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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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Belyakin SN, Maksimov DA, Pobedintseva MA, Laktionov PP, Voronova D. ASIP Promoter Variants Predict the Sesame Coat Color in Shiba Inu Dogs. Vet Sci 2022; 9:vetsci9050222. [PMID: 35622750 PMCID: PMC9146165 DOI: 10.3390/vetsci9050222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Animals exhibit a wide variety of genetically determined coat colors and pigmentation patterns that serve important roles in adaptation and communication. Although the genetics of the main coat colors in dogs have been studied extensively, there are types of coat pigmentation that have not been explained yet. Recently, an association between the variants in the ASIP gene Ventral (VP) and Hair Cycle (HCP) promoters with different coat colors in dogs has been established. Here, we used the new findings as a basis to investigate the genetics of the red sesame coat color in Shiba Inu dogs. Our study revealed that red sesame dogs carry a specific heterozygous ASIP promoter diplotype, VP2-HCP1/VP2-HCP3, where VP2-HCP1 is responsible for the red coat with a dark overlay, and VP2-HCP3 for a tan point-like pattern. This finding explains the inheritance of this coat color pattern and can be used by breeders to produce dogs with this rare phenotype. A comparison of sesame dogs (VP2-HCP1/VP2-HCP3) to a dog homozygous for the VP2-HCP1 promoter haplotype suggests that the incomplete dominance between the ASIP alleles may be involved in the sesame coat formation. These results are in good agreement with the new model explaining how different levels of ASIP gene expression affect the regulation of pigment synthesis in melanocytes.
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Affiliation(s)
- Stepan N. Belyakin
- Genomics Laboratory, Institute of Molecular and Cellular Biology, 630090 Novosibirsk, Russia; (D.A.M.); (M.A.P.); (P.P.L.)
- VetGenomics Laboratory, 630090 Novosibirsk, Russia
- Correspondence:
| | - Daniil A. Maksimov
- Genomics Laboratory, Institute of Molecular and Cellular Biology, 630090 Novosibirsk, Russia; (D.A.M.); (M.A.P.); (P.P.L.)
| | - Maria A. Pobedintseva
- Genomics Laboratory, Institute of Molecular and Cellular Biology, 630090 Novosibirsk, Russia; (D.A.M.); (M.A.P.); (P.P.L.)
| | - Petr P. Laktionov
- Genomics Laboratory, Institute of Molecular and Cellular Biology, 630090 Novosibirsk, Russia; (D.A.M.); (M.A.P.); (P.P.L.)
- Laboratory of Epigenetics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Dinara Voronova
- Russian Nihonken Hozonkai (NIPPO) Club, 129626 Moscow, Russia;
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Frattini S, Polli M, Cortellari M, Negro A, Bionda A, Riva J, Rizzi R, Marelli S, Crepaldi P. Genetic trend of the junctional epidermolysis bullosa in the German shorthaired pointer in Italy. Vet Rec Open 2021; 8:e15. [PMID: 34457315 PMCID: PMC8374380 DOI: 10.1002/vro2.15] [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: 05/14/2020] [Revised: 10/09/2020] [Accepted: 11/12/2020] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Epidermolysis bullosa (EB) is a hereditary heterogeneous group of mechanobullous disorders caused by mutations in several structural skin proteins observed in both humans and animals. In this work, we report the incidence and the genetic trend of the junctional epidermolysis bullosa (JEB), a major type of EB, in the Italian German Shorthaired Pointer (GSPs) population in a 10 years span. METHODS In this study, we monitored the genetic trend of JEB in the Italian population of the GSPs from 2009 to 2018 in 750 animals. The studied mutation was the insertion (4818+207 ins 6.5 kb) of repetitive satellite DNA within intron 35 of the LAMA3 gene. RESULTS Allele frequencies showed a reduction of the mutated (C) allele during the years, with the only exception of 2017, when 13 dogs were diagnosed as carrier for the genetic pathology. A regression logistic analysis was performed, including sex, coat colour and their interaction. Our results showed that there was a statistically significant association with coat colour. CONCLUSIONS The simplicity and the low cost of the analysis for the detection of this pathology suggests that a deeper identification of carrier dogs will allow better breeding strategies and management, leading to a rapid JEB eradication.
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Affiliation(s)
- Stefano Frattini
- Department of Agricultural and Environmental Sciences‐ProductionLandscape, AgroenergyUniversity of MilanMilanItaly
| | - Michele Polli
- Department of Veterinary MedicineUniversity of MilanMilanItaly
| | - Matteo Cortellari
- Department of Agricultural and Environmental Sciences‐ProductionLandscape, AgroenergyUniversity of MilanMilanItaly
| | - Alessio Negro
- Department of Agricultural and Environmental Sciences‐ProductionLandscape, AgroenergyUniversity of MilanMilanItaly
| | - Arianna Bionda
- Department of Agricultural and Environmental Sciences‐ProductionLandscape, AgroenergyUniversity of MilanMilanItaly
| | | | - Rita Rizzi
- Department of Veterinary MedicineUniversity of MilanMilanItaly
| | - Stefano Marelli
- Department of Veterinary MedicineUniversity of MilanMilanItaly
| | - Paola Crepaldi
- Department of Agricultural and Environmental Sciences‐ProductionLandscape, AgroenergyUniversity of MilanMilanItaly
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Brancalion L, Haase B, Wade CM. Canine coat pigmentation genetics: a review. Anim Genet 2021; 53:3-34. [PMID: 34751460 DOI: 10.1111/age.13154] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/21/2021] [Accepted: 10/20/2021] [Indexed: 11/27/2022]
Abstract
Our understanding of canine coat colour genetics and the associated health implications is developing rapidly. To date, there are 15 genes with known roles in canine coat colour phenotypes. Many coat phenotypes result from complex and/or epistatic genetic interactions among variants within and between loci, some of which remain unidentified. Some genes involved in canine pigmentation have been linked to aural, visual and neurological impairments. Consequently, coat pigmentation in the domestic dog retains considerable ethical and economic interest. In this paper we discuss coat colour phenotypes in the domestic dog, the genes and variants responsible for these phenotypes and any proven coat colour-associated health effects.
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Affiliation(s)
- L Brancalion
- Faculty of Science, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, 2006, Australia
| | - B Haase
- Faculty of Science, School of Veterinary Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - C M Wade
- Faculty of Science, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, 2006, Australia
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Dog colour patterns explained by modular promoters of ancient canid origin. Nat Ecol Evol 2021; 5:1415-1423. [PMID: 34385618 PMCID: PMC8484016 DOI: 10.1038/s41559-021-01524-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023]
Abstract
Distinctive colour patterns in dogs are an integral component of canine diversity. Colour pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves but important gaps remain in understanding how these patterns evolved and are genetically controlled. In other mammals, variation at the ASIP gene controls both the temporal and spatial distribution of yellow and black pigments. Here, we identify independent regulatory modules for ventral and hair cycle ASIP expression, and we characterize their action and evolutionary origin. Structural variants define multiple alleles for each regulatory module and are combined in different ways to explain five distinctive dog colour patterns. Phylogenetic analysis reveals that the haplotype combination for one of these patterns is shared with Arctic white wolves and that its hair cycle-specific module probably originated from an extinct canid that diverged from grey wolves more than 2 million years ago. Natural selection for a lighter coat during the Pleistocene provided the genetic framework for widespread colour variation in dogs and wolves.
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Cortellari M, Bionda A, Talenti A, Ceccobelli S, Attard G, Lasagna E, Crepaldi P, Liotta L. Genomic variability of Cirneco dell’Etna and the genetic distance with other dog breeds. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1873076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia, University of Milan, Milano, Italy
| | - Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia, University of Milan, Milano, Italy
| | - Andrea Talenti
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - George Attard
- Department of Rural Sciences and Food Systems, University of Malta, Msida, Malta
- Ministry for Agriculture, Fisheries and Animal Rights, Agency for the Governance of Agricultural Bio-Resources, Marsa, Malta
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia, University of Milan, Milano, Italy
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, University of Messina, Messina, Italy
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Anderson H, Honkanen L, Ruotanen P, Mathlin J, Donner J. Comprehensive genetic testing combined with citizen science reveals a recently characterized ancient MC1R mutation associated with partial recessive red phenotypes in dog. Canine Med Genet 2020; 7:16. [PMID: 33292722 PMCID: PMC7643265 DOI: 10.1186/s40575-020-00095-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/19/2020] [Indexed: 11/23/2022] Open
Abstract
Background The Melanocortin 1 Receptor (MC1R) plays a central role in regulation of coat color determination in various species and is commonly referred to as the “E (extension) Locus”. Allelic variation of the MC1R gene is associated with coat color phenotypes EM (melanistic mask), EG (grizzle/domino) and e1–3 (recessive red) in dogs. In addition, a previous study of archeological dog specimens over 10,000 years of age identified a variant p.R301C in the MC1R gene that may have influenced coat color of early dogs. Results Commercial genotyping of 11,750 dog samples showed the R301C variant of the MC1R gene was present in 35 breeds or breed varieties, at an allele frequency of 1.5% in the tested population. We detected no linkage disequilibrium between R301C and other tested alleles of the E locus. Based on current convention we propose that R301C should be considered a novel allele of the E locus, which we have termed eA for “e ancient red”. Phenotype analysis of owner-provided dog pictures reveals that the eA allele has an impact on coat color and is recessive to wild type E and dominant to the e alleles. In dominant black (KB/*) dogs it can prevent the phenotypic expression of the K locus, and the expressed coat color is solely determined by the A locus. In the absence of dominant black, eA/eA and eA/e genotypes result in the coat color patterns referred to in their respective breed communities as domino in Alaskan Malamute and other Spitz breeds, grizzle in Chihuahua, and pied in Beagle. Conclusions This study demonstrates a large genotype screening effort to identify the frequency and distribution of the MC1R R301C variant, one of the earliest mutations captured by canine domestication, and citizen science empowered characterization of its impact on coat color. Supplementary Information The online version contains supplementary material available at 10.1186/s40575-020-00095-7.
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