × 10 -18 in the Shiba Inu breeds. In addition, principal component analysis based on genotype data revealed the Golden Retrievers, Miniature Dachshunds, and Shiba Inus separated into three clusters. The results of the genotype analysis showed that the Canine Genotypes TM Panel 2.1 Kit could be useful for identity testing and tool of population study of canines in Japan., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Neuronal ceroid lipofuscinosis (NCL) represents a heterogenous group of lysosomal storage diseases resulting in progressive neurodegeneration. We investigated two Small Swiss Hound littermates that showed progressive ataxia and loss of cognitive functions and vision starting around the age of 12 months. Both dogs had to be euthanized a few months after the onset of disease owing to the severity of their clinical signs. Pathological investigation of one affected dog revealed cerebral and cerebellar atrophy with cytoplasmic accumulation of autofluorescent material in degenerating neurons. The clinical signs in combination with the characteristic histopathology led to a tentative diagnosis of NCL. In the subsequent genetic investigation, the genome of one affected dog was sequenced. This revealed a duplication of 18 819 bp within the MFSD8 gene. The duplication breakpoints were located in intron 3 and exon 12 of the gene and were predicted to disrupt the reading frame. Both affected dogs carried the duplication in a homozygous state and there was perfect cosegregation of the genotypes with the phenotype in a large pedigree, consistent with autosomal recessive inheritance. MFSD8 loss-of-function variants are a known cause of NCL7 in human patients, dogs and other mammalian species. The existing knowledge on MFSD8 together with the experimental data strongly suggests that the identified intragenic MFSD8 duplication caused the disease in the Small Swiss Hounds. These results allow their diagnosis to be refined to NCL7 and enable genetic testing in the breed to avoid further unintentional carrier × carrier matings., (© 2024 The Author(s). Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.)

For over 15 years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e., canFam4, UU&#95;Cfam&#95;GSD&#95;1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples and breed relationships revealed by principal component analysis are not affected by the choice of reference genome. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: The ability to learn from humans via observation was considered to be equally present across properly socialized dogs. We showed recently that cooperative working breeds learned from a human demonstrator more effectively. We hypothesized that functional breed selection could affect sensitivity to human attention-eliciting behavior. Accordingly, we ran the first ever study on dogs that compared the effect of ostensive and neutral verbal communication in a social learning scenario. We used the detour paradigm around a transparent V-shaped fence with either ostensive (addressing the receiver both with words and specific, attention-eliciting prosody) or neutral speech (monotonous reciting of a short poem) demonstration. The other features (gestures, movement) of the demonstration sequence were kept identical between the two conditions. We tested (N = 70) companion dogs from 17 cooperative and 16 independent breeds in three 1-min trials. Subjects had to obtain the reward by detouring around the fence., Results: Detour latencies of the cooperative dogs improved after both ostensive and neutral speech demonstrations. The independent dogs did not improve their detour latency in either of the conditions. Remarkably, ostensive verbal utterances elicited longer relative looking time towards the demonstrator, cooperative dogs looked longer at the demonstrator, and longer looking time resulted in more successful detours., Conclusions: Our study provides the first indication that functional breed selection had a significant impact on dogs' sensitivity to ostensive human communication, which, apart from being crucially important for social learning from humans, until now was considered as a uniformly present heritage of domestication in dogs., (© 2024. The Author(s).)

High-throughput genotyping offers great potential to increase our understanding of the genomic basis of canid variation. Braque Français Type Pyrénées (BRA) are smart, agile, and friendly dogs originally developed for tracking, hunting, and retrieving feathered game. On a population of 44 unrelated BRA dogs, single nucleotide polymorphism (SNP) genotype data from the CanineHD Whole-Genome Genotyping BeadChip and evaluation scores for 12 traits related to morphology and hunting performance were available. After quality filtering, 95,859 SNPs on the 38 dog autosomes (CFA) were retained. Phenotypic scores were expressed on a scale from 1 (worst) to 6 (best) and were mostly poorly to moderately correlated except for some morphological traits (e.g. r = 0.81 between the conformation of the head and that of the eye). From GWAS, a total of 378 SNP-phenotype associations with posterior odds of association > 1 have been detected. The strongest associations were found for the eye conformation, for the skull/muzzle ratio, and for connection to the hunter. These included both new and previously identified markers and genes potentially involved with type and behavior traits in BRA. Six of the significant markers mapped within SETDB2, a gene known to be related to pointing behavior in dogs. These results advance our understanding of the genetic basis for morphology and hunting behavior in dogs and identify new variants which are potential targets for further research., Competing Interests: Conflict of interest None of the authors of this paper has a financial or personal relationship with other people or organisations that could inappropriately influence or bias the content of the paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Dog leukocyte antigen (DLA) polymorphisms have been found to be associated with inter-individual variations in the risk, susceptibility, and severity of immune-related phenomena. While DLA class II genes have been extensively studied, less research has been performed on the polymorphisms of DLA class I genes, especially in beagle dogs commonly used as laboratory animals for safety evaluations in drug development. We genotyped four DLA class I genes and four DLA class II genes by locus-specific Sanger sequencing using 93 laboratory beagle dogs derived from two different strains: TOYO and Marshall. The results showed that, for DLA class I genes, 11, 4, 1, and 2 alleles, including a novel allele, were detected in DLA-88, DLA-12/88L, DLA-64, and DLA-79, while, for DLA class II genes, 1, 10, 6, and 7 alleles were detected in DLA-DRA, DLA-DRB1, DLA-DQA1, and DLA-DQB1, respectively. It was estimated that there were 14 DLA haplotypes, six of which had a frequency of ≥ 5%. Furthermore, when comparing the DLA diversity between TOYO and Marshall strains, the most common alleles and haplotypes differed between them. This is the first study to genotype all DLA loci and determine DLA haplotypes including all DLA class I and class II genes in dogs. Integrating information on the DLA diversity of laboratory beagle dogs should reinforce their benefit as an animal model for understanding various diseases associated with a specific DLA type., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Variants in RPGRIP1 and MAP9, termed RPGRIP1ins44 and MAP9del respectively, are both associated with a form of canine progressive retinal atrophy referred to as RPGRIP1-CRD and have both been demonstrated to modify the development and progression of this disease. In the current study both variants were genotyped in at least 50 dogs of 132 diverse breeds and the data reveal that both segregate in multiple breeds. Individually, each variant is common within largely non-overlapping subsets of breed, and there is a negative correlation between their frequencies within breeds that segregate both variants. The frequency of both variants exceeds 0.05 in a single breed only, the Miniature Longhaired Dachshund. These data indicate that both variants are likely to be ancient and predate the development and genetic isolation of modern dog breeds. That both variants are present individually at high frequency in multiple breeds is consistent with the hypothesis that homozygosity of either variant alone is not associated with a clinically relevant phenotype, whereas the negative correlation between the two variants is consistent with the application of selective pressure, from dog breeders, against homozygosity at both loci, probably due to the more severe phenotype associated with homozygosity at both loci., (© 2024 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.)

Neuronal ceroid lipofuscinosis (NCL) is a group of neurodegenerative disorders that occur in humans, dogs, and several other species. NCL is characterised clinically by progressive deterioration of cognitive and motor function, epileptic seizures, and visual impairment. Most forms present early in life and eventually lead to premature death. Typical pathological changes include neuronal accumulation of autofluorescent, periodic acid-Schiff- and Sudan black B-positive lipopigments, as well as marked loss of neurons in the central nervous system. Here, we describe a 19-month-old Schapendoes dog, where clinical signs were indicative of lysosomal storage disease, which was corroborated by pathological findings consistent with NCL. Whole genome sequencing of the affected dog and both parents, followed by variant calling and visual inspection of known NCL genes, identified a missense variant in CLN6 (c.386T>C). The variant is located in a highly conserved region of the gene and predicted to be harmful, which supports a causal relationship. The identification of this novel CLN6 variant enables pre-breeding DNA-testing to prevent future cases of NCL6 in the Schapendoes breed, and presents a potential natural model for NCL6 in humans., (© 2024 The Author(s). Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.)

Recent advances in genomics, coupled with a unique population structure and remarkable levels of variation, have propelled the domestic dog to new levels as a system for understanding fundamental principles in mammalian biology. Central to this advance are more than 350 recognized breeds, each a closed population that has undergone selection for unique features. Genetic variation in the domestic dog is particularly well characterized compared with other domestic mammals, with almost 3000 high-coverage genomes publicly available. Importantly, as the number of sequenced genomes increases, new avenues for analysis are becoming available. Herein, we discuss recent discoveries in canine genomics regarding behavior, morphology, and disease susceptibility. We explore the limitations of current data sets for variant interpretation, tradeoffs between sequencing strategies, and the burgeoning role of long-read genomes for capturing structural variants. In addition, we consider how large-scale collections of whole-genome sequence data drive rare variant discovery and assess the geographic distribution of canine diversity, which identifies Asia as a major source of missing variation. Finally, we review recent comparative genomic analyses that will facilitate annotation of the noncoding genome in dogs., (Published by Cold Spring Harbor Laboratory Press.)

Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago., Competing Interests: Competing interests statement:The authors declare no competing interest.

Background: Brachycephalic obstructive airway syndrome (BOAS), observed in many flat-faced dog breeds, is one of the most urgent welfare problems in pedigree dogs. Various breeding schemes against BOAS have been implemented in many countries during recent years, but their impact on breed health remains unknown. The BOAS breeding test, used by the Finnish Kennel Club (FKC), includes an exercise component with a recovery assessment, BOAS grading by a veterinarian that evaluates upper respiratory signs before and after exercise, and a nostril stenosis assessment. The aim of our study was to evaluate BOAS breeding test results and estimate the heritability of the BOAS grade using parent-offspring regression from FKC data collected during 2017-2022., Results: The majority (80%) of dogs (n = 957) participating in FKC BOAS testing were English Bulldogs, French Bulldogs, and Pugs. In 2022, 89-100% of the litters from these three breeds registered with the FKC had at least one parent tested for BOAS. The proportion of dogs failing the exercise test was highest in English Bulldogs (11%), followed by French Bulldogs (4%) and Pugs (3%). In these three breeds, moderate to severe BOAS signs were reported in 28%, 22% and 30% of dogs, respectively. The proportion of moderate to severe nostril stenosis was highest (71%) in Pugs, followed by French Bulldogs (55%), and English Bulldogs (40%). Estimates of heritability for BOAS grade were separately calculated for these three breeds and for all dogs, and the estimates were moderate to high, ranging from 0.39 to 0.58., Conclusions: The exercise test alone did not sufficiently identify dogs with moderate to severe BOAS signs. To better consider the complex nature of BOAS and breed differences, exercise tolerance, the severity of upper respiratory signs (BOAS grade) and nostril stenosis should all be assessed together in breeding animals. The heritability estimates for veterinary-assessed BOAS grade indicated that BOAS grade could be used in selective breeding to obtain less-affected offspring., (© 2024. The Author(s).)

Previous studies of canid population and evolutionary genetics have relied on high-quality domestic dog reference genomes that have been produced primarily for biomedical and trait mapping studies in dog breeds. However, the absence of highly contiguous genomes from other Canis species like the gray wolf and coyote, that represent additional distinct demographic histories, may bias inferences regarding interspecific genetic diversity and phylogenetic relationships. Here, we present single haplotype de novo genome assemblies for the gray wolf and coyote, generated by applying the trio-binning approach to long sequence reads generated from the genome of a female first-generation hybrid produced from a gray wolf and coyote mating. The assemblies were highly contiguous, with contig N50 sizes of 44.6 and 42.0 Mb for the wolf and coyote, respectively. Genome scaffolding and alignments between the two Canis assemblies and published dog reference genomes showed near complete collinearity, with one exception: a coyote-specific chromosome fission of chromosome 13 and fusion of the proximal portion of that chromosome with chromosome 8, retaining the Canis-typical haploid chromosome number of 2n = 78. We evaluated mapping quality for previous RADseq data from 334 canids and found nearly identical mapping quality and patterns among canid species and regional populations regardless of the genome used for alignment (dog, coyote, or gray wolf). These novel wolf and coyote genome reference assemblies will be important resources for proper and accurate inference of Canis demography, taxonomic evaluation, and conservation genetics., (© The Author(s) 2024. Published by Oxford University Press on behalf of The American Genetic Association. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

RK Wayne has arguably been the most influential geneticist of canids, famously promoting the conservation of wolves in his homeland, the United States. His influence has been felt in other countries and regions outside the contiguous United States, where he inspired others, also including former graduate students and research fellows of his, to use modern molecular techniques to examine the evolutionary biology of canids to inform the conservation and management of wolves. In this review, we focus on the implications of Wayne's work on wolves outside the United States. He envisioned a clear future for wolf conservation research, involving the study of wolves' ecological and genetic diversity, and the description of ecotypes requiring conservation. He also documented widespread hybridization among canids and introgression of DNA from domestic dogs to wolves, a process that started dozens of thousands of years ago. His work therefore calls for innovative studies, such as examining the potential fitness benefits of introgression. Inspired by his results, for example, on the purging of deleterious alleles in small populations, wolf researchers should use novel molecular tools to challenge other conservation genetics paradigms. Overall, RK Wayne's work constitutes a call for answers, which as scientists or citizens concerned with conservation matters, we are obliged to address, as we contribute to monitoring and maintaining biodiversity during our period of dramatic transformations of the biosphere., (© The Author(s) 2024. Published by Oxford University Press on behalf of The American Genetic Association. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

The Edward Novitski Prize recognizes creativity and intellectual ingenuity in the solution of problems in genetics research. The prize honors scientific experimental work-either a single experimental accomplishment or a body of work. Ostrander is recognized for work developing the domestic dog as an experimental system for solving fundamental biological problems and identifying genetic sequences of relevance to human health and disease. Including work on disease and behavioral health, Ostrander has shown a dedication to creative methods for understanding canine genetics and the value of translating research organisms to human genetics., Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest., (Published by Oxford University Press on behalf of The Genetics Society of America 2024.)

The origins and extreme morphological evolution of the modern dog breeds are poorly studied because the founder populations are extinct. Here, we analyse eight 100 to 200 years old dog fur samples obtained from traditional North Swedish clothing, to explore the origin and artificial selection of the modern Nordic Lapphund and Elkhound dog breeds. Population genomic analysis confirmed the Lapphund and Elkhound breeds to originate from the local dog population, and showed a distinct decrease in genetic diversity in agreement with intense breeding. We identified eleven genes under positive selection during the breed development. In particular, the MSRB3 gene, associated with breed-related ear morphology, was selected in all Lapphund and Elkhound breeds, and functional assays showed that a SNP mutation in the 3'UTR region suppresses its expression through miRNA regulation. Our findings demonstrate analysis of near-modern dog artifacts as an effective tool for interpreting the origin and artificial selection of the modern dog breeds., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Recent years have seen a dramatic increase in the number of canine genome assemblies available. Duplications are an important source of evolutionary novelty and are also prone to misassembly. We explored the duplication content of nine canine genome assemblies using both genome self-alignment and read-depth approaches. We find that 8.58% of the genome is duplicated in the canFam4 assembly, derived from the German Shepherd Dog Mischka, including 90.15% of unplaced contigs. Highlighting the continued difficulty in properly assembling duplications, less than half of read-depth and assembly alignment duplications overlap, but the mCanLor1.2 Greenland wolf assembly shows greater concordance. Further study shows the presence of multiple segments that have alignments to four or more duplicate copies. These high-recurrence duplications correspond to gene retrocopies. We identified 3,892 candidate retrocopies from 1,316 parental genes in the canFam4 assembly and find that ∼8.82% of duplicated base pairs involve a retrocopy, confirming this mechanism as a major driver of gene duplication in canines. Similar patterns are found across eight other recent canine genome assemblies, with metrics supporting a greater quality of the PacBio HiFi mCanLor1.2 assembly. Comparison between the wolf and other canine assemblies found that 92% of retrocopy insertions are shared between assemblies. By calculating the number of generations since genome divergence, we estimate that new retrocopy insertions appear, on average, in 1 out of 3,514 births. Our analyses illustrate the impact of retrogene formation on canine genomes and highlight the variable representation of duplicated sequences among recently completed canine assemblies., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Domestic dogs are helpers in outdoor human work and companions for families; thus, individual canine identification and parentage testing are crucial in certain fields, including forensics and breeding programs. In this study, a six-dye fluorescent labeling multiplex amplification system containing 29 canine short tandem repeats (STRs) and the sex-determining marker DAmel was developed. The system was called the Tronfo Canine 30-plex STR Kit and was further validated according to the Scientific Working Group on DNA Analysis Methods and the Organization of Scientific Area Committees for Wildlife Forensics guidelines, including tests for PCR conditions, precision, species specificity, sensitivity, stability, repeatability and reproducibility, a population study, and a study of 16 paternity test cases. The results indicated that the novel canine STR assay was accurate, specific, reproducible, stable, and robust. Complete profiles were obtained with 31.25 pg of canine DNA. Additionally, 500 unrelated canine individuals were investigated using this novel system, and the combined power of discrimination and exclusion values were 0.999999999999999999 and 0.999996451039850, respectively. These results suggest that the Tronfo Canine 30-plex STR Kit is highly polymorphic, informative, and suitable for individual canine identification and parentage testing., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Lhx3 is a LIM-homeodomain transcription factor that affects body size in mammals by regulating the secretion of pituitary hormones. Akita, Shiba Inu, and Mame Shiba Inu dogs are Japanese native dog breeds that have different body sizes. To determine whether Lhx3 plays a role in the differing body sizes of these three dog breeds, we sequenced the Lhx3 gene in the three breeds, which led to the identification of an SNP in codon 280 (S280N) associated with body size. The allele frequency at this SNP differed significantly between the large Akita and the two kinds of smaller Shiba dogs. To validate the function of this SNP on body size, we introduced this change into the Lhx3 gene of mice. Homozygous mutant mice (S279N +/+ ) were found to have significantly increased body lengths and weights compared to heterozygous mutant (S279N +/- ) and wild-type (S279N -/- ) mice several weeks after weaning. These results demonstrate that a nonsynonymous substitution in Lhx3 plays an important role in regulating body size in mammals.

Commercial panels of microsatellite (STR) loci are focused on the use of DNA of the domestic dog (Canis lupus familiaris) and are often inapplicable for genotyping the DNA of the gray wolf (Canis lupus lupus). We propose a CPlex test system, including one hexa- and 12 tetranucleotide autosomal STR loci, as well as two sex loci, that is equally efficient in DNA identification of biological samples of the wolf and the dog. Analysis of molecular variance between samples revealed significant differentiation values (F ST  = 0.0784, p < 0.001), which allows to use the panel to differentiate wolf and dog samples. Population subdivision coefficients (θ-values) were calculated for each of the 13 STR loci of the developed test system. It was shown that the values of the genotype frequency for dogs and wolves, without and with considering the θ-value, differ by three orders of magnitude (for dogs 8.9 × 10 -16 and 2.1 × 10 -14 and for wolves 1.9 × 10 -15 and 4.5 × 10 -14 , respectively). The use of population subdivision coefficients will allow to identify the most reliable results of an expert identification study and the power of exclusion provided by the STR loci of the CPlex test system makes it possible to achieve a reliable level of evidence in forensic DNA analysis of both wolves and dogs. The test system has been validated for use in forensic identification of the dog and wolf based on biological traces found at crime scenes, as well as for individual identification and establishing biological relationship of animals of these species., (© 2024 Stichting International Foundation for Animal Genetics.)

Background: The Bangkaew dog is an indigenous dog breed in the Phitsanulok province of Thailand. This breed is recognized by the Fédération Cynologique Internationale (FCI), a global canine organization. The unique traits of the Bangkaew breed lead to purebred selection for breeding, while only their traits and pedigree from parental history are recorded. Determination of the risk of inbreeding depression and the origin of unknown DNA profiles is essential due to the challenges in predicting puppy characteristics, which are crucial for breed management and conservation., Objective: This study aimed to emphasize that current allelic frequency data for the Bangkaew dog breed must be considered for precise individual identification., Methods: Approximately 82 Bangkaew dogs from various Thai localities were studied using 15 microsatellite markers for genotypic monitoring and individual identification. Maternal genetic inheritance was assessed via mtDNA D-loop analysis., Results: The results revealed high genetic diversity in the Bangkaew breed, indicating low potential for inbreeding. We also found that using a 15 loci microsatellite panel was effective for the identification of Bangkaew dogs. The optimized 10 loci microsatellite genotyping panel developed in this study presents improved identification testing efficiency, promoting both time- and cost-effectiveness., Conclusion: Analysis of microsatellite DNA markers in Bangkaew dogs using an optimized panel of 10 loci selected from 15 loci effectively facilitated individual identification. This approach not only enhances time and cost efficiency, but also provides accurate allelic frequency estimates, which are crucial for the realistic evaluation of DNA evidence., (© 2024. The Author(s) under exclusive licence to The Genetics Society of Korea.)

Ancestral Coast Salish societies in the Pacific Northwest kept long-haired "woolly dogs" that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton," collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.

DNA and traditional knowledge reveal the history of an extinct dog bred for its wool.

Background: Domestication and introduction of dairy animals facilitated the permanent human occupation of the Tibetan Plateau. Yet the history of dairy pastoralism in the Tibetan Plateau remains poorly understood. Little is known how Tibetans adapted to milk and dairy products., Results: We integrated archeological evidence and genetic analysis to show the picture that the dairy ruminants, together with dogs, were introduced from West Eurasia into the Tibetan Plateau since ~ 3600 years ago. The genetic admixture between the exotic and indigenous dogs enriched the candidate lactase persistence (LP) allele 10974A > G of West Eurasian origin in Tibetan dogs. In vitro experiments demonstrate that - 13838G > A functions as a LP allele in Tibetans. Unlike multiple LP alleles presenting selective signatures in West Eurasians and South Asians, the de novo origin of Tibetan-specific LP allele - 13838G > A with low frequency (~ 6-7%) and absence of selection corresponds - 13910C > T in pastoralists across eastern Eurasia steppe., Conclusions: Results depict a novel scenario of genetic and cultural adaptations to diet and expand current understanding of the establishment of dairy pastoralism in the Tibetan Plateau., (© 2023. BioMed Central Ltd., part of Springer Nature.)

We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto's genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto's population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.

This paper is a top-down analysis of the non-protein-coding, canine genome. We demonstrate by use of the y-text-finder method, that the non-protein-coding genome contains lots of hidden y-texts, both short and long, proving that the non-protein-coding genome is the opposite of junk. They are written by means of a y-language of about 28 million y-words separated by stop codons and spelled by nucleotide letters A, C, G, and T. We use the Canis Lupus Familiaris reference genome, Roslin Institute, 2020, from which we select the non-protein-coding part. We show that 70-80 percent of chromosomal y-words are specific for the canine non-protein-coding chromosome, and we show how many y-words any non-protein-coding chromosome shares with any other non-protein-coding chromosome. We demonstrate the peculiar way by which the dog utilizes the nucleotide word-length of y-words to build up its y-language, moreover in a way it shares with the human non-protein-coding genome. In a large table we demonstrate how 18,398 Zipf-qualified y-texts/narratives are distributed over the 40 non-protein-coding chromosomes. 3,812 of these texts/narratives are alpha-qualified and similar in form to human novels. In the last table we compare selected, corresponding characteristics of the human and the canine non-protein-coding genome.

Selective breeding of domestic dogs has generated diverse breeds often optimized for performing specialized tasks. Despite the heritability of breed-typical behavioral traits, identification of causal loci has proven challenging due to the complexity of canine population structure. We overcome longstanding difficulties in identifying genetic drivers of canine behavior by developing a framework for understanding relationships between breeds and the behaviors that define them, utilizing genetic data for over 4,000 domestic, semi-feral, and wild canids and behavioral survey data for over 46,000 dogs. We identify ten major canine genetic lineages and their behavioral correlates and show that breed diversification is predominantly driven by non-coding regulatory variation. We determine that lineage-associated genes converge in neurodevelopmental co-expression networks, identifying a sheepdog-associated enrichment for interrelated axon guidance functions. This work presents a scaffold for canine diversification that positions the domestic dog as an unparalleled system for revealing the genetic origins of behavioral diversity., Competing Interests: Declaration of interests The authors declare no competing interests., (Published by Elsevier Inc.)

Canine atopic dermatitis is an inflammatory skin disease with clinical similarities to human atopic dermatitis. Several dog breeds are at increased risk for developing this disease but previous genetic associations are poorly defined. To identify additional genetic risk factors for canine atopic dermatitis, we here apply a Bayesian mixture model adapted for mapping complex traits and a cross-population extended haplotype test to search for disease-associated loci and selective sweeps in four dog breeds at risk for atopic dermatitis. We define 15 associated loci and eight candidate regions under selection by comparing cases with controls. One associated locus is syntenic to the major genetic risk locus (Filaggrin locus) in human atopic dermatitis. One selection signal in common type Labrador retriever cases positions across the TBC1D1 gene (body weight) and one signal of selection in working type German shepherd controls overlaps the LRP1B gene (brain), near the KYNU gene (psoriasis). In conclusion, we identify candidate genes, including genes belonging to the same biological pathways across multiple loci, with potential relevance to the pathogenesis of canine atopic dermatitis. The results show genetic similarities between dog and human atopic dermatitis, and future across-species genetic comparisons are hereby further motivated., (© 2022. The Author(s).)

Familial cerebellar ataxia with hydrocephalus in Bullmastiffs was described almost 40 years ago as a monogenic autosomal recessive trait. We investigated two young Bullmastiffs showing similar clinical signs. They developed progressive gait and behavioural abnormalities with an onset at around 6 months of age. Neurological assessment was consistent with a multifocal brain disease. Magnetic resonance imaging of the brain showed intra-axial bilateral symmetrical focal lesions localised to the cerebellar nuclei. Based on the juvenile age, nature of neurological deficits and imaging findings, an inherited disorder of the brain was suspected. We sequenced the genome of one affected Bullmastiff. The data were compared with 782 control genomes of dogs from diverse breeds. This search revealed a private homozygous frameshift variant in the MFF gene in the affected dog, XM&#95;038574000.1:c.471&#95;475delinsCGCTCT, that is predicted to truncate 55% of the wild type MFF open reading frame, XP&#95;038429928.1: p.(Glu158Alafs*14). Human patients with pathogenic MFF variants suffer from 'encephalopathy due to defective mitochondrial and peroxisomal fission 2'. Archived samples from two additional affected Bullmastiffs related to the originally described cases were obtained. Genotypes in a cohort of four affected and 70 unaffected Bullmastiffs showed perfect segregation with the disease phenotype. The available data together with information from previous disease reports allow classification of the investigated MFF frameshift variant as pathogenic and probably causative defect of the observed neurological phenotype. In analogy to the human phenotype, we propose to rename this disease 'mitochondrial fission encephalopathy (MFE)'., (© 2022 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.)

The aim of this study was to determine the breed boundary of the Hungarian Short-haired Vizsla (HSV) dog breed. Seventy registered purebred HSV dogs were genotyped on approximately 145,000 SNPs. Principal Component Analysis (PCA) and Admixture analysis certified that they belong to the same population. The outer point of the breed demarcation was a single Hungarian Wire-haired Vizsla (HWV) individual, which was the closest animal genetically to the HSV population in the PCA analysis. Three programs were used for the breed assignment calculations, including the widely used GeneClass2.0 software and two additional approaches developed here: the 'PCA-distance' and 'IBS-central' methods. Both new methods calculate a single number that represents how closely a dog fits into the actual reference population. The former approach calculates this number based on the PCA distances from the median of HSV animals. The latter calculates it from identity by state (IBS) data, measuring the distance from a central animal that is the best representative of the breed. Having no mixed-breed dogs with known HSV genome proportion, admixture animals were simulated by using data of HSV and HWV individuals to calibrate the inclusion/exclusion probabilities for the assignment. The numbers generated from these relatively simple calculations can be used by breeders and clubs to keep their populations under genetic supervision.

Cytochrome P450s (P450s) have been identified and analyzed in dogs and pigs, species that are often used in preclinical drug studies. Moreover, P450s are clinically important for drug therapy not only in humans, but also in species under veterinary care, including dogs and cats. In the present study, seven P450s homologous to human CYP2J2, namely, dog CYP2J2; cat CYP2J2; and pig CYP2J33, CYP2J35, CYP2J91, and CYP2J93, were newly identified and characterized, along with pig CYP2J34 previously identified. The cDNAs of these CYP2Js contain open reading frames of 502 amino acids, except for CYP2J35 (498 amino acids), and share high sequence identity (77%-80%) with human CYP2J2. Phylogenetic analysis revealed that dog and cat CYP2J2 were closely related, whereas pig CYP2Js formed a cluster. All seven CYP2J genes contain nine coding exons and are located in corresponding genomic regions, with the pig CYP2J genes forming a gene cluster. These CYP2J2 mRNAs were predominantly expressed in the small intestine with additional expression in the kidney and brain for dog CYP2J2 and pig CYP2J91 mRNAs, respectively. All seven CYP2Js metabolized human CYP2J2 substrates terfenadine, ebastine, and astemizole, indicating that they are functional enzymes. Dog CYP2J2 and pig CYP2J34 and CYP2J35 efficiently catalyzed ebastine primary hydroxylation and secondary carebastine formation at low substrate concentrations, just as human CYP2J2 does. Velocity - versus-substate plots exhibited sigmoidal relationships for dog CYP2J2, cat CYP2J2, and pig CYP2J33, indicating allosteric interactions. These results suggest that dog, cat, and pig CYP2Js have similar functional characteristics to human CYP2J2, with slight differences in ebastine and astemizole oxidations. SIGNIFICANCE STATEMENT: Dog CYP2J2; cat CYP2J2; and pig CYP2J33, CYP2J34, CYP2J35, CYP2J91, and CYP2J93, homologous to human CYP2J2, were identified and characterized by sequence, phylogenetic, and genomic structure analyses. Intestinal expression patterns of CYP2J mRNAs were characteristic in dogs, cats, and pigs. Dog, cat, and pig CYP2Js likely play roles as drug-metabolizing enzymes in the small intestine, similar to human CYP2J2., (Copyright © 2022 by The American Society for Pharmacology and Experimental Therapeutics.)

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived 1-8 . Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located., (© 2022. The Author(s).)

Atherosclerotic cardiovascular disease resulting from dysregulated lipid metabolism is the leading cause of morbidity and mortality worldwide. Apolipoprotein E (ApoE) plays a critical role in cholesterol metabolism. Knockouts in lipid-metabolizing proteins including ApoE in multiple model organisms such as mice and rats exhibiting elevated levels of cholesterol have been widely used for dissecting the pathology of atherosclerosis, but few of these animal models exhibit advanced atherosclerotic plaques leading to ischemia-induced clinical symptoms, limiting their use for translational studies. Here we report hypercholesterolemia and severe atherosclerosis characterized by stenosis and occlusion of arteries, together with clinical manifestations of stroke and gangrene, in ApoE knockout dogs generated by CRISPR/Cas9 and cloned by somatic cell nuclear transfer technologies. Importantly, the hypercholesterolemia and atherosclerotic complications in F0 mutants are recapitulated in their offspring. As the ApoE-associated atherosclerosis and clinical manifestations in mutant dogs are more similar to that in human patients compared with those in other animal models, these mutant dogs will be invaluable in developing and evaluating new therapies, including endovascular procedures, against atherosclerosis and related disorders., (© 2021. Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature.)

The dog (Canis familiaris) was the first domesticated animal and hundreds of breeds exist today. During domestication, dogs experienced strong selection for temperament, behaviour, and cognitive ability. However, the genetic basis of these abilities is not well-understood. We focused on ancient dog breeds to investigate breed-related differences in social cognitive abilities. In a problem-solving task, ancient breeds showed a lower tendency to look back at humans than other European breeds. In a two-way object choice task, they showed no differences in correct response rate or ability to read human communicative gestures. We examined gene polymorphisms in oxytocin, oxytocin receptor, melanocortin 2 receptor, and a Williams-Beuren syndrome-related gene (WBSCR17), as candidate genes of dog domestication. The single-nucleotide polymorphisms on melanocortin 2 receptor were related to both tasks, while other polymorphisms were associated with the unsolvable task. This indicates that glucocorticoid functions are involved in the cognitive skills acquired during dog domestication., (© 2022. The Author(s).)

Canine mammary gland tumors are very common and represent a potential model of human breast cancer, and microRNA (miRNAs) are promising biomarkers and therapeutic targets for these tumors. Accordingly, we aimed to identify miRNAs differentially expressed in canine mammary gland tumors using next generation sequencing (NGS), with subsequent confirmatory qPCR and target gene analyses. Mammary gland tissue was collected from healthy dogs (n=7) and dogs with suspected tumors (n=80). A subset of samples was analyzed with NGS to identify differentially expressed miRNAs with CLC Genome Workbench. Normal (n=10), tumor-adjacent (n=6), and tumor-bearing (n=76) mammary gland tissue samples were analyzed for the identified miRNAs using qPCR. An in silico analysis (TargetScan) was performed to predict the miRNAs' target genes using gene ontology (GO) terms and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (DAVID). We identified four miRNAs (cfa-miR-1-3p, cfa-miR-133a-3p, cfa-miR-133b-3p, and cfa-miR-133c-3p) as down regulated in canine mammary gland tumor tissues relative to normal and tumor adjacent tissues. KEGG analysis revealed the potential target genes of cfa-miR-1-3p are related to the Rap1 signaling pathway, adherens junction, and Ras signaling pathway, and those of the miR-133 family are related to the TGF-beta signaling pathway, synaptic vesicle cycle, and sphingolipid signaling pathway. In combination, these target genes are related to the regulation of transcription and DNA binding transcription (GO analysis), and the Hippo signaling pathway, adherens junction, and endocytosis (KEGG analysis). Accordingly, we suggest these four miRNAs are promising potential biomarker candidates for canine mammary gland tumors warranting further investigation., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Perception of inanimate objects as animate based on motion cues alone seems to be present in phylogenetically distant species, from birth (humans and chicks). However, we do not know whether the species' social and ecological environment has an influence on this phenomenon. Dogs serve as a unique species to investigate whether selection for specific behavioural traits influences animacy perception. We tested purebred companion dogs, and assigned them into two groups based on the type of work they were originally selected for: (1) Chasers, tracking and chasing prey; (2) Retrievers, mark and remember downed game. We displayed isosceles triangles presenting a chasing pattern vs moving independently, in parallel on a screen. We hypothesised that Chasers prefer to look at chasing and Retrievers eventually focus their visual attention on the independent motion. Overall, we did not find a significant difference between groups regarding the looking duration of dogs or the frequency of their gaze alternation between the chasing and independent motions. Thus it seems that selection for specific traits does not influence the perception of animate entities within the species., (© 2022. The Author(s).)

Genomic imprinting occurs in therian mammals and is a phenomenon whereby the two alleles of a gene are differentially expressed, based on the sex of the parent from whom the alleles were inherited. The allelic differences in expression are the consequence of different epigenetic modifications that are established in the sperm or oocyte during gametogenesis and transmitted at fertilization to offspring. A small minority of genes is regulated in this way but they have important biological functions, and aberrant regulation of imprinted genes contributes to disease aetiology in humans and other animals. The factors driving the evolution of imprinted genes are also of considerable interest, as these genes appear to forego the benefits of diploidy. To broaden the phylogenetic analysis of genomic imprinting, we began a study of imprinted genes in the domestic dog, Canis familiaris. In this report, we show that canine IGF2 and H19 are imprinted, with parent-of origin-dependent monoallelic expression patterns in neonatal umbilical cord. We identify a putative imprint control region associated with the genes, and provide evidence for differential methylation of this region in a somatic tissue (umbilical cord) and for its hypermethylation in the male germline. Canis familiaris is fast becoming a highly informative system for elucidating disease processes and evolution, and the study of imprinted genes in this species may help in understanding how these genes contribute to the generation of morphological and behavioral diversity., (© 2021 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.)