1
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Bryson GT, O’Neill DG, Brand CL, Belshaw Z, Packer RMA. The doodle dilemma: How the physical health of 'Designer-crossbreed' Cockapoo, Labradoodle and Cavapoo dogs' compares to their purebred progenitor breeds. PLoS One 2024; 19:e0306350. [PMID: 39196904 PMCID: PMC11355567 DOI: 10.1371/journal.pone.0306350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/14/2024] [Indexed: 08/30/2024] Open
Abstract
Booming UK ownership of designer-crossbreed dogs resulting from intentional crossing of distinct purebred breeds is often motivated by perceived enhanced health, despite limited evidence supporting a strong 'hybrid vigour' effect in dogs. Improved evidence on the relative health of designer-crossbreed dogs could support prospective owners to make better acquisition decisions when choosing their new dog. This study used a cross-sectional survey of UK owners of three common designer-crossbreeds (Cavapoo, Cockapoo, and Labradoodle) and their progenitor breeds (Cavalier King Charles Spaniel, Cocker Spaniel, Labrador Retriever, and Poodle) to collect owner-reported health disorder information. The authors hypothesised that designer-crossbred breeds have lower odds of common disorders compared to their progenitor breeds. Multivariable analysis accounted for confounding between breeds: dog age, sex, neuter status, and owner age and gender. The odds for the 57 most common disorders were compared across the three designer-crossbreeds with each of their two progenitor breeds (342 comparisons). Valid responses were received for 9,402 dogs. The odds did not differ statistically significantly between the designer-crossbreeds and their relevant progenitor breeds in 86.6% (n = 296) of health comparisons. Designer-crossbreeds had higher odds for 7.0% (n = 24) of disorders studied, and lower odds for 6.4% (n = 22). These findings suggest limited differences in overall health status between the three designer-crossbreeds and their purebred progenitors, challenging widespread beliefs in positive hybrid vigour effects for health in this emerging designer-crossbreed demographic. Equally, the current study did not suggest that designer-crossbreeds have poorer health as has also been purported. Therefore, owners could more appropriately base acquisition decisions between designer-crossbreeds and their purebred progenitors on other factors important to canine welfare such as breeding conditions, temperament, conformation and health of parents.
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Affiliation(s)
- Gina T. Bryson
- Department of Clinical Science and Services, Royal Veterinary College, Hertfordshire, United Kingdom
| | - Dan G. O’Neill
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hertfordshire, United Kingdom
| | - Claire L. Brand
- Department of Clinical Science and Services, Royal Veterinary College, Hertfordshire, United Kingdom
| | - Zoe Belshaw
- EviVet Evidence-Based Veterinary Consultancy, Nottingham, United Kingdom
| | - Rowena M. A. Packer
- Department of Clinical Science and Services, Royal Veterinary College, Hertfordshire, United Kingdom
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2
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Dobos P, Pongrácz P. You talkin' to me? Functional breed selection may have fundamentally influenced dogs' sensitivity to human verbal communicative cues. BMC Biol 2024; 22:183. [PMID: 39183286 PMCID: PMC11346259 DOI: 10.1186/s12915-024-01983-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024] Open
Abstract
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.
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Affiliation(s)
- Petra Dobos
- Department of Ethology, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, 1117, Hungary
| | - Péter Pongrácz
- Department of Ethology, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, 1117, Hungary.
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3
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Kolkmeyer CA, Zambrano Cardona AM, Gansloßer U. Personality Unleashed: Surveying Correlation of Neuter Status and Social Behaviour in Mixed-Breed Male Dogs across Weight Classes. Animals (Basel) 2024; 14:2445. [PMID: 39199978 PMCID: PMC11350830 DOI: 10.3390/ani14162445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024] Open
Abstract
This study investigates the behavioural differences between neutered and intact dogs. A total of 230 questionnaires of neutered (n = 115) and intact (n = 115) mixed-breed male dogs were collected. Small, medium, large, and giant dogs were analysed to investigate a possible influence of body size. The results showed neuters were significantly more stressed than intacts (multinomial logistic regression, p = 0.001). In terms of stress by influences (such as separation anxiety and anxiety at car rides), neutered small, medium, and large dogs were more stressed than giant dogs (multinomial logistic regression, p = 0.05). Neuters were also found to be more aggressive in general (multinomial logistic regression, p = 0.04) and more aggressive on the walk (multinomial logistic regression, p = 0.02). In addition, personality questionnaires revealed significant differences in all characteristics. Neuters were less emotionally calm (multiple ordinal regression, p = 0.03), less trainable and less sociable (each multiple ordinal regression, p < 0.001). They also scored lower on extraversion (multiple ordinal regression, p = 0.04). These findings highlight the importance of further research into the behavioural effects of neutering dogs, as well as the need for evidence-based guidelines for neutering practices.
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Affiliation(s)
- Carina A. Kolkmeyer
- Institut für Zoologie & Evolutionsforschung mit Phyletischem Museum, Ernst-Haeckel-Haus und Biologiedidaktik, Erbertstr. 1, 07743 Jena, Germany;
- Department of Biology, University of Vechta, Driverstrasee 22, 49377 Vechta, Germany
| | - Ana M. Zambrano Cardona
- Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Altensteinstraße 6, 14195 Berlin, Germany;
| | - Udo Gansloßer
- Institut für Zoologie & Evolutionsforschung mit Phyletischem Museum, Ernst-Haeckel-Haus und Biologiedidaktik, Erbertstr. 1, 07743 Jena, Germany;
- Department of Biology, University of Vechta, Driverstrasee 22, 49377 Vechta, Germany
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4
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Coutinho-Lima D, Dreger DL, Doadrio I, Parker HG, Ghanavi HR, Frantz L, Larson G, Ostrander EA, Godinho R. Multiple ancestries and shared gene flow among modern livestock guarding dogs. iScience 2024; 27:110396. [PMID: 39156647 PMCID: PMC11326944 DOI: 10.1016/j.isci.2024.110396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/24/2024] [Accepted: 06/25/2024] [Indexed: 08/20/2024] Open
Abstract
Livestock guarding dogs (LGDs) have been used to protect livestock for millennia. While previous works suggested a single origin of modern LGDs, the degree and source of shared ancestry have not been tested. To address this, we generated genome-wide SNP data from 304 LGDs and combined it with public genomic data from 2,183 modern and 22 ancient dogs. Our findings reveal shared ancestry and extensive gene flow among modern LGD breeds which we attribute to historical livestock migrations. Additionally, admixture between LGDs and free-ranging dogs argues against reproductive isolation as a core mechanism for maintaining the specialized skills of LGDs. Finally, we identify two lineages within modern LGDs and uncover multiple ancestries tracing back to distinct Eurasian ancient dogs, concordant with the absence of a single ancestor. Overall, our work explores the complex evolutionary history of LGDs, offering valuable insights into how human and livestock co-migrations shaped this functional group.
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Affiliation(s)
- Diogo Coutinho-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- BIOPOLIS - Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Dayna L. Dreger
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ignacio Doadrio
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Heidi G. Parker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Laurent Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Faculty of Veterinary Sciences, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- BIOPOLIS - Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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5
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Pongrácz P, Lugosi CA. Cooperative but Dependent-Functional Breed Selection in Dogs Influences Human-Directed Gazing in a Difficult Object-Manipulation Task. Animals (Basel) 2024; 14:2348. [PMID: 39199881 PMCID: PMC11350734 DOI: 10.3390/ani14162348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/05/2024] [Accepted: 08/13/2024] [Indexed: 09/01/2024] Open
Abstract
It is still largely unknown to what extent domestication, ancestry, or recent functional selection are responsible for the behavioral differences in whether dogs look back to a human when presented with a difficult task. Here, we tested whether this ubiquitous human-related response of companion dogs would appear differently in subjects that were selected for either cooperative or independent work tasks. We tested N = 71 dogs from 18 cooperative and 18 independent breeds. Subjects learned in a five-trial warming-up phase that they could easily obtain the reward from a container. In trial six, the reward became impossible to take out from the locked container. When the task was easy, both breed groups behaved similarly, and their readiness to approach the container did not differ between the last 'solvable' and the subsequent 'unsolvable' trial. Task focus, looking at the container, touching the container for the first time, or interacting with the container with a paw or nose did not differ between the breed groups, indicating that their persistence in problem solving was similar. However, in the 'unsolvable' trial, cooperative dogs alternated their gaze more often between the container and the humans than the independent dogs did. The frequency of looking back was also higher in cooperative dogs than in the independent breeds. These are the first empirical results that suggest, in a balanced, representative sample of breeds, that the selection for different levels of cooperativity in working dogs could also affect their human-dependent behavior in a generic problem-solving situation.
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Affiliation(s)
- Péter Pongrácz
- Department of Ethology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary;
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6
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Pongrácz P, Dobos P. Behavioural differences and similarities between dog breeds: proposing an ecologically valid approach for canine behavioural research. Biol Rev Camb Philos Soc 2024. [PMID: 39101379 DOI: 10.1111/brv.13128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/19/2024] [Accepted: 07/26/2024] [Indexed: 08/06/2024]
Abstract
The behaviour of dogs holds great relevance for not only scientists from fundamental and applied research areas, but also due to the widespread roles of dogs in our societies as companions and working animals; their behaviour is also an important factor in animal and human welfare. A large proportion of dogs currently under human supervision belong to one of roughly 400 recognised breeds. Dog breeds can be characterised by distinctive, predictable and reproducible features, including some of their behavioural traits. To the scientist, the comparative analysis of the behaviour of dog breeds provides an opportunity for investigating an array of intriguing phenomena within an easily accessible model organism created from natural and human-driven evolutionary processes. There are many ways to design and conduct breed-related behavioural investigations, but such endeavours should always be based around biologically relevant research questions and lead to ecologically valid conclusions. In this review, we surveyed recent research efforts that included dog behaviour-related comparisons and applied a critical evaluation according to their methods of breed choice and the subsequent research design. Our aim was to assess whether these two fundamentally important components of experimental design provide a solid basis to reach valid conclusions. Based on 97 publications that fulfilled our selection criteria, we identified three primary methods used by researchers to select breeds for their investigations: (i) convenience sampling; (ii) hypothesis-driven, ancestry-based sampling; and (iii) hypothesis-driven, functional sampling. By using the SWOT (Strengths, Weaknesses, Opportunities, Threats) evaluation system, we highlight each of these techniques' merits and shortcomings. We identify when particular methods may be inherently unable to produce biologically meaningful results due to a mismatch between breed choice and the initial research goals. We hope that our evaluation will help researchers adopt best practices in experimental design regarding future dog breed comparisons.
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Affiliation(s)
- Péter Pongrácz
- Department of Ethology, ELTE Eötvös Loránd University, 1117 Pázmány Péter sétány 1/c, Budapest, Hungary
| | - Petra Dobos
- Department of Ethology, ELTE Eötvös Loránd University, 1117 Pázmány Péter sétány 1/c, Budapest, Hungary
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7
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Cahill JA, Smith LA, Gottipati S, Torabi TS, Graim K. Bringing the Genomic Revolution to Comparative Oncology: Human and Dog Cancers. Annu Rev Biomed Data Sci 2024; 7:107-129. [PMID: 38648188 PMCID: PMC11343685 DOI: 10.1146/annurev-biodatasci-102423-111936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Dogs are humanity's oldest friend, the first species we domesticated 20,000-40,000 years ago. In this unequaled collaboration, dogs have inadvertently but serendipitously been molded into a potent human cancer model. Unlike many common model species, dogs are raised in the same environment as humans and present with spontaneous tumors with human-like comorbidities, immunocompetency, and heterogeneity. In breast, bladder, blood, and several pediatric cancers, in-depth profiling of dog and human tumors has established the benefits of the dog model. In addition to this clinical and molecular similarity, veterinary studies indicate that domestic dogs have relatively high tumor incidence rates. As a result, there are a plethora of data for analysis, the statistical power of which is bolstered by substantial breed-specific variability. As such, dog tumors provide a unique opportunity to interrogate the molecular factors underpinning cancer and facilitate the modeling of new therapeutic targets. This review discusses the emerging field of comparative oncology, how it complements human and rodent cancer studies, and where challenges remain, given the rapid proliferation of genomic resources. Increasingly, it appears that human's best friend is becoming an irreplaceable component of oncology research.
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Affiliation(s)
- James A Cahill
- University of Florida Genetics Institute, University of Florida, Gainesville, Florida, USA;
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - Leslie A Smith
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
| | - Soumya Gottipati
- Department of Computer Science, Princeton University, Princeton, New Jersey, USA
| | - Tina Salehi Torabi
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
| | - Kiley Graim
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
- University of Florida Health Cancer Center, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, Florida, USA;
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8
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Mason MJ, Lewis MA. Structure and scaling of the middle ear in domestic dog breeds. J Anat 2024; 245:324-338. [PMID: 38605539 PMCID: PMC11259751 DOI: 10.1111/joa.14049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Although domestic dogs vary considerably in both body size and skull morphology, behavioural audiograms have previously been found to be similar in breeds as distinct as a Chihuahua and a St Bernard. In this study, we created micro-CT reconstructions of the middle ears and bony labyrinths from the skulls of 17 dog breeds, including both Chihuahua and St Bernard, plus a mongrel and a wolf. From these reconstructions, we measured middle ear cavity and ossicular volumes, eardrum and stapes footplate areas and bony labyrinth volumes. All of these ear structures scaled with skull size with negative allometry and generally correlated better with condylobasal length than with maximum or interaural skull widths. Larger dogs have larger ear structures in absolute terms: the volume of the St Bernard's middle ear cavity was 14 times that of the Chihuahua. The middle and inner ears are otherwise very similar in morphology, the ossicular structure being particularly well-conserved across breeds. The expectation that larger ear structures in larger dogs would translate into hearing ranges shifted towards lower frequencies is not consistent with the existing audiogram data. Assuming that the audiograms accurately reflect the hearing of the breeds in question, oversimplifications in existing models of middle ear function or limitations imposed by other parts of the auditory system may be responsible for this paradox.
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Affiliation(s)
- Matthew J. Mason
- Department of Physiology, Development & NeuroscienceUniversity of CambridgeCambridgeUK
| | - Madaleine A. Lewis
- Department of Physiology, Development & NeuroscienceUniversity of CambridgeCambridgeUK
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9
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Donner J, Mellersh C. Frequency of RPGRIP1 and MAP9 genetic modifiers of canine progressive retinal atrophy, in 132 breeds of dog. Anim Genet 2024; 55:687-691. [PMID: 38752391 DOI: 10.1111/age.13443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/10/2024] [Accepted: 04/27/2024] [Indexed: 07/04/2024]
Abstract
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.
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Affiliation(s)
- Jonas Donner
- Wisdom Panel, Mars Petcare Science & Diagnostics, Helsinki, Finland
| | - Cathryn Mellersh
- Department of Veterinary Medicine, Canine Genetics Centre, University of Cambridge, Cambridge, UK
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10
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Garamszegi LZ, Kolm N. The reduction in relative brain size in the domesticated dog is not an evolutionary singularity among the canids. Biol Lett 2024; 20:20240336. [PMID: 39102458 PMCID: PMC11299805 DOI: 10.1098/rsbl.2024.0336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 08/07/2024] Open
Abstract
Domestication has long been considered the most powerful evolutionary engine behind dramatic reductions in brain size in several taxa, and the dog (Canis familiaris) is considered as a typical example that shows a substantial decrease in brain size relative to its ancestor, the grey wolf (Canis lupus). However, to make the case for exceptional evolution of reduced brain size under domestication requires an interspecific approach in a phylogenetic context that can quantify the extent by which domestication reduces brain size in comparison to closely related non-domesticated species responding to different selection factors in the wild. Here, we used a phylogenetic method to identify evolutionary singularities to test if the domesticated dog stands out in terms of relative brain size from other species of canids. We found that the dog does not present unambiguous signature of evolutionary singularity with regard to its small brain size, as the results were sensitive to the considerations about the ancestral trait values upon domestication. However, we obtained strong evidence for the hibernating common raccoon dog (Nyctereutes procyonoides) being an evolutionary outlier for its brain size. Therefore, domestication is not necessarily an exceptional case concerning evolutionary reductions in brain size in an interspecific perspective.
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Affiliation(s)
| | - Niclas Kolm
- Department of Zoology, Stockholm University, Stockholm, Sweden
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11
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Nguyen AK, Schall PZ, Kidd JM. A map of canine sequence variation relative to a Greenland wolf outgroup. Mamm Genome 2024:10.1007/s00335-024-10056-1. [PMID: 39088040 DOI: 10.1007/s00335-024-10056-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024]
Abstract
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_Cfam_GSD_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.
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Affiliation(s)
- Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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12
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Buckley RM, Ostrander EA. Large-scale genomic analysis of the domestic dog informs biological discovery. Genome Res 2024; 34:811-821. [PMID: 38955465 PMCID: PMC11293549 DOI: 10.1101/gr.278569.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
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.
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Affiliation(s)
- Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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13
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Armero AS, Buckley RM, Mboning L, Spatola GJ, Horvath S, Pellegrini M, Ostrander EA. Co-analysis of methylation platforms for signatures of biological aging in the domestic dog reveals previously unexplored confounding factors. Aging (Albany NY) 2024; 16:10724-10748. [PMID: 38985449 PMCID: PMC11272130 DOI: 10.18632/aging.206012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/29/2024] [Indexed: 07/11/2024]
Abstract
Chronological age reveals the number of years an individual has lived since birth. By contrast, biological age varies between individuals of the same chronological age at a rate reflective of physiological decline. Differing rates of physiological decline are related to longevity and result from genetics, environment, behavior, and disease. The creation of methylation biological age predictors is a long-standing challenge in aging research due to the lack of individual pre-mortem longevity data. The consistent differences in longevity between domestic dog breeds enable the construction of biological age estimators which can, in turn, be contrasted with methylation measurements to elucidate mechanisms of biological aging. We draw on three flagship methylation studies using distinct measurement platforms and tissues to assess the feasibility of creating biological age methylation clocks in the dog. We expand epigenetic clock building strategies to accommodate phylogenetic relationships between individuals, thus controlling for the use of breed standard metrics. We observe that biological age methylation clocks are affected by population stratification and require heavy parameterization to achieve effective predictions. Finally, we observe that methylation-related markers reflecting biological age signals are rare and do not colocalize between datasets.
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Affiliation(s)
- Aitor Serres Armero
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reuben M. Buckley
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lajoyce Mboning
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Gabriella J. Spatola
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Altos Labs Inc, Cambridge, United Kingdom
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of Los Angeles, Los Angeles, CA 90095, USA
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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14
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Sanz CR, Sarquis J, Daza MÁ, Miró G. Exploring the impact of epidemiological and clinical factors on the progression of canine leishmaniosis by statistical and whole genome analyses: from breed predisposition to comorbidities. Int J Parasitol 2024; 54:401-414. [PMID: 38570155 DOI: 10.1016/j.ijpara.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 02/25/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
Canine leishmaniosis (CanL), caused by Leishmania infantum, is a complex disease of growing importance in Europe. Clinical manifestations result from the down-modulation of the host immune response through multiple host-parasite interactions. Although several factors might influence CanL progression, this is the first known study evaluating risk factors for its different clinical stages in a large referral hospital population (n = 35.669) from an endemic area, over a 20 year period. Genome-wide scans for selection signatures were also conducted to explore the genomic component of clinical susceptibility to L. infantum infection. The prevalence of CanL was 3.2% (16.7% stage I; 43.6% stage II; 32.1% stage III; 7.6% stage IV). Dog breed (crossbreed), bodyweight (<10 kg), living conditions (indoors), regular deworming treatment, and being vaccinated against Leishmania significantly decreased the transmission risk and the risk for developing severe clinical forms. Conversely, the detection of comorbidities was associated with advanced clinical forms, particularly chronic kidney disease, neoplasia, cryptorchidism, infectious tracheobronchitis and urate urolithiasis, although those did not impact the clinical outcome. Significant associations between an increased risk of severe clinical stages and findings in the anamnesis (renal or skin-related manifestations) and physical examination (ocular findings) were also detected, highlighting their diagnostic value in referred cases of CanL. Sixteen breeds were found to be significantly more susceptible to developing severe stages of leishmaniosis (e.g. Great Dane, Rottweiler, English Springer Spaniel, Boxer, American Staffordshire Terrier, Golden Retriever), while 20 breeds displayed a clinical resistantance phenotype and, thus, are more likely to mount an efficient immune response against L. infantum (e.g. Pointer, Samoyed, Spanish Mastiff, Spanish Greyhound, English Setter, Siberian Husky). Genomic analyses of these breeds retrieved 12 regions under selection, 63 candidate genes and pinpointed multiple biological pathways such as the IRE1 branch of the unfolded protein response, which could play a critical role in clinical susceptibility to L. infantum infection.
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Affiliation(s)
- Carolina R Sanz
- Animal Health Department, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, Madrid 28040, Spain.
| | - Juliana Sarquis
- Animal Health Department, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, Madrid 28040, Spain
| | - María Ángeles Daza
- Veterinary Teaching Hospital, Veterinary Faculty, Complutense University of Madrid, Av. Puerta Hierro s/n, Madrid 28040, Spain; Department of Animal Medicine and Surgery, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, Madrid 28040, Spain
| | - Guadalupe Miró
- Animal Health Department, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, Madrid 28040, Spain; Veterinary Teaching Hospital, Veterinary Faculty, Complutense University of Madrid, Av. Puerta Hierro s/n, Madrid 28040, Spain.
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15
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Dang W, Gao D, Lyu G, Irwin DM, Shang S, Chen J, Zhang J, Zhang S, Wang Z. A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice. Genes (Basel) 2024; 15:739. [PMID: 38927675 PMCID: PMC11202965 DOI: 10.3390/genes15060739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
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.
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Affiliation(s)
- Wanyi Dang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Dali Gao
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Guangqi Lyu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - David M. Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Songyang Shang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Junnan Chen
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Junpeng Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
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16
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Kolkmeyer CA, Baum J, Warlich-Zach N, Gansloßer U. From "Husky" to "Bulldog"- behavioural correlates between castration and breed groups in the domestic dog (Canis lupus familiaris). BMC Vet Res 2024; 20:238. [PMID: 38831350 PMCID: PMC11145769 DOI: 10.1186/s12917-024-04097-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/26/2024] [Indexed: 06/05/2024] Open
Abstract
Neutering dogs is a widespread method and is carried out for various behavioural and husbandry reasons. This study's main objective is to investigate the behavioural correlations between neutering and the breed of male dogs. In order to possibly find breed-dependent differences in the behaviour of intact and castrated dogs, a differentiation between two clades - the "Huskies"(chow chow, shar pei, akita/shiba inu, alaskan malamute, siberian/alaskan husky) and the "Bulldogs" (german boxer, english/french bulldog, old english mastiff, boston terrier, english bull terrier, staffordshire bull terrier, american staffordshire terrier), based on Parker et al. [1], was made.Using an online questionnaire,, 31 neutered and 37 intact male dogs from the clade "Huskies" and 30 neutered and 38 intact male dogs from the clade "Bulldogs", participated in the study (N = 136).The survey included detailed questions on the dogs' personality and any associated issues as well as a behavioural anamnesis. Further questions relating to four of the "big five" personality dimensions based on the "Budapest questionnaire" by Turcsán et al. from 2011 [2] were also added.The results show, that neutered males from both breed clades more frequently displayed aggression toward humans than intact males (multinomial logistic regression, p = 0.002). When it came to aggression towards other dogs, it was the "Huskies" that differed significantly from the "Bulldogs"(multinomial logistic regression, p = 0.04) with being more aggressive. There were also significant differences in stress-related behaviour depending on castration status and breed (multinomial logistic regression, p < 0.001; Cramer's V = 0.33) and only the castration status had an impact on the significance (multinomial logistic regression, p < 0.001). The analysis also revealed significance for stress-indicating behaviour with dependence on neutering status (multinomial logistic regression, p < 0.001) and showed that stress as well as uncertainty are significantly more common in neutered dogs depending on breed and neutering status (multinomial logistic regression, p < 0.001; Cramer's V = 0.42), in that only neutered "Bulldogs" were stressed, but more "Huskies" overall.According to the Budapest questionnaire data, the "Bulldog" clade had considerably greater extraversion scores overall (ordinal regression, p < 0.001) than the "Huskies".Our findings highlight the risks and potential negative effects of neutering. Gonadectomy in no way substitutes for the dog receiving the necessary socialization, training, or bonding. Although in some circumstances it might have a favourable impact on the dog's behaviour, it should not be seen as a panacea for unwanted behaviour. Given that not all behaviours are influenced by sex hormones, every castration decision must be weighed up individually.
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Affiliation(s)
- C A Kolkmeyer
- Department of Biology, University of Vechta, driverstrasee 22, 49377, Vechta, Germany.
- Institut für Zoologie & Evolutionsforschung mit Phyletischem Museum, Ernst-Haeckel-Haus und Biologiedidaktik, Erbertstr.1, Jena, 07743, Thuringia, Germany.
| | - J Baum
- Department of Biology, University of Vechta, driverstrasee 22, 49377, Vechta, Germany
| | - N Warlich-Zach
- Department of Biology, University of Vechta, driverstrasee 22, 49377, Vechta, Germany
| | - U Gansloßer
- Department of Biology, University of Vechta, driverstrasee 22, 49377, Vechta, Germany
- Institut für Zoologie & Evolutionsforschung mit Phyletischem Museum, Ernst-Haeckel-Haus und Biologiedidaktik, Erbertstr.1, Jena, 07743, Thuringia, Germany
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17
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Braman SL, Peterson H, Elbe A, Mani E, Danielson C, Dahman C, Labadie JD, Trepanier LA. Urinary and household chemical exposures in pet dogs with urothelial cell carcinoma. Vet Comp Oncol 2024; 22:217-229. [PMID: 38388159 DOI: 10.1111/vco.12968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Urothelial cell carcinoma (UCC) has been linked to environmental chemical exposures in people, but these risk factors are not well understood in dogs with UCC. We hypothesised that household chemical exposures contribute to the risk of UCC in pet dogs. This prospective cross-sectional case-control study included 37 dogs with UCC and 37 unaffected breed-, sex-, and age-matched controls. Dog owners completed an environmental questionnaire and household samples were collected and analysed for arsenic (in tap water and room dust) and acrolein (in room air). Urine samples from UCC dogs, control dogs, and consenting owners were analysed for inorganic arsenic species, the acrolein metabolite 3-HPMA, and the phenoxy herbicide 2,4-D. Public data on chlorination byproducts (total trihalomethanes) in municipal drinking water were also compared between case and control households. Dogs with UCC were more likely to swim in a pool (15.2%) compared with control dogs (0%) (OR 1.69, 95% CI = 1.69-∞; p = .02). Dogs with UCC also had more than 4-fold higher reported municipal water concentrations of chlorination byproducts (median 28.0 ppb) compared with controls (median 6.9 ppb; p < .0001). Dust arsenic concentrations were unexpectedly lower in case households (median 0.277 ng/cm2) compared with control households (median 0.401 ng/cm2; p = .0002). Other outcomes were not significantly different between groups. These data suggest that dog owners, especially those of breeds known to be at higher risk for UCC, consider limiting access to swimming pools and installing water filtration units that remove total trihalomethanes.
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Affiliation(s)
- Samantha L Braman
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Hannah Peterson
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amy Elbe
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Erin Mani
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Camille Danielson
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christa Dahman
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Julia D Labadie
- Scientific Programs Department, Morris Animal Foundation, Denver, Colorado, USA
| | - Lauren A Trepanier
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
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18
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Parker HG, Harris AC, Plassais J, Dhawan D, Kim EM, Knapp DW, Ostrander EA. Genome-wide analyses reveals an association between invasive urothelial carcinoma in the Shetland sheepdog and NIPAL1. NPJ Precis Oncol 2024; 8:112. [PMID: 38778091 PMCID: PMC11111773 DOI: 10.1038/s41698-024-00591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/14/2024] [Indexed: 05/25/2024] Open
Abstract
Naturally occurring canine invasive urinary carcinoma (iUC) closely resembles human muscle invasive bladder cancer in terms of histopathology, metastases, response to therapy, and low survival rate. The heterogeneous nature of the disease has led to the association of large numbers of risk loci in humans, however most are of small effect. There exists a need for new and accurate animal models of invasive bladder cancer. In dogs, distinct breeds show markedly different rates of iUC, thus presenting an opportunity to identify additional risk factors and overcome the locus heterogeneity encountered in human mapping studies. In the association study presented here, inclusive of 100 Shetland sheepdogs and 58 dogs of other breeds, we identify a homozygous protein altering point mutation within the NIPAL1 gene which increases risk by eight-fold (OR = 8.42, CI = 3.12-22.71), accounting for nearly 30% of iUC risk in the Shetland sheepdog. Inclusion of six additional loci accounts for most of the disease risk in the breed and explains nearly 75% of the phenotypes in this study. When combined with sequence data from tumors, we show that variation in the MAPK signaling pathway is an overarching cause of iUC susceptibility in dogs.
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Affiliation(s)
- Heidi G Parker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Alexander C Harris
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Jocelyn Plassais
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, University of Rennes, 35000, Rennes, France
| | - Deepika Dhawan
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Erika M Kim
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Deborah W Knapp
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
- Purdue University Center for Cancer Research, West Lafayette, IN, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Center, National Institutes of Health, Bethesda, MD, USA.
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19
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Uno Y, Yamato O, Yamazaki H. Transcript abundance of hepatic drug-metabolizing enzymes in two dog breeds compared with 14 species including humans. Drug Metab Pharmacokinet 2024; 55:101002. [PMID: 38452615 DOI: 10.1016/j.dmpk.2024.101002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 03/09/2024]
Abstract
Drug-metabolizing enzymes are important in drug development and therapy, but have not been fully identified and characterized in many species, lines, and breeds. Liver transcriptomic data were analyzed for phase I cytochromes P450, flavin-containing monooxygenases, and carboxylesterases and phase II UDP-glucuronosyltransferases, sulfotransferases, and glutathione S-transferases. Comparisons with a variety of species (humans, rhesus macaques, African green monkeys, baboons, common marmosets, cattle, sheep, pigs, cats, dogs, rabbits, tree shrews, rats, mice, and chickens) revealed both general similarities and differences in the transcript abundances of drug-metabolizing enzymes. Similarly, Beagle and Shiba dogs were examined by next-generation sequencing (RNA-seq). Consequently, no substantial differences in transcript abundance were noted in different breeds of pigs and dogs and in different lines of mice and rats. Therefore, the expression profiles of hepatic drug-metabolizing enzyme transcripts appear to be similar in Shiba and Beagle dogs and pig breeds and the rat and mouse lines analyzed, although some differences were found in other species.
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Affiliation(s)
- Yasuhiro Uno
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima-city, Kagoshima, 890-0065, Japan.
| | - Osamu Yamato
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima-city, Kagoshima, 890-0065, Japan
| | - Hiroshi Yamazaki
- Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan.
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20
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Gnanadesikan GE, Tandon D, Bray EE, Kennedy BS, Tennenbaum SR, MacLean EL, vonHoldt BM. Transposons in the Williams-Beuren Syndrome Critical Region are Associated with Social Behavior in Assistance Dogs. Behav Genet 2024; 54:196-211. [PMID: 38091228 DOI: 10.1007/s10519-023-10166-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 11/08/2023] [Indexed: 02/13/2024]
Abstract
A strong signature of selection in the domestic dog genome is found in a five-megabase region of chromosome six in which four structural variants derived from transposons have previously been associated with human-oriented social behavior, such as attentional bias to social stimuli and social interest in strangers. To explore these genetic associations in more phenotypic detail-as well as their role in training success in a specialized assistance dog program-we genotyped 1001 assistance dogs from Canine Companions for Independence®, including both successful graduates and dogs released from the training program for behaviors incompatible with their working role. We collected phenotypes on each dog using puppy-raiser questionnaires, trainer questionnaires, and both cognitive and behavioral tests. Using Bayesian mixed models, we found strong associations (95% credibility intervals excluding zero) between genotypes and certain behavioral measures, including separation-related problems, aggression when challenged or corrected, and reactivity to other dogs. Furthermore, we found moderate differences in the genotypes of dogs who graduated versus those who did not; insertions in GTF2I showed the strongest association with training success (β = 0.23, CI95% = - 0.04, 0.49), translating to an odds-ratio of 1.25 for one insertion. Our results provide insight into the role of each of these four transposons in canine sociability and may inform breeding and training practices for working dog organizations. Furthermore, the observed importance of the gene GTF2I supports the emerging consensus that variation in GTF2I genotypes and expression have important consequences for social behavior broadly.
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Affiliation(s)
- Gitanjali E Gnanadesikan
- School of Anthropology, University of Arizona, Tucson, AZ, 85721, USA.
- Cognitive Science Program, University of Arizona, Tucson, AZ, 85721, USA.
- Department of Anthropology, Emory University, Atlanta, GA, 30332, USA.
| | - Dhriti Tandon
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Emily E Bray
- School of Anthropology, University of Arizona, Tucson, AZ, 85721, USA
- Canine Companions for Independence, National Headquarters, Santa Rosa, CA, 95402, USA
- College of Veterinary Medicine, University of Arizona, Oro Valley, AZ, 85737, USA
- Department of Psychology, University of Arizona, Tucson, AZ, 85721, USA
| | - Brenda S Kennedy
- Canine Companions for Independence, National Headquarters, Santa Rosa, CA, 95402, USA
| | - Stavi R Tennenbaum
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Evan L MacLean
- School of Anthropology, University of Arizona, Tucson, AZ, 85721, USA
- Cognitive Science Program, University of Arizona, Tucson, AZ, 85721, USA
- College of Veterinary Medicine, University of Arizona, Oro Valley, AZ, 85737, USA
- Department of Psychology, University of Arizona, Tucson, AZ, 85721, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
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21
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Park N, Kim H, Oh J, Kim J, Heo C, Kim J. PAPipe: A Pipeline for Comprehensive Population Genetic Analysis. Mol Biol Evol 2024; 41:msae040. [PMID: 38427787 PMCID: PMC10919927 DOI: 10.1093/molbev/msae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/03/2024] Open
Abstract
Advancements in next-generation sequencing (NGS) technologies have led to a substantial increase in the availability of population genetic variant data, thus prompting the development of various population analysis tools to enhance our understanding of population structure and evolution. The tools that are currently used to analyze population genetic variant data generally require different environments, parameters, and formats of the input data, which can act as a barrier preventing the wide-spread usage of such tools by general researchers who may not be familiar with bioinformatics. To address this problem, we have developed an automated and comprehensive pipeline called PAPipe to perform nine widely used population genetic analyses using population NGS data. PAPipe seamlessly interconnects and serializes multiple steps, such as read trimming and mapping, genetic variant calling, data filtering, and format converting, along with nine population genetic analyses such as principal component analysis, phylogenetic analysis, population tree analysis, population structure analysis, linkage disequilibrium decay analysis, selective sweep analysis, population admixture analysis, sequentially Markovian coalescent analysis, and fixation index analysis. PAPipe also provides an easy-to-use web interface that allows for the parameters to be set and the analysis results to be browsed in intuitive manner. PAPipe can be used to generate extensive results that provide insights that can help enhance user convenience and data usability. PAPipe is freely available at https://github.com/jkimlab/PAPipe.
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Affiliation(s)
- Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyeonji Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jeongmin Oh
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jinseok Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Charyeong Heo
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
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22
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Murgiano L, Niggel JK, Benedicenti L, Cortellari M, Bionda A, Crepaldi P, Liotta L, Aguirre GK, Beltran WA, Aguirre GD. Frameshift Variant in AMPD2 in Cirneco dell'Etna Dogs with Retinopathy and Tremors. Genes (Basel) 2024; 15:238. [PMID: 38397227 PMCID: PMC10887799 DOI: 10.3390/genes15020238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
While the manifestations of many inherited retinal disorders are limited to loss of vision, others are part of a syndrome that affects multiple tissues, particularly the nervous system. Most syndromic retinal disorders are thought to be recessively inherited. Two dogs out of a litter of Cirneco dell' Etna dogs, both males, showed signs of retinal degeneration, along with tremors and signs described as either atypical seizures or paroxysmal dyskinesias, while the other two male littermates were normal. We named this oculo-neurological syndrome CONS (Cirneco oculo-neurological syndrome), and undertook homozygosity mapping and whole-genome sequencing to determine its potential genetic etiology. Notably, we detected a 1-bp deletion in chromosome 6 that was predicted to cause a frameshift and premature stop codon within the canine AMPD2 gene, which encodes adenosine monophosphate deaminase, an enzyme that converts adenosine 5'-monophosphate (AMP) to inosine 5'-monophosphate (IMP). Genotyping of the available Cirneco population suggested perfect segregation between cases and controls for the variant. Moreover, this variant was absent in canine genomic databases comprised of thousands of unaffected dogs. The AMPD2 genetic variant we identified in dogs presents with retinal manifestations, adding to the spectrum of neurological manifestations associated with AMPD2 variants in humans.
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Affiliation(s)
- Leonardo Murgiano
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.K.N.); (W.A.B.); (G.D.A.)
- Sylvia M. Van Sloun Laboratory for Canine Genomic Analysis, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica K. Niggel
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.K.N.); (W.A.B.); (G.D.A.)
- Sylvia M. Van Sloun Laboratory for Canine Genomic Analysis, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leontine Benedicenti
- Matthew J. Ryan Veterinary Hospital, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Matteo Cortellari
- Department of Agricultural and Environmental Sciences—Production, Territory, Agroenergy, University of Milan, 20133 Milan, Italy; (M.C.); (A.B.); (P.C.)
| | - Arianna Bionda
- Department of Agricultural and Environmental Sciences—Production, Territory, Agroenergy, University of Milan, 20133 Milan, Italy; (M.C.); (A.B.); (P.C.)
| | - Paola Crepaldi
- Department of Agricultural and Environmental Sciences—Production, Territory, Agroenergy, University of Milan, 20133 Milan, Italy; (M.C.); (A.B.); (P.C.)
| | - Luigi Liotta
- Department of Veterinary Sciences, University of Messina, 98168 Messina, Italy;
| | - Geoffrey K. Aguirre
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - William A. Beltran
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.K.N.); (W.A.B.); (G.D.A.)
| | - Gustavo D. Aguirre
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.K.N.); (W.A.B.); (G.D.A.)
- Sylvia M. Van Sloun Laboratory for Canine Genomic Analysis, University of Pennsylvania, Philadelphia, PA 19104, USA
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23
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Hrebianchuk AE, Tsybovsky IS. A universal panel of STR loci for the study of polymorphism of the species Canis lupus and forensic identification of dog and wolf. Vavilovskii Zhurnal Genet Selektsii 2024; 28:98-107. [PMID: 38465248 PMCID: PMC10917668 DOI: 10.18699/vjgb-24-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 03/12/2024] Open
Abstract
Commercial panels of microsatellite (STR) loci are intended for DNA analysis of the domestic dog (Canis lupus familiaris) and, therefore, when genotyping the Grey wolf (Canis lupus lupus), most markers reveal significant deviations from the Hardy-Weinberg equilibrium and have a low informative value, which complicates their use in a forensic examination. The aim of this study was to select STR markers that equally effectively reflect population polymorphism in the wolf and the dog, and to create a universal panel for the identification of individuals in forensic science. Based on the study of polymorphisms of 34 STR loci, a CPlex panel of 15 autosomal loci and two sex loci was developed, which is equally suitable for identifying wolfs and dogs. Analysis of molecular variance (AMOVA) between samples revealed significant differentiation values (FST = 0.0828, p < 0.05), which allows the panel to be used for differentiating between wolf and dog samples. For the first time in the forensic examination of objects of animal origin in the Republic of Belarus, population subdivision coefficients (θ-values) were calculated for each of the 15 STR loci of the test system being reported. It was shown that the values of the genotype frequency, when averaged over all studied animals without and with considering the θ-value, differ by three orders of magnitude (3.39 · 10-17 and 4.71 · 10-14, respectively). The use of population subdivision coefficients will provide the researcher with the most relevant results of an expert identification study. The test system was validated in accordance with the protocol of the Scientific Working Group on DNA Analysis Methods. A computational tool was developed to automate the analysis of genetic data on the wolf and dog in the forensic examination; two guides were approved for practicing forensic experts. This methodology is being successfully used in expert practice in investigating cases of illegal hunting, animal abuse and other offenses in the Republic of Belarus.
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Affiliation(s)
- A E Hrebianchuk
- Forensic Examination Committee of the Republic of Belarus, Minsk, Belarus
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24
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McMillan KM, Bielby J, Williams CL, Upjohn MM, Casey RA, Christley RM. Longevity of companion dog breeds: those at risk from early death. Sci Rep 2024; 14:531. [PMID: 38302530 PMCID: PMC10834484 DOI: 10.1038/s41598-023-50458-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/20/2023] [Indexed: 02/03/2024] Open
Abstract
The companion dog is one of the most phenotypically diverse species. Variability between breeds extends not only to morphology and aspects of behaviour, but also to longevity. Despite this fact, little research has been devoted to assessing variation in life expectancy between breeds or evaluating the potential for phylogenetic characterisation of longevity. Using a dataset of 584,734 unique dogs located within the UK, including 284,734 deceased, we present variation in longevity estimates within the following: parental lineage (purebred = 1 breed, crossbred ≥ 2 breeds), breed (n = 155), body size (large, medium, small), sex (male, female) and cephalic index (brachycephalic, mesocephalic, dolichocephalic). Survival estimates were then partitioned amongst phylogenetic clades: providing evidence that canine evolutionary history (via domestication and associated artificial selection) is associated with breed lifespan. This information provides evidence to inform discussions regarding pedigree health, whilst helping current/prospective owners, breeders, policy makers, funding bodies and welfare organisations improve decision making regarding canine welfare.
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Affiliation(s)
| | - Jon Bielby
- Liverpool John Moores University, Liverpool, UK
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25
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Martinez SE, Pandey AV, Perez Jimenez TE, Zhu Z, Court MH. Pharmacogenomics of poor drug metabolism in greyhounds: Canine P450 oxidoreductase genetic variation, breed heterogeneity, and functional characterization. PLoS One 2024; 19:e0297191. [PMID: 38300925 PMCID: PMC10833530 DOI: 10.1371/journal.pone.0297191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/31/2023] [Indexed: 02/03/2024] Open
Abstract
Greyhounds metabolize cytochrome P450 (CYP) 2B11 substrates more slowly than other dog breeds. However, CYP2B11 gene variants associated with decreased CYP2B11 expression do not fully explain reduced CYP2B11 activity in this breed. P450 oxidoreductase (POR) is an essential redox partner for all CYPs. POR protein variants can enhance or repress CYP enzyme function in a CYP isoform and substrate dependent manner. The study objectives were to identify POR protein variants in greyhounds and determine their effect on coexpressed CYP2B11 and CYP2D15 enzyme function. Gene sequencing identified two missense variants (Glu315Gln and Asp570Glu) forming four alleles, POR-H1 (reference), POR-H2 (570Glu), POR-H3 (315Gln, 570Glu) and POR-H4 (315Gln). Out of 68 dog breeds surveyed, POR-H2 was widely distributed across multiple breeds, while POR-H3 was largely restricted to greyhounds and Scottish deerhounds (35% allele frequencies), and POR-H4 was rare. Three-dimensional protein structure modelling indicated significant effects of Glu315Gln (but not Asp570Glu) on protein flexibility through loss of a salt bridge between Glu315 and Arg519. Recombinant POR-H1 (reference) and each POR variant (H2-H4) were expressed alone or with CYP2B11 or CYP2D15 in insect cells. No substantial effects on POR protein expression or enzyme activity (cytochrome c reduction) were observed for any POR variant (versus POR-H1) when expressed alone or with CYP2B11 or CYP2D15. Furthermore, there were no effects on CYP2B11 or CYP2D15 protein expression, or on CYP2D15 enzyme kinetics by any POR variant (versus POR-H1). However, Vmax values for 7-benzyloxyresorufin, propofol and bupropion oxidation by CYP2B11 were significantly reduced by coexpression with POR-H3 (by 34-37%) and POR-H4 (by 65-72%) compared with POR-H1. Km values were unaffected. Our results indicate that the Glu315Gln mutation (common to POR-H3 and POR-H4) reduces CYP2B11 enzyme function without affecting at least one other major canine hepatic P450 (CYP2D15). Additional in vivo studies are warranted to confirm these findings.
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Affiliation(s)
- Stephanie E. Martinez
- Pharmacogenomics Laboratory, Program in Individualized Medicine (PrIMe), Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Amit V. Pandey
- Pediatric Endocrinology, Diabetology, and Metabolism, Department of Biomedical Research, University Children’s Hospital Bern, Switzerland and Translational Hormone Research Program, University of Bern, Bern, Switzerland
| | - Tania E. Perez Jimenez
- Pharmacogenomics Laboratory, Program in Individualized Medicine (PrIMe), Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Zhaohui Zhu
- Pharmacogenomics Laboratory, Program in Individualized Medicine (PrIMe), Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Michael H. Court
- Pharmacogenomics Laboratory, Program in Individualized Medicine (PrIMe), Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
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26
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Moretti R, Massimello G, Chessa S, Sartore S, Tranchero A, Profiti M, Sacchi P. Allele and genotype frequencies for primary hereditary cataract, multifocal retinopathy 1, and degenerative myelopathy in Pyrenean Mountain dog from Italy. Top Companion Anim Med 2024; 58:100844. [PMID: 38081509 DOI: 10.1016/j.tcam.2023.100844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
Pyrenean Mountain Dog (PMD) is an ancient dog breed firstly described in XIV century in the Pyrenees Region and nowadays diffused both in Europe and in the US. Hereditary Cataract (HC), defined as the inherited opacity of the lens, involves clinical signs ranging from reduced vision to glaucoma. A molecular basis of HC was firstly described in Staffordshire Bull Terriers and then reported in multiple canine breeds. The HC-associated variation is a single nucleotide deletion in HSF4 gene that introduces a premature stop codon (c.962del, p.Ala321*). Multifocal Retinopathy 1 (MR) is an ocular disorder characterized by multiple areas of retinal degeneration, caused in various dog breeds (including PMD) by a single nucleotide variant (SNV) in BEST1 gene that generates a premature stop codon (c.73G>A, p.Arg25*). Degenerative Myelopathy (DM) is an adult-onset, progressive neurodegenerative disease and it is associated to a SNV in SOD1 gene causing a change in aminoacidic sequence of the protein (c.118G>A, p.Glu40Lys). This causative variant has been described in various dog breeds, including PMD. Aim of this study was to determine the allele frequencies for the abovementioned three genetic diseases in the Italian breeding PMD population. The survey found no dogs carrying the allele (deletion) associated with HC, while three dogs (6 %) were heterozygous (G/A) for the MR-associated variant, and seven dogs (13 %) were heterozygous (G/A) for the DM-associated alteration, indicating that the variant alleles frequency were 0 %, 3 %, and 7 %, respectively. Appropriate mating management is suggested for the prevention of genetic diseases spreading in the PMD population.
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Affiliation(s)
- R Moretti
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, Grugliasco TO 10095 Italy
| | | | - S Chessa
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, Grugliasco TO 10095 Italy.
| | - S Sartore
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, Grugliasco TO 10095 Italy
| | - A Tranchero
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, Grugliasco TO 10095 Italy
| | - M Profiti
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, Grugliasco TO 10095 Italy
| | - P Sacchi
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, Grugliasco TO 10095 Italy
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27
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Nunney L. The effect of body size and inbreeding on cancer mortality in breeds of the domestic dog: a test of the multi-stage model of carcinogenesis. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231356. [PMID: 38298404 PMCID: PMC10827441 DOI: 10.1098/rsos.231356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Cancer is a leading cause of death in domestic dogs. Deaths due to cancer vary widely among breeds, providing an opportunity for testing the multi-stage model of carcinogenesis. This model underpins evolutionary and basic studies of cancer suppression and predicts a linear increase in cancer with breed size, an expectation complicated by bigger breeds having a shorter lifespan (decreasing risk). Using three independent datasets, the weight and lifespan of breeds provided a good fit of lifetime cancer mortality to the multi-stage model, the fit suggesting many canine cancers are initiated by four driver mutations. Of 85 breeds in more than one dataset, only flat-coated retriever showed significantly elevated cancer mortality, with Scottish terrier, Bernese mountain dog and bullmastiff also showing notable risk (greater than 50% over expected). Analysis of breed clades suggested terriers experience elevated cancer mortality. There was no evidence that the lower mass-specific metabolic rate of larger breeds reduced cancer risk. Residuals indicated increased breed inbreeding shortened expected lifespan, but had no overall effect on cancer mortality. The results provide a baseline for identifying increased breed risk for specific cancers and demonstrate that, unless selection promotes increased cancer suppression, the evolution of larger longer-lived animals leads to a predictable increased cancer risk.
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Affiliation(s)
- Leonard Nunney
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
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28
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Howard CM, Anderson S, Harrington B. Characterization of CD3+/CD20+ canine large-cell lymphoma. J Vet Diagn Invest 2024; 36:86-94. [PMID: 37837199 PMCID: PMC10734595 DOI: 10.1177/10406387231204873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023] Open
Abstract
Immunophenotyping of canine large-cell lymphoma (LCL) for B-cell and T-cell surface antigens is commonly performed to better predict the clinical outcome. Expression of surface antigen CD3 is associated with T-cell malignancies; surface antigen CD20 is expressed on B cells. However, a small subset of canine LCLs expresses both CD3 and CD20 (CD3+/CD20+); this form of lymphoma remains poorly defined at the molecular level. In a retrospective study, we aimed to better characterize immunophenotypic properties and antigen receptor clonality of CD3+/CD20+ LCL. We selected formalin-fixed, paraffin-embedded tissues from 10 cases of CD3+/CD20+ LCL and breed-matched controls of peripheral large T-cell lymphoma (PTCL) and diffuse large B-cell lymphoma (DLBCL). Using PCR for antigen receptor rearrangement (PARR), we identified monoclonal T-cell receptor gamma (TCRγ) rearrangements in all CD3+/CD20+ cases. Three of 10 cases had monoclonal rearrangements in the immunoglobulin heavy chain (IgH), supportive of cross-lineage rearrangement. There was no significant difference in the frequency of antigen receptor rearrangement between CD3+/CD20+ and PTCL cases. In comparison with DLBCL, CD3+/CD20+ LCL had TCRγ rearrangement more frequently and IgH rearrangement less frequently, respectively. Immunolabeling of the B-cell marker PAX5 occurred less frequently in all CD3+/CD20+ LCL cases compared to the DLBCL controls. Immunolabeling for BCL-2 was robust, regardless of immunophenotype. Nuclear Ki67 positivity was variable in CD3+/CD20+ cases, indicating a heterogeneity in proliferation. Overall, cases of canine CD3+/CD20+ LCL had properties similar to PTCL, suggesting a similar histogenesis of these 2 subsets.
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Affiliation(s)
- Cory M. Howard
- Department of Pathobiology and Diagnostic Investigation, Michigan State University College of Veterinary Medicine, East Lansing, MI, USA
- Michigan State University Veterinary Diagnostic Laboratory, Lansing, MI, USA
| | - Steffanie Anderson
- Michigan State University Veterinary Diagnostic Laboratory, Lansing, MI, USA
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29
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Clark JA, Anderson H, Donner J, Pearce-Kelling S, Ekenstedt KJ. Global Frequency Analyses of Canine Progressive Rod-Cone Degeneration-Progressive Retinal Atrophy and Collie Eye Anomaly Using Commercial Genetic Testing Data. Genes (Basel) 2023; 14:2093. [PMID: 38003037 PMCID: PMC10671078 DOI: 10.3390/genes14112093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Hundreds of genetic variants associated with canine traits and disorders have been identified, with commercial tests offered. However, the geographic distributions and changes in allele and genotype frequencies over prolonged, continuous periods of time are lacking. This study utilized a large set of genotypes from dogs tested for the progressive rod-cone degeneration-progressive retinal atrophy (prcd-PRA) G>A missense PRCD variant (n = 86,667) and the collie eye anomaly (CEA)-associated NHEJ1 deletion (n = 33,834) provided by the commercial genetic testing company (Optigen/Wisdom Panel, Mars Petcare Science & Diagnostics). These data were analyzed using the chi-square goodness-of-fit test, time-trend graphical analysis, and regression modeling in order to evaluate how test results changed over time. The results span fifteen years, representing 82 countries and 67 breeds/breed mixes. Both diseases exhibited significant differences in genotype frequencies (p = 2.7 × 10-152 for prcd-PRA and 0.023 for CEA) with opposing graphical trends. Regression modeling showed time progression to significantly affect the odds of a dog being homozygous or heterozygous for either disease, as do variables including breed and breed popularity. This study shows that genetic testing informed breeding decisions to produce fewer affected dogs. However, the presence of dogs homozygous for the disease variant, especially for prcd-PRA, was still observed fourteen years after test availability, potentially due to crosses of unknown carriers. This suggests that genetic testing of dog populations should continue.
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Affiliation(s)
- Jessica A. Clark
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA;
| | - Heidi Anderson
- Wisdom Panel, Mars Petcare Science & Diagnostics, 00581 Helsinki, Finland; (H.A.); (J.D.)
| | - Jonas Donner
- Wisdom Panel, Mars Petcare Science & Diagnostics, 00581 Helsinki, Finland; (H.A.); (J.D.)
| | | | - Kari J. Ekenstedt
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA;
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30
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José-López R. Chemotherapy for the treatment of intracranial glioma in dogs. Front Vet Sci 2023; 10:1273122. [PMID: 38026627 PMCID: PMC10643662 DOI: 10.3389/fvets.2023.1273122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Gliomas are the second most common primary brain tumor in dogs and although they are associated with a poor prognosis, limited data are available relating to the efficacy of standard therapeutic options such as surgery, radiation and chemotherapy. Additionally, canine glioma is gaining relevance as a naturally occurring animal model that recapitulates human disease with fidelity. There is an intense comparative research drive to test new therapeutic approaches in dogs and assess if results translate efficiently into human clinical trials to improve the poor outcomes associated with the current standard-of-care. However, the paucity of data and controversy around most appropriate treatment for intracranial gliomas in dogs make comparisons among modalities troublesome. To further inform therapeutic decision-making, client discussion, and future studies evaluating treatment responses, the outcomes of 127 dogs with intracranial glioma, either presumed (n = 49) or histologically confirmed (n = 78), that received chemotherapy as leading or adjuvant treatment are reviewed here. This review highlights the status of current chemotherapeutic approaches to intracranial gliomas in dogs, most notably temozolomide and lomustine; areas of novel treatment currently in development, and difficulties to consensuate and compare different study observations. Finally, suggestions are made to facilitate evidence-based research in the field of canine glioma therapeutics.
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Affiliation(s)
- Roberto José-López
- Hamilton Specialist Referrals – IVC Evidensia, High Wycombe, United Kingdom
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31
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Yang IS, Jang I, Yang JO, Choi J, Kim MS, Kim KK, Seung BJ, Cheong JH, Sur JH, Nam H, Lee B, Kim J, Kim S. CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris). BMC Genomics 2023; 24:613. [PMID: 37828501 PMCID: PMC10571338 DOI: 10.1186/s12864-023-09655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and transcripts for dogs is relatively incomplete. RESULTS We developed CanISO, a new database to hold a large collection of transcriptome profiles and genomic variations for domestic dogs. CanISO provides 87,692 novel transcript isoforms and 60,992 known isoforms from whole transcriptome sequencing of canine tumors (N = 157) and their matched normal tissues (N = 64). CanISO also provides genomic variation information for 210,444 unique germline single nucleotide polymorphisms (SNPs) from the whole exome sequencing of 183 dogs, with a query system that searches gene- and transcript-level information as well as covered SNPs. Transcriptome profiles can be compared with corresponding human transcript isoforms at a tissue level, or between sample groups to identify tumor-specific gene expression and alternative splicing patterns. CONCLUSIONS CanISO is expected to increase understanding of the dog genome and transcriptome, as well as its functional associations with humans, such as shared/distinct mechanisms of cancer. CanISO is publicly available at https://www.kobic.re.kr/caniso/ .
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Affiliation(s)
- In Seok Yang
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Insu Jang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Jin Ok Yang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Jinhyuk Choi
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Min-Seo Kim
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Ka-Kyung Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Byung-Joon Seung
- Department of Veterinary Pathology, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Korea
| | - Jae-Ho Cheong
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Jung-Hyang Sur
- Department of Veterinary Pathology, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Korea
| | - Hojung Nam
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Korea
| | - Byungwook Lee
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea.
| | - Junho Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea.
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32
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Soh PXY, Khatkar MS, Williamson P. Lymphoma in Border Collies: Genome-Wide Association and Pedigree Analysis. Vet Sci 2023; 10:581. [PMID: 37756103 PMCID: PMC10536503 DOI: 10.3390/vetsci10090581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
There has been considerable interest in studying cancer in dogs and its potential as a model system for humans. One area of research has been the search for genetic risk variants in canine lymphoma, which is amongst the most common canine cancers. Previous studies have focused on a limited number of breeds, but none have included Border Collies. The aims of this study were to identify relationships between Border Collie lymphoma cases through an extensive pedigree investigation and to utilise relationship information to conduct genome-wide association study (GWAS) analyses to identify risk regions associated with lymphoma. The expanded pedigree analysis included 83,000 Border Collies, with 71 identified lymphoma cases. The analysis identified affected close relatives, and a common ancestor was identified for 54 cases. For the genomic study, a GWAS was designed to incorporate lymphoma cases, putative "carriers", and controls. A case-control GWAS was also conducted as a comparison. Both analyses showed significant SNPs in regions on chromosomes 18 and 27. Putative top candidate genes from these regions included DLA-79, WNT10B, LMBR1L, KMT2D, and CCNT1.
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Affiliation(s)
- Pamela Xing Yi Soh
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia;
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Mehar Singh Khatkar
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia;
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA 5371, Australia
| | - Peter Williamson
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia;
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia;
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33
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Hansen Wheat C, Larsson L, Berner P, Temrin H. Commentary by Gácsi et al. (2023) highlights general misconceptions within the field of dog domestication and dog-wolf comparisons. Ecol Evol 2023; 13:e10466. [PMID: 37736276 PMCID: PMC10509154 DOI: 10.1002/ece3.10466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 08/18/2023] [Indexed: 09/23/2023] Open
Affiliation(s)
| | - Linn Larsson
- Department of ZoologyStockholm UniversityStockholmSweden
| | | | - Hans Temrin
- Department of ZoologyStockholm UniversityStockholmSweden
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34
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Meadows JRS, Kidd JM, Wang GD, Parker HG, Schall PZ, Bianchi M, Christmas MJ, Bougiouri K, Buckley RM, Hitte C, Nguyen AK, Wang C, Jagannathan V, Niskanen JE, Frantz LAF, Arumilli M, Hundi S, Lindblad-Toh K, Ginja C, Agustina KK, André C, Boyko AR, Davis BW, Drögemüller M, Feng XY, Gkagkavouzis K, Iliopoulos G, Harris AC, Hytönen MK, Kalthoff DC, Liu YH, Lymberakis P, Poulakakis N, Pires AE, Racimo F, Ramos-Almodovar F, Savolainen P, Venetsani S, Tammen I, Triantafyllidis A, vonHoldt B, Wayne RK, Larson G, Nicholas FW, Lohi H, Leeb T, Zhang YP, Ostrander EA. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 2023; 24:187. [PMID: 37582787 PMCID: PMC10426128 DOI: 10.1186/s13059-023-03023-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/25/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. RESULTS We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. CONCLUSIONS We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
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Affiliation(s)
- Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA.
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Katia Bougiouri
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Christophe Hitte
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Julia E Niskanen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E14NS, UK and Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, D-80539, Munich, Germany
| | - Meharji Arumilli
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catarina Ginja
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | | | - Catherine André
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Xin-Yao Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Konstantinos Gkagkavouzis
- Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Giorgos Iliopoulos
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Alexander C Harris
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Daniela C Kalthoff
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Petros Lymberakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Nikolaos Poulakakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | | | - Peter Savolainen
- Department of Gene Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, 17121, Solna, Sweden
| | - Semina Venetsani
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Imke Tammen
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Alexandros Triantafyllidis
- Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-7246, USA
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK
| | - Frank W Nicholas
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.
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Li WL, Liu YH, Li JX, Ding MT, Adeola AC, Isakova J, Aldashev AA, Peng MS, Huang X, Xie G, Chen X, Yang WK, Zhou WW, Ghanatsaman ZA, Olaogun SC, Sanke OJ, Dawuda PM, Hytönen MK, Lohi H, Esmailizadeh A, Poyarkov AD, Savolainen P, Wang GD, Zhang YP. Multiple Origins and Genomic Basis of Complex Traits in Sighthounds. Mol Biol Evol 2023; 40:msad158. [PMID: 37433053 PMCID: PMC10401622 DOI: 10.1093/molbev/msad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/13/2023] Open
Abstract
Sighthounds, a distinctive group of hounds comprising numerous breeds, have their origins rooted in ancient artificial selection of dogs. In this study, we performed genome sequencing for 123 sighthounds, including one breed from Africa, six breeds from Europe, two breeds from Russia, and four breeds and 12 village dogs from the Middle East. We gathered public genome data of five sighthounds and 98 other dogs as well as 31 gray wolves to pinpoint the origin and genes influencing the morphology of the sighthound genome. Population genomic analysis suggested that sighthounds originated from native dogs independently and were comprehensively admixed among breeds, supporting the multiple origins hypothesis of sighthounds. An additional 67 published ancient wolf genomes were added for gene flow detection. Results showed dramatic admixture of ancient wolves in African sighthounds, even more than with modern wolves. Whole-genome scan analysis identified 17 positively selected genes (PSGs) in the African population, 27 PSGs in the European population, and 54 PSGs in the Middle Eastern population. None of the PSGs overlapped in the three populations. Pooled PSGs of the three populations were significantly enriched in "regulation of release of sequestered calcium ion into cytosol" (gene ontology: 0051279), which is related to blood circulation and heart contraction. In addition, ESR1, JAK2, ADRB1, PRKCE, and CAMK2D were under positive selection in all three selected groups. This suggests that different PSGs in the same pathway contributed to the similar phenotype of sighthounds. We identified an ESR1 mutation (chr1: g.42,177,149 T > C) in the transcription factor (TF) binding site of Stat5a and a JAK2 mutation (chr1: g.93,277,007 T > A) in the TF binding site of Sox5. Functional experiments confirmed that the ESR1 and JAK2 mutation reduced their expression. Our results provide new insights into the domestication history and genomic basis of sighthounds.
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Affiliation(s)
- Wu-Lue Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jin-Xiu Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Meng-Ting Ding
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Jainagul Isakova
- Laboratory of Molecular and Cell Biology, Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan
| | - Almaz A Aldashev
- Laboratory of Molecular and Cell Biology, Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Xuezhen Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Guoli Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei-Kang Yang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zeinab Amiri Ghanatsaman
- Animal Science Research Department, Fars Agricultural and Natural Resources research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran
| | - Sunday C Olaogun
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oscar J Sanke
- Ministry of Agriculture and Natural Resources, Taraba State Government, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Animal Science, Faculty of Agriculture, National University of Lesotho, Roma, Southern Africa
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Andrey D Poyarkov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Science, Moscow, Russia
| | - Peter Savolainen
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, Solna, Sweden
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
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Bionda A, Cortellari M, Liotta L, Crepaldi P. The Shepherd and the Hunter: A Genomic Comparison of Italian Dog Breeds. Animals (Basel) 2023; 13:2438. [PMID: 37570247 PMCID: PMC10417656 DOI: 10.3390/ani13152438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Shepherd and hunting dogs have undergone divergent selection for specific tasks, resulting in distinct phenotypic and behavioural differences. Italy is home to numerous recognized and unrecognized breeds of both types, providing an opportunity to compare them genomically. In this study, we analysed SNP data obtained from the CanineHD BeadChip, encompassing 116 hunting dogs (representing 6 breeds) and 158 shepherd dogs (representing 9 breeds). We explored the population structure, genomic background, and phylogenetic relationships among the breeds. To compare the two groups, we employed three complementary methods for selection signature detection: FST, XP-EHH, and ROH. Our results reveal a clear differentiation between shepherd and hunting dogs as well as between gun dogs vs. hounds and guardian vs. herding shepherd dogs. The genomic regions distinguishing these groups harbour several genes associated with domestication and behavioural traits, including gregariousness (WBSRC17) and aggressiveness (CDH12 and HTT). Additionally, genes related to morphology, such as size and coat colour (ASIP and TYRP1) and texture (RSPO2), were identified. This comparative genomic analysis sheds light on the genetic underpinnings of the phenotypic and behavioural variations observed in Italian hunting and shepherd dogs.
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Affiliation(s)
- Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
| | - Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, University of Messina, Viale Palatucci 13, 98168 Messina, Italy;
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
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O'Neill DG, McMillan KM, Church DB, Brodbelt DC. Dog breeds and conformations in the UK in 2019: VetCompass canine demography and some consequent welfare implications. PLoS One 2023; 18:e0288081. [PMID: 37494312 PMCID: PMC10370710 DOI: 10.1371/journal.pone.0288081] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
INTRODUCTION Growing concerns over health and welfare impacts from extreme phenotypes in dogs have created an urgent need for reliable demographic information on the national breed structures of dogs. METHODS This study included all dogs under primary veterinary care in the UK during 2019 at practices participating in VetCompass. Demographic data on these dogs were analysed to report on the frequency of common breeds and also to report on conformation, bodyweight, sex and neuter associations with these breeds. RESULTS The study included 2,237,105 dogs under UK veterinary care in 2019. Overall, 69.4% (n = 1,551,462) were classified as purebred, 6.7% (149,308) as designer-crossbred and 24.0% (536,335) as nondesigner-crossbred. Across 800 unique breed names, the most frequent breeds at any age were nondesigner-crossbred (n = 536,335, 24.0%), Labrador Retriever (154,222, 6.9%) and Jack Russell Terrier (101,294, 4.5%). Among 229,624 (10.3%) dogs aged under one year, the most frequent breeds were nondesigner-crossbred (n = 45,995, 20.0%), French Bulldog (16,036, 7.0%) and Cockapoo (14,321, 6.2%). Overall, based on breed characteristics, 17.6% (395,739) were classified as brachycephalic, 43.1% (969,403) as mesaticephalic and 8.3% (186,320) as dolichocephalic. Of 1,551,336 dogs that were classifiable based on breed, 52.6% (815,673) were chondrodystrophic. Of 1,462,925 dogs that were classifiable, there were 54.6% (n = 798,426) short haired, 32.6% (476,883) medium haired and 12.8% (186,934) long haired. Of 1,547,653 dogs that were classifiable for ear carriage, 24.5% (n = 379,581) were erect, 28.1% (434,273) were semi-erect, 19.7% (305,475) were v-shaped drop and 27.7% (428,324) were pendulous. Overall, there was a 1.09:1.00 ratio of male (n = 1,163,512; 52.2%) to female dogs (n = 1,067,552; 47.8%). CONCLUSIONS Health and welfare issues linked to popular breeds with extreme phenotypes suggest that there is much work to do to help owners to make more welfare-friendly decisions when choosing which type of dog to own.
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Affiliation(s)
- Dan G O'Neill
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Kirsten M McMillan
- DataSEA (Science, Engineering & Analytics), Research Team, Strategy & Transformation, Dogs Trust, London, United Kingdom
| | - David B Church
- Clinical Science and Services, The Royal Veterinary College, Hatfield, United Kingdom
| | - Dave C Brodbelt
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
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Caddiell RMP, Cunningham RM, White PA, Lascelles BDX, Gruen ME. Pain sensitivity differs between dog breeds but not in the way veterinarians believe. FRONTIERS IN PAIN RESEARCH 2023; 4:1165340. [PMID: 37435196 PMCID: PMC10332458 DOI: 10.3389/fpain.2023.1165340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/08/2023] [Indexed: 07/13/2023] Open
Abstract
Background Veterinarians hold distinct breed-specific pain sensitivity beliefs that differ from the general public but are highly consistent with one another. This is remarkable as there is no current scientific evidence for biological differences in pain sensitivity across dog breeds. Therefore, the present study evaluated whether pain sensitivity thresholds differ across a set of dog breeds and, if so, whether veterinarians' pain sensitivity ratings explain these differences or whether these ratings are attributed to behavioral characteristics. Methods Pain sensitivity thresholds [using quantitative sensory testing (QST) methods] and canine behaviors (using owner questionnaires and emotional reactivity tests) were prospectively measured across selected dog breeds. Adult, healthy dogs from 10 dog breeds/breed types were recruited, representing breeds subjectively rated by veterinarians as high (chihuahua, German shepherd, Maltese, Siberian husky), average (border collie, Boston terrier, Jack Russell terrier), or low (golden retriever, pitbull, Labrador retriever) pain sensitivity. A final sample of 149 dogs was included in statistical analyses. Results Veterinarians' pain sensitivity ratings provided a minimal explanation for pain sensitivity thresholds measured using QST in dogs; however, dog breeds did differ in their pain sensitivity thresholds across the QST methods evaluated. Breed differences were observed for some aspects of emotional reactivity tests; however, these behavioral differences did not explain the differences in pain sensitivity thresholds found. Veterinarians' pain sensitivity ratings were positively associated with dog approach scores for the disgruntled stranger test suggesting that the way dogs greet strangers may be a factor influencing veterinarians' ratings of pain sensitivity across dog breeds. Conclusions and clinical relevance Overall, these findings highlight a need to investigate biological mechanisms that may explain breed differences in pain sensitivity because this may inform pain management recommendations. Further, future research should focus on when and how these breed-specific pain sensitivity beliefs developed in veterinarians, as veterinarians' beliefs could impact the recognition and treatment of pain for canine patients.
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Affiliation(s)
- Rachel M. P. Caddiell
- Comparative Behavioral Research, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Translational Research in Pain, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Rachael M. Cunningham
- Comparative Behavioral Research, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Translational Research in Pain, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Philip A. White
- Department of Statistics, College of Physical and Mathematical Sciences, Brigham Young University, Provo, UT, United States
| | - B. Duncan X. Lascelles
- Translational Research in Pain, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Comparative Pain Research and Education Center, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Thurston Arthritis Centre, UNC School of Medicine, Chapel Hill, NC, United States
- Center for Translational Pain Research, Department of Anesthesiology, Duke University, Durham, NC, United States
| | - Margaret E. Gruen
- Comparative Behavioral Research, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Comparative Pain Research and Education Center, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
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Churakov G, Kuritzin A, Chukharev K, Zhang F, Wünnemann F, Ulyantsev V, Schmitz J. A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees. Syst Biol 2023; 72:649-661. [PMID: 36688484 DOI: 10.1093/sysbio/syac082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/04/2022] [Accepted: 12/23/2022] [Indexed: 01/24/2023] Open
Abstract
Retrophylogenomics makes use of genome-wide retrotransposon presence/absence insertion patterns to resolve questions in phylogeny and population genetics. In the genomics era, evaluating high-throughput data requires the associated development of appropriately powerful statistical tools. The currently used KKSC 3-lineage statistical test for estimating the significance of retrophylogenomic data is limited by the number of possible tree topologies it can assess in one step. To improve on this, we have extended the analysis to simultaneously compare four lineages, enabling us to evaluate ten distinct presence/absence insertion patterns for 26 possible tree topologies plus 129 trees with different incidences of hybridization or introgression. The new tool provides statistics for cases involving multiple ancestral hybridizations/introgressions, ancestral incomplete lineage sorting, bifurcation, and polytomy. The test is embedded in a user-friendly web R application (http://retrogenomics.uni-muenster.de:3838/hammlet/) and is available for use by the scientific community. [ancestral hybridization/introgression; ancestral incomplete lineage sorting (ILS); empirical distribution; KKSC-statistics; 4-lineage (4-LIN) insertion polymorphism; polytomy; retrophylogenomics.].
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Affiliation(s)
- Gennady Churakov
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
- Department of Biochemistry, Institute of Experimental Medicine, St. Petersburg, Russia
| | - Andrej Kuritzin
- Department of System Analysis, Saint Petersburg State Institute of Technology, St. Petersburg, Russia
| | - Konstantin Chukharev
- Information Technologies, Mechanics and Optics, University Saint Petersburg, St. Petersburg, Russia
| | - Fengjun Zhang
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
| | - Florian Wünnemann
- Institute for Computational Biomedicine, University Heidelberg, Heidelberg, Germany
| | - Vladimir Ulyantsev
- Information Technologies, Mechanics and Optics, University Saint Petersburg, St. Petersburg, Russia
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
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Ahn B, Kang M, Jeon H, Kim JS, Jiang H, Ha J, Park C. Origin and population structure of native dog breeds in the Korean peninsula and East Asia. iScience 2023; 26:106982. [PMID: 37378348 PMCID: PMC10291505 DOI: 10.1016/j.isci.2023.106982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/13/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
To study the ancestry and phylogenetic relationships of native Korean dog breeds to other Asian dog populations, we analyzed nucleotide variations in whole-genome sequences of 205 canid individuals. Sapsaree, Northern Chinese indigenous dog, and Tibetan Mastiff were largely related to West Eurasian ancestry. Jindo, Donggyeongi, Shiba, Southern Chinese indigenous (SCHI), Vietnamese indigenous dogs (VIET), and Indonesian indigenous dogs were related to Southeast and East Asian ancestry. Among East Asian dog breeds, Sapsaree presented the highest haplotype sharing with German Shepherds, indicating ancient admixture of European ancestry to modern East Asian dog breeds. SCHI showed greater haplotype sharing with New Guinea singing dogs, VIET, and Jindo than with other Asian breeds. The predicted divergence time of East Asian populations from their common ancestor was approximately 2,000 to 11,000 years ago. Our results expand understanding of the genetic history of dogs in the Korean peninsula to the Asian continent and Oceanic region.
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Affiliation(s)
- Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jong-Seok Kim
- Department of Korean Jindo and Domestic Animal, Jindo 58927, Republic of Korea
| | - Hao Jiang
- College of Animal Science, Jilin University, Changchun, Jilin 130119, China
| | - Jihong Ha
- Korean Sapsaree Foundation, Gyeongsan 38412, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
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Dobos P, Pongrácz P. Would You Detour with Me? Association between Functional Breed Selection and Social Learning in Dogs Sheds Light on Elements of Dog-Human Cooperation. Animals (Basel) 2023; 13:2001. [PMID: 37370511 DOI: 10.3390/ani13122001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Interspecific social learning is a main synchronizing mechanism that enables dogs to adapt to the anthropogenic niche. It is not known whether dogs in general possess the capacity of learning from humans or whether more recent selective events have affected their ability to learn from humans. We hypothesized that cooperative and independent working dog breeds may behave differently in a social learning task. Dogs (N = 78 from 16 cooperative and 18 independent breeds) had to detour a transparent, V-shaped wire mesh fence. The experiment consisted of three one-minute-long trials. The control condition did not include a demonstration. In the demonstration condition, the experimenter placed a reward in the inside corner by walking around the fence. Cooperative dogs reached the target significantly faster, while independent dogs did not detour faster in trials 2 and 3 after the human demonstration. Detour latencies were not associated with the keeping conditions and training level of the subjects. As we assembled both test groups from several genetically distantly related breeds, we can exclude the explanation that higher cooperativity emerged only in particular clades of dogs; instead, functional selection for particular working tasks could enhance capacities that affect a wide range of socio-cognitive traits in dogs.
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Affiliation(s)
- Petra Dobos
- Department of Ethology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary
| | - Péter Pongrácz
- Department of Ethology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary
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Li Z, Wang Z, Chen Z, Voegeli H, Lichtman JH, Smith P, Liu J, DeWan AT, Hoh J. Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds. BMC Genomics 2023; 24:302. [PMID: 37277710 DOI: 10.1186/s12864-023-09390-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND In light of previous studies that profiled breed-specific traits or used genome-wide association studies to refine loci associated with characteristic morphological features in dogs, the field has gained tremendous genetic insights for known dog traits observed among breeds. Here we aim to address the question from a reserve perspective: whether there are breed-specific genotypes that may underlie currently unknown phenotypes. This study provides a complete set of breed-specific genetic signatures (BSGS). Several novel BSGS with significant protein-altering effects were highlighted and validated. RESULTS Using the next generation whole-genome sequencing technology coupled with unsupervised machine learning for pattern recognitions, we constructed and analyzed a high-resolution sequence map for 76 breeds of 412 dogs. Genomic structures including novel single nucleotide polymorphisms (SNPs), SNP clusters, insertions, deletions (INDELs) and short tandem repeats (STRs) were uncovered mutually exclusively among breeds. We also partially validated some novel nonsense variants by Sanger sequencing with additional dogs. Four novel nonsense BSGS were found in the Bernese Mountain Dog, Samoyed, Bull Terrier, and Basset Hound, respectively. Four INDELs resulting in either frame-shift or codon disruptions were found in the Norwich Terrier, Airedale Terrier, Chow Chow and Bernese Mountain Dog, respectively. A total of 15 genomic regions containing three types of BSGS (SNP-clusters, INDELs and STRs) were identified in the Akita, Alaskan Malamute, Chow Chow, Field Spaniel, Keeshond, Shetland Sheepdog and Sussex Spaniel, in which Keeshond and Sussex Spaniel each carried one amino-acid changing BSGS in such regions. CONCLUSION Given the strong relationship between human and dog breed-specific traits, this study might be of considerable interest to researchers and all. Novel genetic signatures that can differentiate dog breeds were uncovered. Several functional genetic signatures might indicate potentially breed-specific unknown phenotypic traits or disease predispositions. These results open the door for further investigations. Importantly, the computational tools we developed can be applied to any dog breeds as well as other species. This study will stimulate new thinking, as the results of breed-specific genetic signatures may offer an overarching relevance of the animal models to human health and disease.
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Affiliation(s)
- Zicheng Li
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA.
| | - Zuoheng Wang
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Zhiyuan Chen
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Heidi Voegeli
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Judith H Lichtman
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Peter Smith
- Department of Comparative Medicine, School of Medicine, Yale University, New Haven, CT, 06510, USA
| | - Ju Liu
- Medical Research Center, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, 16766 Jingshi Road, Jinan, Shandong, 250014, China
| | - Andrew T DeWan
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA
- Center for Perinatal Pediatric and Environmental Epidemiology, Yale University, New Haven, CT, 06510, USA
| | - Josephine Hoh
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA.
- Department of Ophthalmology and Visual Science, School of Medicine, Yale University, New Haven, CT, 06510, USA.
- Department of Applied Mathematics, Yale University, New Haven, CT, 06510, USA.
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Zapata I, Eyre AW, Alvarez CE. Psychological Stress Is Associated with Increased Cancer Risk in Dogs. Animals (Basel) 2023; 13:1869. [PMID: 37889770 PMCID: PMC10251977 DOI: 10.3390/ani13111869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 10/29/2023] Open
Abstract
Although there is evidence that psychological stress may be associated with increased cancer risk, the effect of stress on cancer risk is difficult to study, both in humans, due to socioeconomic factors, and in animal models, due to questionable biological relevance. Here, we test whether heritable canine temperament that increases psychological stress is associated with cancer risk. The study data are breed-specific averages of incidences of multiple cancer types and of temperament classes. The latter are derived from a latent class analysis of behavioral questionnaires completed by owners (C-BARQ). We thus classified the dogs according to whether they are calm vs. reactive within and across breeds. Using meta-analysis approaches, we modeled the risk of multiple cancer types in calm vs. reactive dogs. We adjusted for breed averages of body mass and lifespan, which are common confounders that impact cancer. Our study confirms that body size has a significant effect of on risk of multiple types of cancers in dogs and shows for the first time that temperament also has a moderate effect. These findings suggest dog models of heritable psychological stress are suitable for molecular epidemiological and translational studies on its effects on cancer risk.
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Affiliation(s)
- Isain Zapata
- Department of Biomedical Sciences, Rocky Vista University College of Osteopathic Medicine, Englewood, CO 80112, USA
| | | | - Carlos E Alvarez
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- Department of Veterinary Clinical Sciences, The Ohio State University College of Veterinary Medicine, Columbus, OH 43210, USA
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Salonen M, Mikkola S, Niskanen JE, Hakanen E, Sulkama S, Puurunen J, Lohi H. Breed, age, and social environment are associated with personality traits in dogs. iScience 2023; 26:106691. [PMID: 37168553 PMCID: PMC10165416 DOI: 10.1016/j.isci.2023.106691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 05/13/2023] Open
Abstract
Personality in pets and other domesticated animals is important for their well-being and it can also influence human-animal relationships. Genetic and environmental factors influencing unwanted behavior in dogs are somewhat well known, but the factors influencing dog personality remain understudied. Here we examined environmental and demographic factors associated with seven broad personality traits in a survey of over 11,000 dogs. We utilized linear models and extensive model validation to examine the factors that have the most significant influences on personality and calculated effect sizes to assess the importance of these variables. Breed and age had the strongest associations with dog personality traits. Some environmental factors, especially puppyhood socialization, were also associated with personality. All factors had small effect sizes, highlighting that a lot of variation in personality remains unexplained. Our results indicate that personality traits are complex and strikingly similar in dogs, humans, and other nonhuman animals.
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Affiliation(s)
- Milla Salonen
- Department of Medical and Clinical Genetics, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Folkhälsan Research Center, Uusimaa, 00290 Helsinki, Finland
- Department of Biology, University of Turku, Turku, 20014 Southwest Finland, Finland
- Corresponding author
| | - Salla Mikkola
- Department of Medical and Clinical Genetics, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Folkhälsan Research Center, Uusimaa, 00290 Helsinki, Finland
| | - Julia E. Niskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Folkhälsan Research Center, Uusimaa, 00290 Helsinki, Finland
| | - Emma Hakanen
- Department of Medical and Clinical Genetics, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Folkhälsan Research Center, Uusimaa, 00290 Helsinki, Finland
| | - Sini Sulkama
- Department of Medical and Clinical Genetics, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Folkhälsan Research Center, Uusimaa, 00290 Helsinki, Finland
| | - Jenni Puurunen
- Department of Medical and Clinical Genetics, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Folkhälsan Research Center, Uusimaa, 00290 Helsinki, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Uusimaa, 00014 Helsinki, Finland
- Folkhälsan Research Center, Uusimaa, 00290 Helsinki, Finland
- Corresponding author
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45
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Hu G, Do DN, Manafiazar G, Kelvin AA, Sargolzaei M, Plastow G, Wang Z, Miar Y. Population genomics of American mink using genotype data. Front Genet 2023; 14:1175408. [PMID: 37274788 PMCID: PMC10234291 DOI: 10.3389/fgene.2023.1175408] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/14/2023] [Indexed: 06/07/2023] Open
Abstract
Understanding the genetic structure of the target population is critically important to develop an efficient genomic selection program in domestic animals. In this study, 2,973 American mink of six color types from two farms (Canadian Centre for Fur Animal Research (CCFAR), Truro, NS and Millbank Fur Farm (MFF), Rockwood, ON) were genotyped with the Affymetrix Mink 70K panel to compute their linkage disequilibrium (LD) patterns, effective population size (Ne), genetic diversity, genetic distances, and population differentiation and structure. The LD pattern represented by average r 2, decreased to <0.2 when the inter-marker interval reached larger than 350 kb and 650 kb for CCFAR and MFF, respectively, and suggested at least 7,700 and 4,200 single nucleotide polymorphisms (SNPs) be used to obtain adequate accuracy for genomic selection programs in CCFAR and MFF respectively. The Ne for five generations ago was estimated to be 76 and 91 respectively. Our results from genetic distance and diversity analyses showed that American mink of the various color types had a close genetic relationship and low genetic diversity, with most of the genetic variation occurring within rather than between color types. Three ancestral genetic groups was considered the most appropriate number to delineate the genetic structure of these populations. Black (in both CCFAR and MFF) and pastel color types had their own ancestral clusters, while demi, mahogany, and stardust color types were admixed with the three ancestral genetic groups. This study provided essential information to utilize the first medium-density SNP panel for American mink in their genomic studies.
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Affiliation(s)
- Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Ghader Manafiazar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Alyson A. Kelvin
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc, Plain City, OH, United States
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
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46
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Kijan C, Hugen S, Thomas RE, Oberbauer AM, Leegwater PAJ, Fieten H, German AJ, Mandigers PJJ. The Histopathological Characteristic of Gastric Carcinoma in the Belgian Tervueren and Groenendael Dog: A Comparison of Two Classification Methods. Animals (Basel) 2023; 13:ani13091532. [PMID: 37174569 PMCID: PMC10177043 DOI: 10.3390/ani13091532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/27/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
Gastric carcinoma is generally considered to be a rare disease in dogs, carrying a grave prognosis. However, in the Tervueren and Groenendael varieties of the Belgian Shepherd dog breed, the disease is highly prevalent. While histopathology is the gold standard for diagnosing gastric carcinoma, there is no general consensus on the methods for histological classification in these cases. Biopsies of a group of 61 dogs with confirmed gastric carcinoma (45 Tervueren and 16 Groenendael) were examined and classified according to World Health Organization (WHO) and Laurén classifications. Kaplan-Meier curves were used to compare survival between the different subtypes and simple and multiple linear regression were used to analyse the association between age of onset and breed variant, sex, neuter status, location of the tumour, inflammation score, and Laurén and WHO classifications. Mean age at diagnosis was significantly different in Groenendael (10.1 ± 2.01) and Tervueren dogs (8.5 ± 1.90). The Laurén classification resulted in 29 (48%) diffuse- and 32 (52%) intestinal-type tumours. Applying the WHO classification resulted in 30 (49%) tubular carcinoma growth patterns and 31 (51%) others. Median survival time was significantly reduced for the diffuse type as compared to the intestinal type according to the Laurén classification, with the same median survival time results for tubular compared to non-tubular subtypes according to the WHO classification (median survival time of 61 vs. 182 days, respectively). Using the WHO and Lauren classification on tumour biopsies may help the practising clinician in the prognostication of gastric carcinoma in Tervueren and Groenendael dogs.
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Affiliation(s)
- Christina Kijan
- Expertise Centre Genetics, Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Sanne Hugen
- Expertise Centre Genetics, Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Rachel E Thomas
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Anita M Oberbauer
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Peter A J Leegwater
- Expertise Centre Genetics, Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Hille Fieten
- Expertise Centre Genetics, Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Alexander J German
- Institute of Life Course and Medical Sciences, University of Liverpool, Leahurst Campus, Wirral, Neston CH64 7TE, UK
| | - Paul J J Mandigers
- Expertise Centre Genetics, Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands
- IVC Evidensia Referral Hospital Arnhem, Meander 10, 6825 MB Arnhem, The Netherlands
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47
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Davis KM, Partin AM, Burghardt GM, Springer CM, Albright JD. A Descriptive Methodology for Studying the Ontogeny of Object Play and Breed Differences in Dogs ( Canis lupus familiaris). Animals (Basel) 2023; 13:ani13081371. [PMID: 37106934 PMCID: PMC10135149 DOI: 10.3390/ani13081371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
Play behavior is a prominent aspect of juvenile behavior for many animals, yet early development, especially play with objects, has received little attention. Our previous study on object play introduced our general methods, focusing on litter differences in the developmental trajectory of object play and toy preferences. Here, we present a detailed ethogram of more than 30 observed object play behaviors. We focus on breed differences in the development of play in the three following breeds: Welsh Terriers, Vizslas, and standard Poodles. Puppies were video recorded from 3 to 7 weeks of age at half-week intervals upon the introduction of a standard set of five toys into their home environments. Ten minutes of video from each session for each puppy were analyzed using the Noldus Observer XT program. Aside from analyzing individual behaviors, they were also grouped into three behavioral categories. These were behaviors that occurred only in a solitary context, only in a social context, or in both contexts. Solitary object play developed first, and social object play developed later across breeds. There was a significant three-way interaction between breed, developmental age, and the context in which play occurred. Pairwise comparisons within each breed, age, and context are discussed, but a prominent result is that the onset of many behaviors occurred later in Welsh Terriers compared to the other breeds.
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Affiliation(s)
- Karen M Davis
- Department of Psychology, SUNY Potsdam, Potsdam, NY 13676, USA
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, USA
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Adam M Partin
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, USA
| | - Gordon M Burghardt
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, USA
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Cary M Springer
- Office of Information Technology, Research Computing Support, University of Tennessee, Knoxville, TN 37996, USA
| | - Julia D Albright
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA
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48
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Hsu WT, Williamson P, Khatkar MS. Identification of Genomic Signatures in Bullmastiff Dogs Using Composite Selection Signals Analysis of 23 Purebred Clades. Animals (Basel) 2023; 13:ani13071149. [PMID: 37048405 PMCID: PMC10093657 DOI: 10.3390/ani13071149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Dog breeds represent canine sub-populations with distinctive phenotypic features and limited genetic diversity. We have established a resource to study breed-specific genetic diversity. Utilising genetic resources within our laboratory biobank, public domain genotype data and the phylogenetic framework of 23 breed clades, the primary objective for this study was to identify genomic regions that differentiate the Bullmastiff breed. Through application of a composite index analysis (CSS), genomic signatures were identified in Bullmastiffs when compared to the formative breeds, Mastiffs and Bulldogs, and to 22 other breed groups. Significant regions were identified on 15 chromosomes, with the most differentiated regions found on CFA1, CFA9, and CFA18. These regions may reflect genetic drift following establishment of the breed or the effects of selective breeding during development of the modern Bullmastiff. This was supported by analysis of genes from the identified genomic regions, including 458 genes from the multi-clade analysis, which revealed enriched pathways that may be related to characteristic traits and distinct morphology of the breed. The study demonstrates the utility of the CSS method in breed-specific genome analysis and advances our understanding of genetic diversity in Bullmastiff dogs.
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Affiliation(s)
- Wei-Tse Hsu
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Peter Williamson
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mehar Singh Khatkar
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
- School of Animal and Veterinary Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Roseworthy, SA 5371, Australia
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49
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Miyamae J, Okano M, Katakura F, Kulski JK, Moritomo T, Shiina T. Large-Scale Polymorphism Analysis of Dog Leukocyte Antigen Class I and Class II Genes ( DLA-88, DLA-12/88L and DLA-DRB1) and Comparison of the Haplotype Diversity between Breeds in Japan. Cells 2023; 12:cells12050809. [PMID: 36899945 PMCID: PMC10001263 DOI: 10.3390/cells12050809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Polymorphisms of canine leukocyte antigen (DLA) class I (DLA-88 and DLA-12/88L) and class II (DLA-DRB1) genes are important for disease susceptibility studies, but information on the genetic diversity among dog breeds is still lacking. To better elucidate the polymorphism and genetic diversity between breeds, we genotyped DLA-88, DLA-12/88L, and DLA-DRB1 loci using 829 dogs of 59 breeds in Japan. Genotyping by Sanger sequencing identified 89, 43, and 61 alleles in DLA-88, DLA-12/88L, and DLA-DRB1 loci, respectively, and a total of 131 DLA-88-DLA-12/88L-DLA-DRB1 haplotypes (88-12/88L-DRB1) were detected more than once. Of the 829 dogs, 198 were homozygotes for one of the 52 different 88-12/88L-DRB1 haplotypes (homozygosity rate: 23.8%). Statistical modeling suggests that 90% of the DLA homozygotes or heterozygotes with one or other of the 52 different 88-12/88L-DRB1 haplotypes within somatic stem cell lines would benefit graft outcome after 88-12/88L-DRB1-matched transplantation. As previously reported for DLA class II haplotypes, the diversity of 88-12/88L-DRB1 haplotypes varied remarkably between breeds but was relatively conserved within most breeds. Therefore, the genetic characteristics of high DLA homozygosity rate and poor DLA diversity within a breed are useful for transplantation therapy, but they may affect biological fitness as homozygosity progresses.
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Affiliation(s)
- Jiro Miyamae
- Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoino-oka, Imabari 794-8555, Japan
- Correspondence: ; Tel.: +81-898-52-9126
| | - Masaharu Okano
- Department of Legal Medicine, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
| | - Fumihiko Katakura
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - Jerzy K. Kulski
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara 259-1143, Japan
| | - Tadaaki Moritomo
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara 259-1143, Japan
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50
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Spatola GJ, Buckley RM, Dillon M, Dutrow EV, Betz JA, Pilot M, Parker HG, Bogdanowicz W, Thomas R, Chyzhevskyi I, Milinevsky G, Kleiman N, Breen M, Ostrander EA, Mousseau TA. The dogs of Chernobyl: Demographic insights into populations inhabiting the nuclear exclusion zone. SCIENCE ADVANCES 2023; 9:eade2537. [PMID: 36867701 PMCID: PMC9984172 DOI: 10.1126/sciadv.ade2537] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The 1986 Chernobyl nuclear disaster initiated a series of catastrophic events resulting in long-term and widespread environmental contamination. We characterize the genetic structure of 302 dogs representing three free-roaming dog populations living within the power plant itself, as well as those 15 to 45 kilometers from the disaster site. Genome-wide profiles from Chernobyl, purebred and free-breeding dogs, worldwide reveal that the individuals from the power plant and Chernobyl City are genetically distinct, with the former displaying increased intrapopulation genetic similarity and differentiation. Analysis of shared ancestral genome segments highlights differences in the extent and timing of western breed introgression. Kinship analysis reveals 15 families, with the largest spanning all collection sites within the radioactive exclusion zone, reflecting migration of dogs between the power plant and Chernobyl City. This study presents the first characterization of a domestic species in Chernobyl, establishing their importance for genetic studies into the effects of exposure to long-term, low-dose ionizing radiation.
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Affiliation(s)
- Gabriella J Spatola
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megan Dillon
- North Carolina State University, Raleigh NC 27695, USA
| | - Emily V Dutrow
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
- Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Rachel Thomas
- North Carolina State University, Raleigh NC 27695, USA
| | | | - Gennadi Milinevsky
- Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- International Center of Future Science, College of Physics, Jilin University, Changchun 130012, China
| | | | - Matthew Breen
- North Carolina State University, Raleigh NC 27695, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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