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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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2
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Estabrooks T, Gurinovich A, Pietruska J, Lewis B, Harvey G, Post G, Lambert L, Miller A, Rodrigues L, White ME, Lopes C, London CA, Megquier K. Identification of genomic alterations with clinical impact in canine splenic hemangiosarcoma. Vet Comp Oncol 2023; 21:623-633. [PMID: 37734854 DOI: 10.1111/vco.12925] [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: 11/23/2022] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 09/23/2023]
Abstract
Canine hemangiosarcoma (HSA) is an aggressive cancer of endothelial cells with short survival times. Understanding the genomic landscape of HSA may aid in developing therapeutic strategies for dogs and may also inform therapies for the rare and aggressive human cancer angiosarcoma. The objectives of this study were to build a framework for leveraging real-world genomic and clinical data that could provide the foundation for precision medicine in veterinary oncology, and to determine the relationships between genomic and clinical features in canine splenic HSA. One hundred and nine dogs with primary splenic HSA treated by splenectomy that had tumour sequencing via the FidoCure® Precision Medicine Platform targeted sequencing panel were enrolled. Patient signalment, weight, metastasis at diagnosis and overall survival time were retrospectively evaluated. The incidence of genomic alterations in individual genes and their relationship to patient variables including outcome were assessed. Somatic mutations in TP53 (n = 44), NRAS (n = 20) and PIK3CA (n = 19) were most common. Survival was associated with presence of metastases at diagnosis and germline variants in SETD2 and NOTCH1. Age at diagnosis was associated with somatic NRAS mutations and breed. TP53 and PIK3CA somatic mutations were found in larger dogs, while germline SETD2 variants were found in smaller dogs. We identified both somatic mutations and germline variants associated with clinical variables including age, breed and overall survival. These genetic changes may be useful prognostic factors and provide insight into the genomic landscape of hemangiosarcoma.
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Affiliation(s)
- Timothy Estabrooks
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, USA
| | | | - Jodie Pietruska
- MassBio, UMass Chan Medical School, Worcester, Massachusetts, USA
| | | | | | - Gerald Post
- One Health Company, Palo Alto, California, USA
| | | | | | | | | | | | - Cheryl A London
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, USA
| | - Kate Megquier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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3
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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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4
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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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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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Heinrich J, Berger C, Berger B, Hecht W, Phillips C, Parson W. The LASSIE MPS panel: Predicting externally visible traits in dogs for forensic purposes. Forensic Sci Int Genet 2023; 66:102893. [PMID: 37290253 DOI: 10.1016/j.fsigen.2023.102893] [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: 03/03/2023] [Revised: 05/28/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Predicting the outward appearance of dogs via their DNA, also known as Canine DNA Phenotyping, is a young, emerging field of research in forensic genetics. The few previous studies published in this respect were restricted to the consecutive analysis of single DNA markers, a process that is time- and sample-consuming and therefore not a viable option for limited forensic specimens. Here, we report on the development and evaluation of a Massively Parallel Sequencing (MPS) based molecular genetic assay, the LASSIE MPS Panel. This panel aims to predict externally visible as well as skeletal traits, which include coat color, coat pattern, coat structure, tail morphology, skull shape, ear shape, eye color and body size from DNA using 44 genetic markers in a single molecular genetic assay. A biostatistical naïve Bayes classification approach was applied to identify the most informative marker combinations for predicting phenotypes. Overall, the predictive performance was characterized by a very high classification success for some of the trait categories, and high to moderate success for others. The performance of the developed predictive framework was further evaluated using blind samples from three randomly selected dog individuals, whose appearance was well predicted.
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Affiliation(s)
- Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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Mondino A, Khan M, Case B, Giovagnoli S, Thomson A, Lascelles BDX, Gruen M, Olby N. Activity patterns are associated with fractional lifespan, memory, and gait speed in aged dogs. Sci Rep 2023; 13:2588. [PMID: 36788306 PMCID: PMC9929073 DOI: 10.1038/s41598-023-29181-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023] Open
Abstract
Maintaining an active lifestyle is considered a hallmark of successful aging. Physical activity significantly reduces the risk of cognitive decline and Alzheimer's disease in humans. However, pain and lack of motivation are important barriers to exercise. Dogs are a remarkable model for translational studies in aging and cognition as they are prone to Canine Cognitive Dysfunction syndrome, which has many similarities with Alzheimer's disease. According to owner reports, changes in activity levels are characteristic of this syndrome, with decreased daytime activity, but also excessive pacing, especially at sleep time. We used physical activity monitors to record the activity of 27 senior dogs and evaluated the association between activity level and age, fractional lifespan, cognitive status measured by an owner questionnaire and cognitive tests. We also assessed the relationship between activity and joint/spinal pain, and the off/on leash gait speed ratio (a potential marker of gait speed reserve and motivation). We found that activity patterns in dogs are associated with fractional lifespan and working memory. Additionally, dogs with higher on/off leash gait speed are more active in the afternoon of weekdays. These results encourage future studies evaluating how physical activity can improve or delay cognitive impairment in senior dogs.
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Affiliation(s)
- Alejandra Mondino
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Michael Khan
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Beth Case
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Sara Giovagnoli
- Department of Psychology "Renzo Canestrari", University of Bologna, Bologna, Italy
| | - Andrea Thomson
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - B Duncan X Lascelles
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
- Translational Research in Pain, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
- Comparative Pain Research and Education Centre, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
- Thurston Arthritis Center, UNC School of Medicine, Chapel Hill, NC, USA
- Department of Anesthesiology, Center for Translational Pain Research, Duke University, Durham, NC, USA
| | - Margaret Gruen
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Natasha Olby
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.
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Dzomba EF, Van Der Nest MA, Mthembu JNT, Soma P, Snyman MA, Chimonyo M, Muchadeyi FC. Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders. Front Genet 2023; 13:932272. [PMID: 36685923 PMCID: PMC9847500 DOI: 10.3389/fgene.2022.932272] [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: 04/29/2022] [Accepted: 11/22/2022] [Indexed: 01/05/2023] Open
Abstract
Merino sheep are a breed of choice across the world, popularly kept for their wool and mutton value. They are often reared as a pure breed or used in crossbreeding and are a common component in synthetic breed development. This study evaluated genetic diversity, population structure, and breed divergence in 279 animals of Merino and Merino-based sheep breeds in South Africa using the Illumina Ovine SNP 50K BeadChip. The sheep breeds analysed included the three Merino-derived breeds of Dohne Merino (n = 50); Meatmaster (n = 47); and Afrino (n = 52) and five presumed ancestral populations of Merinos (Merino (n = 46); South African Merino (n = 10); and South African Mutton Merino (n = 8)); and the non-Merino founding breeds of Damara (n = 20); Ronderib Afrikaner (n = 17); and Nguni (n = 29). Highest genetic diversity values were observed in the Dohne Merino (DM), with H o = 0.39 ± 0.01, followed by the Meatmaster and South African Merino (SAM), with H o = 0.37 ± 0.03. The level of inbreeding ranged from 0.0 ± 0.02 (DM) to 0.27 ± 0.05 (Nguni). Analysis of molecular variance (AMOVA) showed high within-population variance (>80%) across all population categories. The first principal component (PC1) separated the Merino, South African Mutton Merino (SAMM), DM, and Afrino (AFR) from the Meatmaster, Damara, Nguni, and Ronderib Afrikaner (RDA). PC2 aligned each Merino-derived breed with its presumed ancestors and separated the SAMM from the Merino and SAM. The iHS analysis yielded selection sweeps across the AFR (12 sweeps), Meatmaster (four sweeps), and DM (29 sweeps). Hair/wool trait genes such as FGF12; metabolic genes of ICA1, NXPH1, and GPR171; and immune response genes of IL22, IL26, IFNAR1, and IL10RB were reported. Other genes include HMGA, which was observed as selection signatures in other populations; WNT5A, important in the development of the skeleton and mammary glands; ANTXR2, associated with adaptation to variation in climatic conditions; and BMP2, which has been reported as strongly selected in both fat-tailed and thin-tailed sheep. The DM vs. SAMM shared all six sweep regions on chromosomes 1, 10, and 11 with AFR vs. SAMM. Genes such as FGF12 on OAR 1:191.3-194.7 Mb and MAP2K4 on OAR 11:28.6-31.3 Mb were observed. The selection sweep on chromosome 10 region 28.6-30.3 Mb harbouring the RXFP2 for polledness was shared between the DM vs. Merino, the Meatmaster vs. Merino, and the Meatmaster vs. Nguni. The DM vs. Merino and the Meatmaster vs. Merino also shared an Rsb-based selection sweep on chromosome 1 region 268.5-269.9 Mb associated with the Calpain gene, CAPN7. The study demonstrated some genetic similarities between the Merino and Merino-derived breeds emanating from common founding populations and some divergence driven by breed-specific selection goals. Overall, information regarding the evolution of these composite breeds from their founding population will guide future breed improvement programs and management and conservation efforts.
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Affiliation(s)
- E. F. Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa,*Correspondence: E. F. Dzomba,
| | - M. A. Van Der Nest
- Agricultural Research Council Biotechnology Platform, Private Bag X5 Onderstepoort, Pretoria, South Africa
| | - J. N. T. Mthembu
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - P Soma
- Agricultural Research Council, Animal Production and Improvement, Pretoria, South Africa
| | - M. A. Snyman
- Grootfontein Agricultural Development Institute, Middelburg, South Africa
| | - M. Chimonyo
- Discipline of Animal and Poultry Science, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - F. C. Muchadeyi
- Agricultural Research Council Biotechnology Platform, Private Bag X5 Onderstepoort, Pretoria, South Africa
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Selection Signatures in Italian Livestock Guardian and Herding Shepherd Dogs. Vet Sci 2022; 10:vetsci10010003. [PMID: 36669004 PMCID: PMC9862740 DOI: 10.3390/vetsci10010003] [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: 10/21/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Livestock guardian (LGD) and herding shepherd (HSD) dogs have distinct morphological and behavioural characteristics, long selected by farmers and breeders, to accomplish different tasks. This study aimed to find the genomic regions that best differentiate and characterise Italian LGD and HSD. Genomic data of 158 dogs of four LGD and five HSD breeds, obtained with the 170K canine SNPchip, were collected. The two groups were compared using FST and XP-EHH analyses, identifying regions containing 29 genes. Moreover, 16 islands of runs of homozygosity were found in LGD, and 15 in HSD; 4 of them were partially shared. Among the genes found that better differentiated HSD and LGD, several were associated with dog domestication and behavioural aspects; particularly, MSRB3 and LLPH were linked to herding behaviour in previous studies. Others, DYSK, MAP2K5, and RYR, were related to body size and muscle development. Prick ears prevailed in sampled HSD, and drop ears in LGD; this explains the identification of WIF1 and MSRB3 genes. Unexpectedly, a number of genes were also associated with eye development and functionality. These results shed further light on the differences that human selection introduced in dogs aimed at different duties, even in a limited geographic area such as Italy.
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Binversie EE, Momen M, Rosa GJM, Davis BW, Muir P. Across-breed genetic investigation of canine hip dysplasia, elbow dysplasia, and anterior cruciate ligament rupture using whole-genome sequencing. Front Genet 2022; 13:913354. [PMID: 36531249 PMCID: PMC9755188 DOI: 10.3389/fgene.2022.913354] [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: 04/05/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
Here, we report the use of genome-wide association study (GWAS) for the analysis of canine whole-genome sequencing (WGS) repository data using breed phenotypes. Single-nucleotide polymorphisms (SNPs) were called from WGS data from 648 dogs that included 119 breeds from the Dog10K Genomes Project. Next, we assigned breed phenotypes for hip dysplasia (Orthopedic Foundation for Animals (OFA) HD, n = 230 dogs from 27 breeds; hospital HD, n = 279 dogs from 38 breeds), elbow dysplasia (ED, n = 230 dogs from 27 breeds), and anterior cruciate ligament rupture (ACL rupture, n = 279 dogs from 38 breeds), the three most important canine spontaneous complex orthopedic diseases. Substantial morbidity is common with these diseases. Previous within- and between-breed GWAS for HD, ED, and ACL rupture using array SNPs have identified disease-associated loci. Individual disease phenotypes are lacking in repository data. There is a critical knowledge gap regarding the optimal approach to undertake categorical GWAS without individual phenotypes. We considered four GWAS approaches: a classical linear mixed model, a haplotype-based model, a binary case-control model, and a weighted least squares model using SNP average allelic frequency. We found that categorical GWAS was able to validate HD candidate loci. Additionally, we discovered novel candidate loci and genes for all three diseases, including FBX025, IL1A, IL1B, COL27A1, SPRED2 (HD), UGDH, FAF1 (ED), TGIF2 (ED & ACL rupture), and IL22, IL26, CSMD1, LDHA, and TNS1 (ACL rupture). Therefore, categorical GWAS of ancestral dog populations may contribute to the understanding of any disease for which breed epidemiological risk data are available, including diseases for which GWAS has not been performed and candidate loci remain elusive.
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Affiliation(s)
- Emily E. Binversie
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Mehdi Momen
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Guilherme J. M. Rosa
- Department of Animal and Dairy Sciences, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Peter Muir
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States,*Correspondence: Peter Muir,
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Abstract
As the most phenotypically diverse mammalian species that shares human environments and access to sophisticated healthcare, domestic dogs have unique potential to inform our understanding of the determinants of aging. Here we outline key concepts in the study of aging and illustrate the value of research with dogs, which can improve dog health and support translational discoveries. We consider similarities and differences in aging and age-related diseases in dogs and humans and summarize key advances in our understanding of genetic and environmental risk factors for morbidity and mortality in dogs. We address health outcomes ranging from cancer to cognitive function and highlight emerging research opportunities from large-scale cohort studies in companion dogs. We conclude that studying aging in dogs could overcome many limitations of laboratory models, most notably, the ability to assess how aging-associated pathways influence aging in real-world environments similar to those experienced by humans.
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Affiliation(s)
- Audrey Ruple
- Department of Population Health Sciences, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA;
| | - Evan MacLean
- School of Anthropology and College of Veterinary Medicine, University of Arizona, Tucson, Arizona, USA;
| | - Noah Snyder-Mackler
- School of Life Sciences, Center for Evolution and Medicine, and School for Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA;
| | - Kate E. Creevy
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Daniel Promislow
- Department of Laboratory Medicine & Pathology and Department of Biology, University of Washington School of Medicine, Seattle, Washington, USA;
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Zapata I, Lilly ML, Herron ME, Serpell JA, Alvarez CE. Genetic testing of dogs predicts problem behaviors in clinical and nonclinical samples. BMC Genomics 2022; 23:102. [PMID: 35130840 PMCID: PMC8819838 DOI: 10.1186/s12864-022-08351-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 01/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Very little is known about the etiology of personality and psychiatric disorders. Because the core neurobiology of many such traits is evolutionarily conserved, dogs present a powerful model. We previously reported genome scans of breed averages of ten traits related to fear, anxiety, aggression and social behavior in multiple cohorts of pedigree dogs. As a second phase of that discovery, here we tested the ability of markers at 13 of those loci to predict canine behavior in a community sample of 397 pedigree and mixed-breed dogs with individual-level genotype and phenotype data. RESULTS We found support for all markers and loci. By including 122 dogs with veterinary behavioral diagnoses in our cohort, we were able to identify eight loci associated with those diagnoses. Logistic regression models showed subsets of those loci could predict behavioral diagnoses. We corroborated our previous findings that small body size is associated with many problem behaviors and large body size is associated with increased trainability. Children in the home were associated with anxiety traits; illness and other animals in the home with coprophagia; working-dog status with increased energy and separation-related problems; and competitive dogs with increased aggression directed at familiar dogs, but reduced fear directed at humans and unfamiliar dogs. Compared to other dogs, Pit Bull-type dogs were not defined by a set of our markers and were not more aggressive; but they were strongly associated with pulling on the leash. Using severity-threshold models, Pit Bull-type dogs showed reduced risk of owner-directed aggression (75th quantile) and increased risk of dog-directed fear (95th quantile). CONCLUSIONS Our association analysis in a community sample of pedigree and mixed-breed dogs supports the interbreed mapping. The modeling shows some markers are predictive of behavioral diagnoses. Our findings have broad utility, including for clinical and breeding purposes, but we caution that thorough understanding is necessary for their interpretation and use.
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Affiliation(s)
- Isain Zapata
- Department of Veterinary Clinical Sciences, The Ohio State University College of Veterinary Medicine, Columbus, OH, 43210, USA. .,Department of Biomedical Sciences, Rocky Vista University College of Osteopathic Medicine, Parker, CO, 80134, USA.
| | - M Leanne Lilly
- Department of Veterinary Clinical Sciences, The Ohio State University College of Veterinary Medicine, Columbus, OH, 43210, USA
| | - Meghan E Herron
- Department of Veterinary Clinical Sciences, The Ohio State University College of Veterinary Medicine, Columbus, OH, 43210, USA
| | - James A Serpell
- Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Carlos E Alvarez
- Department of Veterinary Clinical Sciences, The Ohio State University College of Veterinary Medicine, Columbus, OH, 43210, USA. .,Center for Clinical and Translational Research, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA. .,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA.
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13
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Lee MO, Li J, Davis BW, Upadhyay S, Al Muhisen HM, Suva LJ, Clement TM, Andersson L. Hmga2 deficiency is associated with allometric growth retardation, infertility, and behavioral abnormalities in mice. G3 (BETHESDA, MD.) 2022; 12:6456304. [PMID: 34878116 PMCID: PMC9210324 DOI: 10.1093/g3journal/jkab417] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/23/2021] [Indexed: 05/13/2023]
Abstract
The high mobility group AT-hook 2 (HMGA2) protein works as an architectural regulator by binding AT-rich DNA sequences to induce conformational changes affecting transcription. Genomic deletions disrupting HMGA2 coding sequences and flanking noncoding sequences cause dwarfism in mice and rabbits. Here, CRISPR/Cas9 was used in mice to generate an Hmga2 null allele that specifically disrupts only the coding sequence. The loss of one or both alleles of Hmga2 resulted in reduced body size of 20% and 60%, respectively, compared to wild-type littermates as well as an allometric reduction in skull length in Hmga2-/- mice. Both male and female Hmga2-/- mice are infertile, whereas Hmga2+/- mice are fertile. Examination of reproductive tissues of Hmga2-/- males revealed a significantly reduced size of testis, epididymis, and seminal vesicle compared to controls, and 70% of knock-out males showed externalized penis, but no cryptorchidism was observed. Sperm analyses revealed severe oligospermia in mutant males and slightly decreased sperm viability, increased DNA damage but normal sperm chromatin compaction. Testis histology surprisingly revealed a normal seminiferous epithelium, despite the significant reduction in testis size. In addition, Hmga2-/- mice showed a significantly reduced exploratory behavior. In summary, the phenotypic effects in mouse using targeted mutagenesis confirmed that Hmga2 is affecting prenatal and postnatal growth regulation, male reproductive tissue development, and presents the first indication that Hmga2 function is required for normal mouse behavior. No specific effect, despite an allometric reduction, on craniofacial development was noted in contrast to previous reports of an altered craniofacial development in mice and rabbits carrying deletions of both coding and noncoding sequences at the 5' part of Hmga2.
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Affiliation(s)
- Mi Ok Lee
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Jingyi Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Srijana Upadhyay
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Hadil M Al Muhisen
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Larry J Suva
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Tracy M Clement
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
- Corresponding author: Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Vet Med Research Bldg., 588 Raymond Stotzer Pw, TX 77843, USA.
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14
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Review on Selected Aggression Causes and the Role of Neurocognitive Science in the Diagnosis. Animals (Basel) 2022; 12:ani12030281. [PMID: 35158605 PMCID: PMC8833765 DOI: 10.3390/ani12030281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Aggression in dogs is often a reason for abandonment and/or euthanasia. Recently, knowledge about aggression has been subjected to more detailed analysis. In recent years, it has been studied in terms of factors affecting it, such as diet (especially nutritional supplements) and physiology (endocrine system). In addition, recently, new methods of brain research, such as neurocognitive research, have appeared, which enable a significant increase in knowledge about dog behavior, including aggression. Abstract Aggression as a behavior is not always desirable, often ends in abandonment and/or euthanasia. However, it is possible to prevent the occurrence of unwanted aggression in domestic dogs. Aggression is not a fully understood phenomenon. In recent years, many studies have focused on the influence of diet and physiology (including the endocrine system) on the emergence of behavioral disorders. In particular, the emphasis was put on nutritional additives such as fatty acids, amino acids, and probiotics. In addition, the possibility of using neurocognition in the observation of abnormal behavior in dogs has also been discussed, which may allow for a more detailed determination of the basis of aggressive behavior in dogs. In this review, the concepts related to aggression and its potential causes have been gathered. In addition, the possible influence of diet and hormones on aggression in dogs has been discussed, as well as the application of neurocognition in the possibility of its diagnosis.
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15
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Giska I, Pimenta J, Farelo L, Boursot P, Hackländer K, Jenny H, Reid N, Montgomery WI, Prodöhl PA, Alves PC, Melo-Ferreira J. The evolutionary pathways for local adaptation in mountain hares. Mol Ecol 2022; 31:1487-1503. [PMID: 34995383 PMCID: PMC9303332 DOI: 10.1111/mec.16338] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022]
Abstract
Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole‐genome sequencing, we identify genetic signatures of local adaptation in mountain hares (Lepus timidus) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. Demographic modelling suggested that the split of these mountain hares occurred around 20 thousand years ago, providing the opportunity to study adaptive evolution over a short timescale. Using genome‐wide scans, we identified signatures of extreme differentiation among hares from distinct geographic areas that overlap with area‐specific selective sweeps, suggesting targets for local adaptation. Several identified candidate genes are associated with traits related to the uniqueness of the different environments inhabited by the three groups of mountain hares, including coat colour, ability to live at high altitudes and variation in body size. In Irish mountain hares, a variant of ASIP, a gene previously implicated in introgression‐driven winter coat colour variation in mountain and snowshoe hares (L. americanus), may underlie brown winter coats, reinforcing the repeated nature of evolution at ASIP moulding adaptive seasonal colouration. Comparative genomic analyses across several hare species suggested that mountain hares’ adaptive variants appear predominantly species‐specific. However, using coalescent simulations, we also show instances where the candidate adaptive variants have been introduced via introgressive hybridization. Our study shows that standing adaptive variation, including that introgressed from other species, was a crucial component of the post‐glacial dynamics of species.
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Affiliation(s)
- Iwona Giska
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - João Pimenta
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, 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
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pierre Boursot
- Institut des Sciences de l'Évolution Montpellier (ISEM), Université Montpellier, CNRS, IRD, Montpellier, France
| | - Klaus Hackländer
- Institute of Wildlife Biology and Game Management, University of Natural Resources and Life Sciences, Vienna, Austria.,Deutsche Wildtier Stiftung (German Wildlife Foundation), Hamburg, Germany
| | - Hannes Jenny
- Department of Wildlife and Fishery Service Grison, Chur, Switzerland
| | - Neil Reid
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - W Ian Montgomery
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Paulo A Prodöhl
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, 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
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, 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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16
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Raymond PW, Velie BD, Wade CM. Forensic DNA phenotyping: Canis familiaris breed classification and skeletal phenotype prediction using functionally significant skeletal SNPs and indels. Anim Genet 2021; 53:247-263. [PMID: 34963196 DOI: 10.1111/age.13165] [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: 10/21/2020] [Revised: 11/30/2021] [Accepted: 12/12/2021] [Indexed: 11/29/2022]
Abstract
This review highlights a novel application of breed identification and prediction of skeletal traits in forensic investigations using canine DNA evidence. Currently, genotyping methods used for canine breed classification involve the application of highly polymorphic short tandem repeats in addition to larger commercially available SNP arrays. Both applications face technical challenges. An additional approach to breed identification could be through genotyping SNPs and indels that characterise the array of skeletal differences displayed across domestic dog populations. Research has shown that a small number of genetic variants of large effect drive differences in skeletal phenotypes among domestic dog breeds. This feature makes functionally significant canine skeletal variants a cost-effective target for forensic investigators to classify individuals according to their breed. Further analysis of these skeletal variants would enable the prediction of external appearance. To date, functionally significant genes with genetic variants associated with differences in size, bulk, skull shape, ear shape, limb length, digit type, and tail morphology have been uncovered. Recommendations of a cost-effective genotyping method that can be readily designed and applied by forensic investigators have been given. Further advances to improve the field of canine skeletal forensic DNA phenotyping include the refinement of phenotyping methods, further biological validation of the skeletal genetic variants and establishing a publicly available database for storage of allele frequencies of the skeletal genetic variants in the wider domestic dog population.
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Affiliation(s)
- Patrick W Raymond
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Brandon D Velie
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Claire M Wade
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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17
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The effect of inbreeding, body size and morphology on health in dog breeds. Canine Med Genet 2021; 8:12. [PMID: 34852838 PMCID: PMC8638537 DOI: 10.1186/s40575-021-00111-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background Dog breeds are known for their distinctive body shape, size, coat color, head type and behaviors, features that are relatively similar across members of a breed. Unfortunately, dog breeds are also characterized by distinct predispositions to disease. We explored the relationships between inbreeding, morphology and health using genotype based inbreeding estimates, body weight and insurance data for morbidity. Results The average inbreeding based on genotype across 227 breeds was Fadj = 0.249 (95% CI 0.235–0.263). There were significant differences in morbidity between breeds with low and high inbreeding (H = 16.49, P = 0.0004). There was also a significant difference in morbidity between brachycephalic breeds and non-brachycephalic breeds (P = 0.0048) and between functionally distinct groups of breeds (H = 14.95 P < 0.0001). Morbidity was modeled using robust regression analysis and both body weight (P < 0.0001) and inbreeding (P = 0.013) were significant (r2 = 0.77). Smaller less inbred breeds were healthier than larger more inbred breeds. Conclusions In this study, body size and inbreeding along with deleterious morphologies contributed to increases in necessary health care in dogs. Supplementary Information The online version contains supplementary material available at 10.1186/s40575-021-00111-4.
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18
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Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis. Animals (Basel) 2021; 11:ani11113136. [PMID: 34827868 PMCID: PMC8614278 DOI: 10.3390/ani11113136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 12/14/2022] Open
Abstract
As a companion and hunting dog, height, length, length to height ratio (LHR) and body-weight are the vital economic traits for Jindo dog. Human selection and targeted breeding have produced an extraordinary diversity in these traits. Therefore, the identification of causative markers, genes and pathways that help us to understand the genetic basis of this variability is essential for their selection purposes. Here, we performed a genome-wide association study (GWAS) combined with enrichment analysis on 757 dogs using 118,879 SNPs. The genomic heritability (h2) was 0.33 for height and 0.28 for weight trait in Jindo. At p-value < 5 × 10-5, ten, six, thirteen and eleven SNPs on different chromosomes were significantly associated with height, length, LHR and body-weight traits, respectively. Based on our results, HHIP, LCORL and NCAPG for height, IGFI and FGFR3 for length, DLK1 and EFEMP1 for LHR and PTPN2, IGFI and RASAL2 for weight can be the potential candidate genes because of the significant SNPs located in their intronic or upstream regions. The gene-set enrichment analysis highlighted here nine and seven overlapping significant (p < 0.05) gene ontology (GO) terms and pathways among traits. Interestingly, the highlighted pathways were related to hormone synthesis, secretion and signalling were generally involved in the metabolism, growth and development process. Our data provide an insight into the significant genes and pathways if verified further, which will have a significant effect on the breeding of the Jindo dog's population.
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19
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Fossati P, Ruffo G. Purebred dogs and cats: A proposal for a better protection. J Vet Behav 2021. [DOI: 10.1016/j.jveb.2021.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Interface of Human/Wildlife Interactions: An Example of a Bold Coyote (Canis latrans) in Atlanta, GA, USA. DIVERSITY 2021. [DOI: 10.3390/d13080372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
There is arguably no other North American species that better illustrates the complexities of the human-wildlife interface than the coyote. In this study, a melanistic coyote in metropolitan Atlanta, Georgia was exhibiting unusually bold behaviors that included encounters with humans, domestic dogs, and attempts to enter homes. After tracking this coyote (nicknamed Carmine) across a highly urbanized landscape with participatory science, including at least 80 publicly reported sightings, he was captured and relocated to a wildlife sanctuary. Genome-wide analyses revealed 92.8% coyote ancestry, 1.7% gray wolf ancestry, and 5.5% domestic dog ancestry. The dog alleles in Carmine’s genome were estimated to have been acquired by his ancestors 14–29 years ago. Despite his bold behavior, Carmine did not carry any mutations known to shape hypersociability in canines. He did, however, carry a single copy of the dominant mutation responsible for his melanistic coat color. This detailed study of Carmine dispels common assumptions about the reticent coyote personality and the origins of behavior. His unusual bold behavior created a higher level of human-coyote interaction. He now serves as a public ambassador for human-wildlife coexistence, urging the global community to reconsider mythologies about wildlife and promote coexistence with them in landscapes significantly altered by human activity in our rapidly changing world.
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21
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Shan S, Xu F, Brenig B. Genome-Wide Association Studies Reveal Neurological Genes for Dog Herding, Predation, Temperament, and Trainability Traits. Front Vet Sci 2021; 8:693290. [PMID: 34368281 PMCID: PMC8335642 DOI: 10.3389/fvets.2021.693290] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association study (GWAS) using dog breed standard values as phenotypic measurements is an efficient way to identify genes associated with morphological and behavioral traits. As a result of strong human purposeful selections, several specialized behavioral traits such as herding and hunting have been formed in different modern dog breeds. However, genetic analyses on this topic are rather limited due to the accurate phenotyping difficulty for these complex behavioral traits. Here, 268 dog whole-genome sequences from 130 modern breeds were used to investigate candidate genes underlying dog herding, predation, temperament, and trainability by GWAS. Behavioral phenotypes were obtained from the American Kennel Club based on dog breed standard descriptions or groups (conventional categorization of dog historical roles). The GWAS results of herding behavior (without body size as a covariate) revealed 44 significantly associated sites within five chromosomes. Significantly associated sites on CFA7, 9, 10, and 20 were located either in or near neuropathological or neuronal genes including THOC1, ASIC2, MSRB3, LLPH, RFX8, and CHL1. MSRB3 and CHL1 genes were reported to be associated with dog fear. Since herding is a restricted hunting behavior by removing killing instinct, 36 hounds and 55 herding dogs were used to analyze predation behavior. Three neuronal-related genes (JAK2, MEIS1, and LRRTM4) were revealed as candidates for predation behavior. The significantly associated variant of temperament GWAS was located within ACSS3 gene. The highest associated variant in trainability GWAS is located on CFA22, with no variants detected above the Bonferroni threshold. Since dog behaviors are correlated with body size, we next incorporate body mass as covariates into GWAS; and significant signals around THOC1, MSRB3, LLPH, RFX8, CHL1, LRRTM4, and ACSS3 genes were still detected for dog herding, predation, and temperament behaviors. In humans, these candidate genes are either involved in nervous system development or associated with mental disorders. In conclusion, our results imply that these neuronal or psychiatric genes might be involved in biological processes underlying dog herding, predation, and temperament behavioral traits.
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Affiliation(s)
- Shuwen Shan
- Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
| | - Fangzheng Xu
- Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
| | - Bertram Brenig
- Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
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22
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Berger C, Heinrich J, Berger B, Hecht W, Parson W. Towards Forensic DNA Phenotyping for Predicting Visible Traits in Dogs. Genes (Basel) 2021; 12:genes12060908. [PMID: 34208207 PMCID: PMC8230911 DOI: 10.3390/genes12060908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
The popularity of dogs as human companions explains why these pets regularly come into focus in forensic cases such as bite attacks or accidents. Canine evidence, e.g., dog hairs, can also act as a link between the victim and suspect in a crime case due to the close contact between dogs and their owners. In line with human DNA identification, dog individualization from crime scene evidence is mainly based on the analysis of short tandem repeat (STR) markers. However, when the DNA profile does not match a reference, additional information regarding the appearance of the dog may provide substantial intelligence value. Key features of the dog's appearance, such as the body size and coat colour are well-recognizable and easy to describe even to non-dog experts, including most investigating officers and eyewitnesses. Therefore, it is reasonable to complement eyewitnesses' testimonies with externally visible traits predicted from associated canine DNA samples. Here, the feasibility and suitability of canine DNA phenotyping is explored from scratch in the form of a proof of concept study. To predict the overall appearance of an unknown dog from its DNA as accurately as possible, the following six traits were chosen: (1) coat colour, (2) coat pattern, (3) coat structure, (4) body size, (5) ear shape, and (6) tail length. A total of 21 genetic markers known for high predicting values for these traits were selected from previously published datasets, comprising 15 SNPs and six INDELS. Three of them belonged to SINE insertions. The experiments were designed in three phases. In the first two stages, the performance of the markers was tested on DNA samples from dogs with well-documented physical characteristics from different breeds. The final blind test, including dogs with initially withheld appearance information, showed that the majority of the selected markers allowed to develop composite sketches, providing a realistic impression of the tested dogs. We regard this study as the first attempt to evaluate the possibilities and limitations of forensic canine DNA phenotyping.
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Affiliation(s)
- Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
- Correspondence: ; Tel.: +43-512-9003-70640
| | - Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
| | - Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, 35390 Giessen, Germany;
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
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23
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McCune S, Promislow D. Healthy, Active Aging for People and Dogs. Front Vet Sci 2021; 8:655191. [PMID: 34164450 PMCID: PMC8215343 DOI: 10.3389/fvets.2021.655191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/05/2021] [Indexed: 01/08/2023] Open
Abstract
Dogs act as companions who provide us with emotional and physical support. Their shorter lifespans compel us to learn about the challenges and gifts of caring for older individuals. Our companion dogs can be exemplars of healthy or unhealthy aging, and sentinels of environmental factors that might increase or decrease our own healthy lifespan. In recent years, the field of aging has emphasized not just lifespan, but healthspan—the period of healthy, active lifespan. This focus on healthy, active aging is reflected in the World Health Organization's current focus on healthy aging for the next decade and the 2016 Healthy Aging in Action initiative in the US. This paper explores the current research into aging in both people and companion dogs, and in particular, how the relationship between older adults and dogs impacts healthy, active aging for both parties. The human-dog relationship faces many challenges as dogs, and people, age. We discuss potential solutions to these challenges, including suggestions for ways to continue contact with dogs if dog ownership is no longer possible for an older person. Future research directions are outlined in order to encourage the building of a stronger evidence base for the role of dogs in the lives of older adults.
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Affiliation(s)
- Sandra McCune
- School of Psychology, School of Life Sciences, University of Lincoln, Lincoln, United Kingdom.,Animal Matters Consultancy Ltd., Stamford, United Kingdom
| | - Daniel Promislow
- Department of Lab Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States.,Department of Biology, University of Washington, Seattle, WA, United States
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24
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O'Brien MJ, Beijerink NJ, Wade CM. Genetics of canine myxomatous mitral valve disease. Anim Genet 2021; 52:409-421. [PMID: 34028063 DOI: 10.1111/age.13082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2021] [Indexed: 12/26/2022]
Abstract
Myxomatous mitral valve disease (MMVD) is the most common heart disease and cause of cardiac death in domestic dogs. MMVD is characterised by slow progressive myxomatous degeneration from the tips of the mitral valves onwards with subsequent mitral valve regurgitation, and left atrial and ventricular dilatation. Although the disease usually has a long asymptomatic period, in dogs with severe disease, mortality is typically secondary to left-sided congestive heart failure. Although it is not uncommon for dogs to survive long enough in the asymptomatic period to die from unrelated causes; a proportion of dogs rapidly advance into congestive heart failure. Heightened prevalence in certain breeds, such as the Cavalier King Charles Spaniel, has indicated that MMVD is under a genetic influence. The genetic characterisation of the factors that underlie the difference in progression of disease is of strong interest to those concerned with dog longevity and welfare. Advanced genomic technologies have the potential to provide information that may impact treatment, prevalence, or severity of MMVD through the elucidation of pathogenic mechanisms and the detection of predisposing genetic loci of major effect. Here we describe briefly the clinical nature of the disorder and consider the physiological mechanisms that might impact its occurrence in the domestic dog. Using results from comparative genomics we suggest possible genetic approaches for identifying genetic risk factors within breeds. The Cavalier King Charles Spaniel breed represents a robust resource for uncovering the genetic basis of MMVD.
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Affiliation(s)
- M J O'Brien
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - N J Beijerink
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia.,Veterinaire Specialisten Vught, Reutsedijk 8a, Vught, 5264 PC, The Netherlands
| | - C M Wade
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
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25
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Serres-Armero A, Davis BW, Povolotskaya IS, Morcillo-Suarez C, Plassais J, Juan D, Ostrander EA, Marques-Bonet T. Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Res 2021; 31:762-774. [PMID: 33863806 PMCID: PMC8092016 DOI: 10.1101/gr.266049.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 02/26/2021] [Indexed: 01/02/2023]
Abstract
Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole genome CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray technologies. We have taken advantage of this data set to perform the first CNV-based genome-wide association study (GWAS) in canids. We identify 96 loci that display copy number differences across breeds, which are statistically associated with a previously compiled set of breed-specific morphometrics and disease susceptibilities. Among these, we highlight the discovery of a long-range interaction involving a CNV near MED13L and TBX3, which could influence breed standard height. Integration of the CNVs with chromatin interactions, long noncoding RNA expression, and single nucleotide variation highlights a subset of specific loci and genes with potential functional relevance and the prospect to explain trait variation between dog breeds.
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Affiliation(s)
- Aitor Serres-Armero
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Brian W Davis
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Inna S Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Carlos Morcillo-Suarez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David Juan
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tomas Marques-Bonet
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia 08201, Spain
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26
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Gnanadesikan GE, Hare B, Snyder-Mackler N, Call J, Kaminski J, Miklósi Á, MacLean EL. Breed Differences in Dog Cognition Associated with Brain-Expressed Genes and Neurological Functions. Integr Comp Biol 2020; 60:976-990. [PMID: 32726413 DOI: 10.1093/icb/icaa112] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Given their remarkable phenotypic diversity, dogs present a unique opportunity for investigating the genetic bases of cognitive and behavioral traits. Our previous work demonstrated that genetic relatedness among breeds accounts for a substantial portion of variation in dog cognition. Here, we investigated the genetic architecture of breed differences in cognition, seeking to identify genes that contribute to variation in cognitive phenotypes. To do so, we combined cognitive data from the citizen science project Dognition.com with published breed-average genetic polymorphism data, resulting in a dataset of 1654 individuals with cognitive phenotypes representing 49 breeds. We conducted a breed-average genome-wide association study to identify specific polymorphisms associated with breed differences in inhibitory control, communication, memory, and physical reasoning. We found five single nucleotide polymorphisms (SNPs) that reached genome-wide significance after Bonferroni correction, located in EML1, OR52E2, HS3ST5, a U6 spliceosomal RNA, and a long noncoding RNA. When we combined results across multiple SNPs within the same gene, we identified 188 genes implicated in breed differences in cognition. This gene set included more genes than expected by chance that were (1) differentially expressed in brain tissue and (2) involved in nervous system functions including peripheral nervous system development, Wnt signaling, presynapse assembly, and synaptic vesicle exocytosis. These results advance our understanding of the genetic underpinnings of complex cognitive phenotypes and identify specific genetic variants for further research.
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Affiliation(s)
- Gitanjali E Gnanadesikan
- School of Anthropology, University of Arizona, Tucson, AZ, USA.,Cognitive Science Program, University of Arizona, Tucson, AZ, USA
| | - Brian Hare
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA.,Center for Cognitive Neuroscience, Duke University, Durham, NC, USA
| | - Noah Snyder-Mackler
- Department of Psychology, University of Washington, Seattle, WA, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Josep Call
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK
| | - Juliane Kaminski
- Department of Psychology, University of Portsmouth, Portsmouth, UK
| | - Ádám Miklósi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary.,MTA-ELTE Comparative Ethology Research Group, Budapest, Hungary
| | - Evan L MacLean
- School of Anthropology, University of Arizona, Tucson, AZ, USA.,Cognitive Science Program, University of Arizona, Tucson, AZ, USA.,Psychology Department, University of Arizona, Tucson, AZ, USA.,College of Veterinary Medicine, University of Arizona, Tucson, AZ, USA
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27
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Doherty A, Lopes I, Ford CT, Monaco G, Guest P, de Magalhães JP. A scan for genes associated with cancer mortality and longevity in pedigree dog breeds. Mamm Genome 2020; 31:215-227. [PMID: 32661568 PMCID: PMC7496057 DOI: 10.1007/s00335-020-09845-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/29/2020] [Indexed: 12/20/2022]
Abstract
Selective breeding of the domestic dog (Canis lupus familiaris) rigidly retains desirable features, and could inadvertently fix disease-causing variants within a breed. We combine phenotypic data from > 72,000 dogs with a large genotypic dataset to search for genes associated with cancer mortality and longevity in pedigree dog breeds. We validated previous findings that breeds with higher average body weight have higher cancer mortality rates and lower life expectancy. We identified a significant positive correlation between life span and cancer mortality residuals corrected for body weight, implying that long-lived breeds die more frequently from cancer compared to short-lived breeds. We replicated a number of known genetic associations with body weight (IGF1, GHR, CD36, SMAD2 and IGF2BP2). Subsequently, we identified five genetic variants in known cancer-related genes (located within SIPA1, ADCY7 and ARNT2) that could be associated with cancer mortality residuals corrected for confounding factors. One putative genetic variant was marginally significantly associated with longevity residuals that had been corrected for the effects of body weight; this genetic variant is located within PRDX1, a peroxiredoxin that belongs to an emerging class of pro-longevity associated genes. This research should be considered as an exploratory analysis to uncover associations between genes and longevity/cancer mortality.
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Affiliation(s)
- Aoife Doherty
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Inês Lopes
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Christopher T Ford
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Gianni Monaco
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Patrick Guest
- School of Biology, Medical and Biological Sciences Building, University of St. Andrews, North Haugh, St. Andrews, KY16 9TF, UK
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK.
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28
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Bannasch DL, Baes CF, Leeb T. Genetic Variants Affecting Skeletal Morphology in Domestic Dogs. Trends Genet 2020; 36:598-609. [PMID: 32487495 DOI: 10.1016/j.tig.2020.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/25/2022]
Abstract
Purebred dog breeds provide a powerful resource for the discovery of genetic variants affecting skeletal morphology. Domesticated and subsequently purebred dogs have undergone strong artificial selection for a broad range of skeletal variation, which include both the size and shapes of their bones. While the phenotypic variation between breeds is high, within-breed morphological variation is typically low. Approaches for defining genetic variants associated with canine morphology include quantitative within-breed analyses, as well as across-breed analyses, using breed standards as proxies for individual measurements. The ability to identify variants across the genomes of individual dogs can now be paired with precise measures of morphological variation to define the genetic interactions and the phenotypic effect of variants on skeletal morphology.
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Affiliation(s)
- Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
| | - Christine F Baes
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
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29
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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30
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Watowich MM, MacLean EL, Hare B, Call J, Kaminski J, Miklósi Á, Snyder-Mackler N. Age influences domestic dog cognitive performance independent of average breed lifespan. Anim Cogn 2020; 23:795-805. [PMID: 32356029 DOI: 10.1007/s10071-020-01385-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 04/12/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022]
Abstract
Across mammals, increased body size is positively associated with lifespan. However, within species, this relationship is inverted. This is well illustrated in dogs (Canis familiaris), where larger dogs exhibit accelerated life trajectories: growing faster and dying younger than smaller dogs. Similarly, some age-associated traits (e.g., growth rate and physiological pace of aging) exhibit accelerated trajectories in larger breeds. Yet, it is unknown whether cognitive performance also demonstrates an accelerated life course trajectory in larger dogs. Here, we measured cognitive development and aging in a cross-sectional study of over 4000 dogs from 66 breeds using nine memory and decision-making tasks performed by citizen scientists as part of the Dognition project. Specifically, we tested whether cognitive traits follow a compressed (accelerated) trajectory in larger dogs, or the same trajectory for all breeds, which would result in limited cognitive decline in larger breeds. We found that all breeds, regardless of size or lifespan, tended to follow the same quadratic trajectory of cognitive aging-with a period of cognitive development in early life and decline in later life. Taken together, our results suggest that cognitive performance follows similar age-related trajectories across dog breeds, despite remarkable variation in developmental rates and lifespan.
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Affiliation(s)
- Marina M Watowich
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Evan L MacLean
- School of Anthropology, University of Arizona, Tucson, AZ, 85721, USA.,Department of Psychology, University of Arizona, Tucson, AZ, 85721, USA.,Cognitive Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Brian Hare
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA.,Center for Cognitive Neuroscience, Duke University, Durham, NC, 27708, USA
| | - Josep Call
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK
| | - Juliane Kaminski
- Centre for Comparative and Evolutionary Psychology, Department of Psychology, University of Portsmouth, Portsmouth, UK
| | - Ádám Miklósi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary.,MTA-ELTE Comparative Ethology Research Group, Budapest, Hungary
| | - Noah Snyder-Mackler
- Department of Biology, University of Washington, Seattle, WA, 98195, USA. .,Center for Evolution & Medicine, Arizona State University, Tempe, AZ, 85287, USA. .,School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA. .,Department of Psychology, University of Washington, Seattle, WA, 98195, USA. .,Nathan Shock Center of Excellence in the Basic Biology of Aging, Department of Pathology, University of Washington, Seattle, WA, 98195, USA. .,Center for Studies in Demography and Ecology, University of Washington, Seattle, WA, 98195, USA.
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31
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Liu S, Jiang S, Dong XG, Cui R, Ling Y, Zhao C. Novel Variants in the HMGA2 Gene Are Associated With Withers Height in Debao Pony. J Equine Vet Sci 2020; 88:102948. [PMID: 32303316 DOI: 10.1016/j.jevs.2020.102948] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/28/2019] [Accepted: 01/27/2020] [Indexed: 10/25/2022]
Abstract
The Debao pony is a well-known dwarf horse breed in China. High-mobility group AT-hook 2 (HMGA2) gene is regarded as one of the important candidate genes regulating body height in horses. The aim of this study was to study the association between mutations in HMGA2 gene and withers height in Debao ponies. The polymorphisms in all exons and partial introns of the HMGA2 gene were screened with sequencing across 180 Debao ponies. And the association between the DNA variants and withers height was analyzed. Seven genetic variants were identified in HMGA2 gene, including six novel variants. Among them, six mutations were located in two closed linked blocks. The three novel variants (In1-1, E5-1, and E5-2) in the 1st intron and the fifth exon and a known mutation (In1-2) had significant association with withers height in Debao ponies. These results suggest that the four variants have the potential to be used as genetic markers for dwarf horse breeding activities.
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Affiliation(s)
- Shuqin Liu
- Equine Center, China Agricultural University, Beijing, China; College of Animal Science and Technology, China Agricultural University, Beijing, China; National Engineering Laboratory for Animal Breeding, Beijing, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China
| | - Shunyan Jiang
- Equine Center, China Agricultural University, Beijing, China; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiang Gui Dong
- Equine Center, China Agricultural University, Beijing, China; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ran Cui
- Equine Center, China Agricultural University, Beijing, China; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yao Ling
- Equine Center, China Agricultural University, Beijing, China; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chunjiang Zhao
- Equine Center, China Agricultural University, Beijing, China; College of Animal Science and Technology, China Agricultural University, Beijing, China; National Engineering Laboratory for Animal Breeding, Beijing, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China; Beijing Key Laboratory of Animal Genetic Improvement, Beijing, China.
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32
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Srikanth K, Kim NY, Park W, Kim JM, Kim KD, Lee KT, Son JH, Chai HH, Choi JW, Jang GW, Kim H, Ryu YC, Nam JW, Park JE, Kim JM, Lim D. Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse. Sci Rep 2019; 9:16672. [PMID: 31723199 PMCID: PMC6853925 DOI: 10.1038/s41598-019-53102-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/18/2019] [Indexed: 12/16/2022] Open
Abstract
The Jeju horse, indigenous to the Jeju Island in Korea may have originated from Mongolian horses. Adaptations to the local harsh environment have conferred Jeju horse with unique traits such as small-sized body, stocky head, and shorter limbs. These characteristics have not been studied previously at the genomic level. Therefore, we sequenced and compared the genome of 41 horses belonging to 6 breeds. We identified numerous breed-specific non-synonymous SNPs and loss-of-function mutants. Demographic and admixture analyses showed that, though Jeju horse is genetically the closest to the Mongolian breeds, its genetic ancestry is independent of that of the Mongolian breeds. Genome wide selection signature analysis revealed that genes such as LCORL, MSTN, HMGA2, ZFAT, LASP1, PDK4, and ACTN2, were positively selected in the Jeju horse. RNAseq analysis showed that several of these genes were also differentially expressed in Jeju horse compared to Thoroughbred horse. Comparative muscle fiber analysis showed that, the type I muscle fibre content was substantially higher in Jeju horse compared to Thoroughbred horse. Our results provide insights about the selection of complex phenotypic traits in the small-sized Jeju horse and the novel SNPs identified will aid in designing high-density SNP chip for studying other native horse breeds.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Nam-Young Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju-do, 63242, Republic of Korea
| | - WonCheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jae-Min Kim
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Kyung-Tai Lee
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Ju-Hwan Son
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jung-Woo Choi
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Gul-Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | | | - Youn-Chul Ryu
- Division of Biotechnology, Jeju National University, Jeju, 63243, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Ansung-si, 17546, Republic of Korea.
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
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33
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Sándor S, Kubinyi E. Genetic Pathways of Aging and Their Relevance in the Dog as a Natural Model of Human Aging. Front Genet 2019; 10:948. [PMID: 31681409 PMCID: PMC6813227 DOI: 10.3389/fgene.2019.00948] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Aging research has experienced a burst of scientific efforts in the last decades as the growing ratio of elderly people has begun to pose an increased burden on the healthcare and pension systems of developed countries. Although many breakthroughs have been reported in understanding the cellular mechanisms of aging, the intrinsic and extrinsic factors that contribute to senescence on higher biological levels are still barely understood. The dog, Canis familiaris, has already served as a valuable model of human physiology and disease. The possible role the dog could play in aging research is still an open question, although utilization of dogs may hold great promises as they naturally develop age-related cognitive decline, with behavioral and histological characteristics very similar to those of humans. In this regard, family dogs may possess unmatched potentials as models for investigations on the complex interactions between environmental, behavioral, and genetic factors that determine the course of aging. In this review, we summarize the known genetic pathways in aging and their relevance in dogs, putting emphasis on the yet barely described nature of certain aging pathways in canines. Reasons for highlighting the dog as a future aging and gerontology model are also discussed, ranging from its unique evolutionary path shared with humans, its social skills, and the fact that family dogs live together with their owners, and are being exposed to the same environmental effects.
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Affiliation(s)
- Sára Sándor
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
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34
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MacLean EL, Snyder-Mackler N, vonHoldt BM, Serpell JA. Highly heritable and functionally relevant breed differences in dog behaviour. Proc Biol Sci 2019; 286:20190716. [PMID: 31575369 DOI: 10.1098/rspb.2019.0716] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Variation across dog breeds presents a unique opportunity to investigate the evolution and biological basis of complex behavioural traits. We integrated behavioural data from more than 14 000 dogs from 101 breeds with breed-averaged genotypic data (n = 5697 dogs) from over 100 000 loci in the dog genome. We found high levels of among-breed heritability for 14 behavioural traits (the proportion of trait variance attributable to genetic similarity among breeds). We next identified 131 single nucleotide polymorphisms associated with breed differences in behaviour, which were found in genes that are highly expressed in the brain and enriched for neurobiological functions and developmental processes, suggesting that they may be functionally associated with behavioural differences. Our results shed light on the heritability and genetic architecture of complex behavioural traits and identify dogs as a powerful model in which to address these questions.
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Affiliation(s)
- Evan L MacLean
- School of Anthropology, University of Arizona, Tucson, AZ, USA.,Department of Psychology, University of Arizona, Tucson, AZ, USA
| | - Noah Snyder-Mackler
- Department of Psychology, University of Washington, Seattle, WA, USA.,Center for Studies in Demography and Ecology, University of Washington, Seattle, WA, USA.,Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - James A Serpell
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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35
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Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies. PLoS Genet 2019; 15:e1008003. [PMID: 31525180 PMCID: PMC6762211 DOI: 10.1371/journal.pgen.1008003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/26/2019] [Accepted: 08/19/2019] [Indexed: 12/11/2022] Open
Abstract
Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference genome. SNP arrays of this density are sufficient for detecting genetic associations within breeds but are underpowered for finding associations across multiple breeds or in mixed-breed dogs, where linkage disequilibrium rapidly decays between markers, even though such studies would hold particular promise for mapping complex diseases and traits. Here we introduce an imputation reference panel, consisting of 365 diverse, whole-genome sequenced dogs and wolves, which increases the number of markers that can be queried in genome-wide association studies approximately 130-fold. Using previously genotyped dogs, we show the utility of this reference panel in identifying potentially novel associations, including a locus on CFA20 significantly associated with cranial cruciate ligament disease, and fine-mapping for canine body size and blood phenotypes, even when causal loci are not in strong linkage disequilibrium with any single array marker. This reference panel resource will improve future genome-wide association studies for canine complex diseases and other phenotypes. Complex traits are controlled by more than one gene and as such are difficult to map. For complex trait mapping in the domestic dog, researchers use the current array of 173,000 variants, with only minimal success. Here, we use a method called imputation to increase the number of variants–from 173,000 to 24 million–that can be queried in canine association studies. We use sequence data from the whole genomes of 365 dogs and wolves to accurately predict variants, in a separate cohort of dogs, that are not present on the array. Using dog body size, blood phenotypes, and a common orthopedic disease that involves rupture of the cranial cruciate ligament, we show that the increase in variants results in an increase in mapping power, through the identification of new associations and the narrowing of regions of interest. This imputation panel is particularly important because of its usefulness in improving complex trait mapping in the dog, which has significant implications for discovery of variants in humans with similar diseases.
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36
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The impact of incorrectly recorded parentage on inferred genotypes over multiple generations. Canine Genet Epidemiol 2019; 6:6. [PMID: 31360528 PMCID: PMC6639963 DOI: 10.1186/s40575-019-0074-3] [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: 05/15/2019] [Accepted: 07/08/2019] [Indexed: 11/30/2022] Open
Abstract
The absence of selective pressure against recessive deleterious mutations in the heterozygous state means that virtually every individual will carry several such mutations which have arisen over time. The inflation in frequency of a few of these mutations due to selective processes during domestication and breed formation have left modern domestic dog breeds with a high burden of genetic disease due to mutations at single genes. This has stimulated research into the causal mutations, and a consequential market in DNA tests, which enable breeders to distinguish heterozygotes from wild type homozygotes and determine pairings that will avoid producing diseased progeny. The genotypes of progeny of parents with known genotypes themselves may in some cases be definitively inferred. Importantly, two parents homozygous for non-disease causing alleles, will produce progeny with the same genotype, which may be assigned to the offspring (e.g. as ‘hereditary clear’) without the need for further testing. However, the veracity of assigned genotypes is dependent on the parentage being recorded without error, which is not the case in most species. Simulations presented here demonstrate that a modest rate of false paternity can result in a notable proportion of ‘hereditary clear’ assignments being false when ‘hereditary clear’ status is assigned across a number of generations (error rates exceeding 5% after 6 generations with a disease causing mutation frequency of 0.2). Erroneous assignment of ‘hereditary clear’ genotypes risks the production of puppies with the very disease for which a DNA test is available allowing avoidance. In light of these findings and to reduce the risks of producing puppies destined to be affected by such diseases, the Kennel Club has determined to limit the assignment of ‘hereditary clear’ status of registered dogs to 2 generations, with effect from January 2022.
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Ostrander EA, Wang GD, Larson G, vonHoldt BM, Davis BW, Jagannathan V, Hitte C, Wayne RK, Zhang YP. Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health. Natl Sci Rev 2019; 6:810-824. [PMID: 31598383 PMCID: PMC6776107 DOI: 10.1093/nsr/nwz049] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/14/2019] [Accepted: 04/09/2019] [Indexed: 12/18/2022] Open
Abstract
Dogs are the most phenotypically diverse mammalian species, and they possess more known heritable disorders than any other non-human mammal. Efforts to catalog and characterize genetic variation across well-chosen populations of canines are necessary to advance our understanding of their evolutionary history and genetic architecture. To date, no organized effort has been undertaken to sequence the world's canid populations. The Dog10K Consortium (http://www.dog10kgenomes.org) is an international collaboration of researchers from across the globe who will generate 20× whole genomes from 10 000 canids in 5 years. This effort will capture the genetic diversity that underlies the phenotypic and geographical variability of modern canids worldwide. Breeds, village dogs, niche populations and extended pedigrees are currently being sequenced, and de novo assemblies of multiple canids are being constructed. This unprecedented dataset will address the genetic underpinnings of domestication, breed formation, aging, behavior and morphological variation. More generally, this effort will advance our understanding of human and canine health.
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Affiliation(s)
- Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford OX1 3TG, UK
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-1014, USA
| | - Brian W Davis
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland
| | | | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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Cattai A, Bizzotto R, Cagnardi P, Di Cesare F, Franci P. A pharmacokinetic model optimized by covariates for propofol target-controlled infusion in dogs. Vet Anaesth Analg 2019; 46:568-578. [PMID: 31326349 DOI: 10.1016/j.vaa.2019.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/28/2019] [Accepted: 04/11/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVE To develop a population pharmacokinetic model for propofol target-controlled infusion (TCI) in dogs and to evaluate its performance for use in the clinical setting. STUDY DESIGN Prospective clinical study. ANIMALS A group of 40 client-owned dogs undergoing general anaesthesia for magnetic resonance imaging. METHODS Propofol was administered to 26 premedicated dogs and arterial blood samples were collected during the infusion and over 240 minutes after terminating the infusion. Propofol concentrations were measured by high-performance liquid chromatography. A population pharmacokinetic analysis was performed using a nonlinear mixed-effects modelling approach, allowing inter- and intra-individual variability estimation and quantitative evaluation of the influence of the following covariates: weight, body condition score, age, size-related age (Age_size), sex, premedication type, size and contrast agent administration. A final model was obtained using a stepwise approach in which individual covariate effects on each pharmacokinetic variable were incorporated. The performance of the developed TCI model was subsequently evaluated while inducing and maintaining anaesthesia in 14 premedicated dogs and assessed by comparing predicted and measured concentrations at specific time points. RESULTS Propofol pharmacokinetics was best described by a three-compartment model. Weight, Age_size, premedication and sex showed significant pharmacokinetic effects. Addition of the significant covariate/variable associations to the final model resulted in a reduction of the objective function value from 285.53 to -22.34. The median values of prediction error and absolute performance error were 3.1% and 28.4%, respectively. Induction targets between 4.0 and 6.5 μg mL-1 allowed intubation within 5.0 ± 0.9 minutes. Anaesthesia was achieved with targets between 3.0 and 6.5 μg mL-1. Mean time to extubation was 9.7 ± 2.6 minutes. All dogs recovered smoothly and without complications. CONCLUSIONS AND CLINICAL RELEVANCE Overall predictive performance of the pharmacokinetic model-driven infusion developed was clinically acceptable for administering propofol to dogs in routine anaesthesia.
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Affiliation(s)
- Andrea Cattai
- Department of Animal Medicine, Production and Health, Università degli Studi di Padova, Padua, Italy.
| | | | - Petra Cagnardi
- Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, Milan, Italy
| | - Federica Di Cesare
- Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, Milan, Italy
| | - Paolo Franci
- Department of Animal Medicine, Production and Health, Università degli Studi di Padova, Padua, Italy
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Plassais J, Kim J, Davis BW, Karyadi DM, Hogan AN, Harris AC, Decker B, Parker HG, Ostrander EA. Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology. Nat Commun 2019; 10:1489. [PMID: 30940804 PMCID: PMC6445083 DOI: 10.1038/s41467-019-09373-w] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 03/06/2019] [Indexed: 01/14/2023] Open
Abstract
Domestic dog breeds are characterized by an unrivaled diversity of morphologic traits and breed-associated behaviors resulting from human selective pressures. To identify the genetic underpinnings of such traits, we analyze 722 canine whole genome sequences (WGS), documenting over 91 million single nucleotide and small indels, creating a large catalog of genomic variation for a companion animal species. We undertake both selective sweep analyses and genome wide association studies (GWAS) inclusive of over 144 modern breeds, 54 wild canids and a hundred village dogs. Our results identify variants of strong impact associated with 16 phenotypes, including body weight variation which, when combined with existing data, explain greater than 90% of body size variation in dogs. We thus demonstrate that GWAS and selection scans performed with WGS are powerful complementary methods for expanding the utility of companion animal systems for the study of mammalian growth and biology.
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Affiliation(s)
- Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jaemin Kim
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Brian W Davis
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Texas A&M University, College Station, TX, 77840, USA
| | - Danielle M Karyadi
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Laboratory of Genetic Susceptibility, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA
| | - Andrew N Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alex C Harris
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Brennan Decker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Heidi G Parker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, 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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Liang J, Zhang Y, Wang L, Liu X, Yan H, Wang L, Zhang L. Molecular cloning of WIF1 and HMGA2 reveals ear-preferential expression while uncovering a missense mutation associated with porcine ear size in WIF1. Anim Genet 2019; 50:157-161. [PMID: 30815903 DOI: 10.1111/age.12759] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2018] [Indexed: 02/01/2023]
Abstract
Considerable diversity exists in porcine ear size, which is an important morphological feature of pig breeds. Previously, we localized four crucial candidate genes-high mobility group AT-hook 2 (HMGA2), LEM domain-containing 3 (LEMD3), methionine sulfoxide reductase B3 (MSRB3) and Wnt inhibitory factor 1 (WIF1)-on Sus Scrofa chromosome 5 affecting porcine ear size, then cloned LEMD3 and MSBR3. In this study, we performed rapid amplification of cDNA ends to obtain full-length cDNA sequences of 2338-bp WIF1 and 2998-bp HMGA2. Using quantitative real-time PCR, we revealed that WIF1 expression was highest in ear cartilage of 60-day-old pigs and that this is therefore a better candidate gene for ear size than HMGA2. We further screened coding sequence variants in both genes and identified only one missense mutation (WIF1:c.1167C>G) in a conserved epidermal growth factor-like domain from the mammalian WIF1 protein. The protein-altering mutation was significantly associated with ear size across the Large White × Minzhu hybrid and Beijing Black pig populations. When WIF1:c.1167C>G was included as fixed effect in the model to re-run a genome-wide association study in the Large White × Minzhu intercross population the P-value of the peak SNP on SSC5 from re-running the genome-wide association study dropped from 2.45E-12 to 7.33E-05. Taken together, the WIF1:c.1167C>G could be an important mutation associated with ear size. Our findings provide helpful information for further studies of the molecular mechanisms controlling porcine ear size.
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Affiliation(s)
- J Liang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Y Zhang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - L Wang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - X Liu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - H Yan
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - L Wang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - L Zhang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Chen C, Liu C, Xiong X, Fang S, Yang H, Zhang Z, Ren J, Guo Y, Huang L. Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p. Genet Sel Evol 2018; 50:72. [PMID: 30587124 PMCID: PMC6307293 DOI: 10.1186/s12711-018-0442-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 12/18/2018] [Indexed: 01/30/2023] Open
Abstract
Background The size and type of ears are important conformation characteristics that distinguish pig breeds. A significant quantitative trait locus (QTL) for ear size has been identified on SSC5 (SSC for Sus scrofa chromosome) but the underlying causative gene and mutation remain unknown. Thus, our aim was to identify the gene responsible for enlarged ears in pig. Results First, we narrowed down the QTL region on SSC5 to a 137.85-kb interval that harbors only the methionine sulfoxide reductase B3 (MSRB3) gene. Then, we identified a 38.7-kb copy number variation (CNV) that affects the last two exons of MSRB3 and could be the candidate causative mutation for this QTL. This CNV showed complete concordance with genotype at the QTL of the founder animals in a white Duroc × Erhualian F2 intercross and was found only in pigs from six Chinese indigenous breeds with large ears and from the Landrace breed with half-floppy ears. Moreover, it accounted for the significant association with ear size on SSC5 across the five pig populations tested. eQTL mapping revealed that this CNV was significantly associated with the expression of the microRNA (miRNA) miR-584-5p, which interacts with MSRB3, one of its target genes. In vivo and in vitro experiments confirmed that miR-584-5p inhibits the translation of MSRB3 mRNA. Taken together, these results led us to conclude that presence of the 38.7-kb CNV in the genome of some pig breeds affects ear size by altering the expression of miR-584-5p, which consequently hinders the expression of one of its target genes (e.g. MSRB3). Conclusions Our findings shed insight into the underlying mechanism of development of external ears in mammals and contribute to a better understanding of how the presence of CNV can regulate gene expression. Electronic supplementary material The online version of this article (10.1186/s12711-018-0442-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Chenlong Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.,Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Xinwei Xiong
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shaoming Fang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Hui Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhiyan Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yuanmei Guo
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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Genetic diversity and population structure of African village dogs based on microsatellite and immunity-related molecular markers. PLoS One 2018; 13:e0199506. [PMID: 29940023 PMCID: PMC6016929 DOI: 10.1371/journal.pone.0199506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 06/10/2018] [Indexed: 11/19/2022] Open
Abstract
The village and street dogs represent a unique model of canine populations. In the absence of selective breeding and veterinary care, they are subject mostly to natural selection. Their analyses contribute to understanding general mechanisms governing the genetic diversity, evolution and adaptation. In this study, we analyzed the genetic diversity and population structure of African village dogs living in villages in three different geographical areas in Northern Kenya. Data obtained for neutral microsatellite molecular markers were compared with those computed for potentially non-neutral markers of candidate immunity-related genes. The neutral genetic diversity was similar to other comparable village dog populations studied so far. The overall genetic diversity in microsatellites was higher than the diversity of European pure breeds, but it was similar to the range of diversity observed in a group composed of many European breeds, indicating that the African population has maintained a large proportion of the genetic diversity of the canine species as a whole. Microsatellite marker diversity indicated that the entire population is subdivided into three genetically distinct, although closely related subpopulations. This genetical partitioning corresponded to their geographical separation and the observed gene flow well correlated with the communication patterns among the three localities. In contrast to neutral microsatellites, the genetic diversity in immunity-related candidate SNP markers was similar across all three subpopulations and to the European group. It seems that the genetic structure of this particular population of Kenyan village dogs is mostly determined by geographical and anthropogenic factors influencing the gene flow between various subpopulations rather than by biological factors, such as genetic contribution of original migrating populations and/or the pathogen-mediated selection. On the other hand, the study of oldest surviving dogs suggested a biological mechanism, i.e. a possible advantage of the overal heterozygosity marked by the the microsatellite loci analyzed.
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High mobility group A2 (HMGA2) deficiency in pigs leads to dwarfism, abnormal fetal resource allocation, and cryptorchidism. Proc Natl Acad Sci U S A 2018; 115:5420-5425. [PMID: 29735702 PMCID: PMC6003518 DOI: 10.1073/pnas.1721630115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Expression of HMGA2 is strongly associated with body size and growth in mice and humans. In mice, inactivation of one or both alleles of Hmga2 results in body-size reductions of 20% and 60%, respectively. In humans, microdeletions involving the HMGA2 locus result in short stature, suggesting the function of the HMGA2 protein is conserved among mammals. To test this hypothesis, we generated HMGA2-deficient pigs via gene editing and somatic cell nuclear transfer (SCNT). Examination of growth parameters revealed that HMGA2-/+ male and female pigs were on average 20% lighter and smaller than HMGA2+/+ matched controls (P < 0.05). HMGA2-/- boars showed significant size reduction ranging from 35 to 85% of controls depending on age (P < 0.05), and organ weights were also affected (P < 0.05). HMGA2-/+ gilts and boars exhibited normal reproductive development and fertility, while HMGA2-/- boars were sterile due to undescended testes (cryptorchidism). Crossbreeding HMGA2-/+ boars and gilts produced litters lacking the HMGA2-/- genotype. However, analysis of day (D) D40 and D78 pregnancies indicated that HMGA2-/- fetuses were present at the expected Mendelian ratio, but placental abnormalities were seen in the D78 HMGA2-/- concepti. Additionally, HMGA2-/- embryos generated by gene editing and SCNT produced multiple pregnancies and viable offspring, indicating that lack of HMGA2 is not lethal per se. Overall, our results show that the effect of HMGA2 with respect to growth regulation is highly conserved among mammals and opens up the possibility of regulating body and organ size in a variety of mammalian species including food and companion animals.
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Rochus CM, Tortereau F, Plisson-Petit F, Restoux G, Moreno-Romieux C, Tosser-Klopp G, Servin B. Revealing the selection history of adaptive loci using genome-wide scans for selection: an example from domestic sheep. BMC Genomics 2018; 19:71. [PMID: 29357834 PMCID: PMC5778797 DOI: 10.1186/s12864-018-4447-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 01/11/2018] [Indexed: 01/11/2023] Open
Abstract
Background One of the approaches to detect genetics variants affecting fitness traits is to identify their surrounding genomic signatures of past selection. With established methods for detecting selection signatures and the current and future availability of large datasets, such studies should have the power to not only detect these signatures but also to infer their selective histories. Domesticated animals offer a powerful model for these approaches as they adapted rapidly to environmental and human-mediated constraints in a relatively short time. We investigated this question by studying a large dataset of 542 individuals from 27 domestic sheep populations raised in France, genotyped for more than 500,000 SNPs. Results Population structure analysis revealed that this set of populations harbour a large part of European sheep diversity in a small geographical area, offering a powerful model for the study of adaptation. Identification of extreme SNP and haplotype frequency differences between populations listed 126 genomic regions likely affected by selection. These signatures revealed selection at loci commonly identified as selection targets in many species (“selection hotspots”) including ABCG2, LCORL/NCAPG, MSTN, and coat colour genes such as ASIP, MC1R, MITF, and TYRP1. For one of these regions (ABCG2, LCORL/NCAPG), we could propose a historical scenario leading to the introgression of an adaptive allele into a new genetic background. Among selection signatures, we found clear evidence for parallel selection events in different genetic backgrounds, most likely for different mutations. We confirmed this allelic heterogeneity in one case by resequencing the MC1R gene in three black-faced breeds. Conclusions Our study illustrates how dense genetic data in multiple populations allows the deciphering of evolutionary history of populations and of their adaptive mutations. Electronic supplementary material The online version of this article (10.1186/s12864-018-4447-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christina Marie Rochus
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France. .,UFR Génétique, Élevage et Reproduction, AgroParisTech, Université Paris-Saclay, 752 31, Paris, France. .,Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden.
| | - Flavie Tortereau
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France
| | | | - Gwendal Restoux
- UFR Génétique, Élevage et Reproduction, AgroParisTech, Université Paris-Saclay, 752 31, Paris, France.,Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, 752 31, Paris, France
| | - Carole Moreno-Romieux
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France
| | - Gwenola Tosser-Klopp
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France
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Mazzatenta A, Carluccio A, Robbe D, Giulio CD, Cellerino A. The companion dog as a unique translational model for aging. Semin Cell Dev Biol 2017; 70:141-153. [DOI: 10.1016/j.semcdb.2017.08.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
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Ostrander EA, Wayne RK, Freedman AH, Davis BW. Demographic history, selection and functional diversity of the canine genome. Nat Rev Genet 2017; 18:705-720. [DOI: 10.1038/nrg.2017.67] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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47
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vonHoldt BM, Shuldiner E, Koch IJ, Kartzinel RY, Hogan A, Brubaker L, Wanser S, Stahler D, Wynne CDL, Ostrander EA, Sinsheimer JS, Udell MAR. Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs. SCIENCE ADVANCES 2017; 3:e1700398. [PMID: 28776031 PMCID: PMC5517105 DOI: 10.1126/sciadv.1700398] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/15/2017] [Indexed: 05/04/2023]
Abstract
Although considerable progress has been made in understanding the genetic basis of morphologic traits (for example, body size and coat color) in dogs and wolves, the genetic basis of their behavioral divergence is poorly understood. An integrative approach using both behavioral and genetic data is required to understand the molecular underpinnings of the various behavioral characteristics associated with domestication. We analyze a 5-Mb genomic region on chromosome 6 previously found to be under positive selection in domestic dog breeds. Deletion of this region in humans is linked to Williams-Beuren syndrome (WBS), a multisystem congenital disorder characterized by hypersocial behavior. We associate quantitative data on behavioral phenotypes symptomatic of WBS in humans with structural changes in the WBS locus in dogs. We find that hypersociability, a central feature of WBS, is also a core element of domestication that distinguishes dogs from wolves. We provide evidence that structural variants in GTF2I and GTF2IRD1, genes previously implicated in the behavioral phenotype of patients with WBS and contained within the WBS locus, contribute to extreme sociability in dogs. This finding suggests that there are commonalities in the genetic architecture of WBS and canine tameness and that directional selection may have targeted a unique set of linked behavioral genes of large phenotypic effect, allowing for rapid behavioral divergence of dogs and wolves, facilitating coexistence with humans.
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Affiliation(s)
- Bridgett M. vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Corresponding author.
| | - Emily Shuldiner
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Translational Genetics and Genomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Disorders, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Ilana Janowitz Koch
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rebecca Y. Kartzinel
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Andrew Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Brubaker
- Department of Animal and Rangeland Sciences, Oregon State University, OR 97331, USA
| | - Shelby Wanser
- Department of Animal and Rangeland Sciences, Oregon State University, OR 97331, USA
| | - Daniel Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY 82190, USA
| | - Clive D. L. Wynne
- Department of Psychology, Arizona State University, Tempe, AZ 85287, USA
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Janet S. Sinsheimer
- Departments of Human Genetics and Biomathematics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Monique A. R. Udell
- Department of Animal and Rangeland Sciences, Oregon State University, OR 97331, USA
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48
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Abstract
The genetic architecture of behavioral traits in dogs is of great interest to owners, breeders, and professionals involved in animal welfare, as well as to scientists studying the genetics of animal (including human) behavior. The genetic component of dog behavior is supported by between-breed differences and some evidence of within-breed variation. However, it is a challenge to gather sufficiently large datasets to dissect the genetic basis of complex traits such as behavior, which are both time-consuming and logistically difficult to measure, and known to be influenced by nongenetic factors. In this study, we exploited the knowledge that owners have of their dogs to generate a large dataset of personality traits in Labrador Retrievers. While accounting for key environmental factors, we demonstrate that genetic variance can be detected for dog personality traits assessed using questionnaire data. We identified substantial genetic variance for several traits, including fetching tendency and fear of loud noises, while other traits revealed negligibly small heritabilities. Genetic correlations were also estimated between traits; however, due to fairly large SEs, only a handful of trait pairs yielded statistically significant estimates. Genomic analyses indicated that these traits are mainly polygenic, such that individual genomic regions have small effects, and suggested chromosomal associations for six of the traits. The polygenic nature of these traits is consistent with previous behavioral genetics studies in other species, for example in mouse, and confirms that large datasets are required to quantify the genetic variance and to identify the individual genes that influence behavioral traits.
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49
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Domyan ET, Shapiro MD. Pigeonetics takes flight: Evolution, development, and genetics of intraspecific variation. Dev Biol 2016; 427:241-250. [PMID: 27847323 DOI: 10.1016/j.ydbio.2016.11.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 10/28/2016] [Accepted: 11/10/2016] [Indexed: 11/26/2022]
Abstract
Intensive artificial selection over thousands of years has produced hundreds of varieties of domestic pigeon. As Charles Darwin observed, the morphological differences among breeds can rise to the magnitude of variation typically observed among different species. Nevertheless, different pigeon varieties are interfertile, thereby enabling forward genetic and genomic approaches to identify genes that underlie derived traits. Building on classical genetic studies of pigeon variation, recent molecular investigations find a spectrum of coding and regulatory alleles controlling derived traits, including plumage color, feather growth polarity, and limb identity. Developmental and genetic analyses of pigeons are revealing the molecular basis of variation in a classic example of extreme intraspecific diversity, and have the potential to nominate genes that control variation among other birds and vertebrates in general.
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Affiliation(s)
- Eric T Domyan
- Department of Biology, Utah Valley University, Orem, UT, United States.
| | - Michael D Shapiro
- Department of Biology, University of Utah, Salt Lake City, UT, United States.
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50
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Friedenberg SG, Meurs KM, Mackay TFC. Evaluation of artificial selection in Standard Poodles using whole-genome sequencing. Mamm Genome 2016; 27:599-609. [PMID: 27510710 DOI: 10.1007/s00335-016-9660-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 07/28/2016] [Indexed: 12/11/2022]
Abstract
Identifying regions of artificial selection within dog breeds may provide insights into genetic variation that underlies breed-specific traits or diseases-particularly if these traits or disease predispositions are fixed within a breed. In this study, we searched for runs of homozygosity (ROH) and calculated the d i statistic (which is based upon F ST) to identify regions of artificial selection in Standard Poodles using high-coverage, whole-genome sequencing data of 15 Standard Poodles and 49 dogs across seven other breeds. We identified consensus ROH regions ≥1 Mb in length and common to at least ten Standard Poodles covering 0.6 % of the genome, and d i regions that most distinguish Standard Poodles from other breeds covering 3.7 % of the genome. Within these regions, we identified enriched gene pathways related to olfaction, digestion, and taste, as well as pathways related to adrenal hormone biosynthesis, T cell function, and protein ubiquitination that could contribute to the pathogenesis of some Poodle-prevalent autoimmune diseases. We also validated variants related to hair coat and skull morphology that have previously been identified as being under selective pressure in Poodles, and flagged additional polymorphisms in genes such as ITGA2B, CBX4, and TNXB that may represent strong candidates for other common Poodle disorders.
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Affiliation(s)
- Steven G Friedenberg
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27607, USA.
| | - Kathryn M Meurs
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27607, USA
| | - Trudy F C Mackay
- Department of Biological Sciences, College of Sciences, North Carolina State University, 3510 Thomas Hall, Raleigh, NC, 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27607, USA
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