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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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Slavney AJ, Kawakami T, Jensen MK, Nelson TC, Sams AJ, Boyko AR. Five genetic variants explain over 70% of hair coat pheomelanin intensity variation in purebred and mixed breed domestic dogs. PLoS One 2021; 16:e0250579. [PMID: 34043658 PMCID: PMC8158882 DOI: 10.1371/journal.pone.0250579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/08/2021] [Indexed: 11/19/2022] Open
Abstract
In mammals, the pigment molecule pheomelanin confers red and yellow color to hair, and the intensity of this coloration is caused by variation in the amount of pheomelanin. Domestic dogs exhibit a wide range of pheomelanin intensity, ranging from the white coat of the Samoyed to the deep red coat of the Irish Setter. While several genetic variants have been associated with specific coat intensity phenotypes in certain dog breeds, they do not explain the majority of phenotypic variation across breeds. In order to gain further insight into the extent of multigenicity and epistatic interactions underlying coat pheomelanin intensity in dogs, we leveraged a large dataset obtained via a direct-to-consumer canine genetic testing service. This consisted of genome-wide single nucleotide polymorphism (SNP) genotype data and owner-provided photos for 3,057 pheomelanic mixed breed and purebred dogs from 63 breeds and varieties spanning the full range of canine coat pheomelanin intensity. We first performed a genome-wide association study (GWAS) on 2,149 of these dogs to search for additional genetic variants that underlie intensity variation. GWAS identified five loci significantly associated with intensity, of which two (CFA15 29.8 Mb and CFA20 55.8 Mb) replicate previous findings and three (CFA2 74.7 Mb, CFA18 12.9 Mb, CFA21 10.9 Mb) have not previously been reported. In order to assess the combined predictive power of these loci across dog breeds, we used our GWAS data set to fit a linear model, which explained over 70% of variation in coat pheomelanin intensity in an independent validation dataset of 908 dogs. These results introduce three novel pheomelanin intensity loci, and further demonstrate the multigenic nature of coat pheomelanin intensity determination in domestic dogs.
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Affiliation(s)
- Andrea J. Slavney
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Takeshi Kawakami
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Meghan K. Jensen
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Thomas C. Nelson
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Aaron J. Sams
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Adam R. Boyko
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York, United States of America
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Tsunoi T, Noju K, Eto T, Suzuki H. A 1-bp deletion in Mc1r in a Norway rat (Rattus norvegicus) from Sado Island, Japan gives rise to a yellowish color variant: an insight into mammalian MC1R variants. Genes Genet Syst 2021; 96:89-97. [PMID: 33994400 DOI: 10.1266/ggs.20-00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The melanocortin-1 receptor gene (MC1R) controls production of the pigments eumelanin and pheomelanin. Changes in MC1R lead to variation in coat color in mammals, which can range from entirely black (melanism) to yellowish. In this study, we report a case of a wild-caught Norway rat (Rattus norvegicus) from Sado Island, Japan with a yellowish coat color. Upon sequencing the whole coding region of the Mc1r gene (954 bp), we found a 1-bp deletion at site 337 (c.337del), indicative of a frameshift mutation, which was characterized as a severe loss-of-function or null mutation. A spectrophotometer was used to measure coat color, revealing that the rat had a distinctly lighter coat, based on lightness score, than mice with homozygous similar loss-of-function mutations. This implies that loss-of-function mutations can yield different phenotypes in murine rodents. The loss-of-function-mutant rat exhibited a contrasting coat pattern consisting of darker and lighter colors along its dorsal and ventral sides, respectively. Similar patterns have been observed in homozygous MC1R-deficient mutants in other mammals, implying that the countershading pattern can still be expressed despite the absence of MC1R in the melanocyte.
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Affiliation(s)
- Takeru Tsunoi
- Graduate School of Environmental Science, Hokkaido University
| | - Koki Noju
- Graduate School of Science, Hokkaido University
| | - Takeshi Eto
- Faculty of Agriculture, University of the Ryukyus
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University
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Bychkova E, Viktorovskaya O, Filippova E, Eliseeva Z, Barabanova L, Sotskaya M, Markov A. Identification of a candidate genetic variant for the Himalayan color pattern in dogs. Gene 2020; 769:145212. [PMID: 33039541 DOI: 10.1016/j.gene.2020.145212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/11/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022]
Abstract
Acromelanism is a temperature-dependent hypopigmentation pattern commonly manifested as the Himalayan coat color found in rabbits, rats, mice, minks, and gerbils, wherein the extreme "points" are dark and the torso is pale. It is known as the Siamese pattern in cats. Himalayan color is genetically determined by the allelic variant ch of the locus C, later identified as the tyrosinase gene TYR. The tyrosinase functions at the initial steps of melanin production, and alteration of its activity by sequence changes results in pigmentation defects in vertebrates. The presence of acromelanism in dogs has not been described until now. We analyzed a DNA sample of a dachshund with a unique coat color resembling the Himalayan type. Sequencing of the coding part of the TYR gene from the proband revealed a homozygous variant (c.230G > A) in exon 1, leading to an amino acid substitution (p.R77Q) in a conserved region of the protein. The proband's mother, which is black-and-tan, is a heterozygous carrier of the c.230A allele, while none of the 210 dogs of different breeds, unrelated to the proband, carried the c.230A allele. These results suggest that the identified sequence variant is likely the cause of the Himalayan coloration of the proband.
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Affiliation(s)
- Elina Bychkova
- Center of Veterinary Genetics ZOOGEN, Saint Petersburg 194156, Russia; Animal Genetics Laboratory, Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg 199034, Russia.
| | | | | | - Zhanna Eliseeva
- Animal Genetics Laboratory, Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg 199034, Russia
| | - Larisa Barabanova
- Animal Genetics Laboratory, Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg 199034, Russia
| | - Maria Sotskaya
- Moscow State University of Psychology and Education, Moscow 127051, Russia
| | - Anton Markov
- Center of Veterinary Genetics ZOOGEN, Saint Petersburg 194156, Russia
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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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Hédan B, Cadieu E, Botherel N, Dufaure de Citres C, Letko A, Rimbault M, Drögemüller C, Jagannathan V, Derrien T, Schmutz S, Leeb T, André C. Identification of a Missense Variant in MFSD12 Involved in Dilution of Phaeomelanin Leading to White or Cream Coat Color in Dogs. Genes (Basel) 2019; 10:E386. [PMID: 31117290 PMCID: PMC6562630 DOI: 10.3390/genes10050386] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 11/17/2022] Open
Abstract
White coat color in mammals has been selected several times during the domestication process. Numerous dog breeds are fixed for one form of white coat color that involves darkly pigmented skin. The genetic basis of this color, due to the absence of pigment in the hairs, was suggested to correspond to extreme dilution of the phaeomelanin, by both the expression of only phaeomelanin (locus E) and its extreme dilution (locus I). To go further, we performed genome-wide association studies (GWAS) using a multiple breed approach. The first GWAS, using 34 white dogs and 128 non-white dogs, including White Shepherds, Poodles, Cotons de Tulear and Bichons allowed us to identify two significantly associated loci on the locus E and a novel locus on chromosome 20. A second GWAS using 15 other breeds presenting extreme phaeomelanin dilution confirmed the position of locus I on the chromosome 20 (position 55 Mb pcorrected = 6 × 10-13). Using whole-genome sequencing, we identified a missense variant in the first exon of MFSD12, a gene recently identified to be involved in human, mouse and horse pigmentation. We confirmed the role of this variant in phaeomelanin dilution of numerous canine breeds, and the conserved role of MFSD12 in mammalian pigmentation.
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Affiliation(s)
- Benoit Hédan
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France.
| | - Edouard Cadieu
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France.
| | - Nadine Botherel
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France.
| | | | - Anna Letko
- Institute of Genetics, University of Bern, 3001 Bern, Swizterland.
| | - Maud Rimbault
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France.
| | - Cord Drögemüller
- Institute of Genetics, University of Bern, 3001 Bern, Swizterland.
| | | | - Thomas Derrien
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France.
| | - Sheila Schmutz
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Swizterland.
| | - Catherine André
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France.
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Ziółkowski M, Redlarska A, Adamus-Fiszer K, Kania-Gierdziewicz J. Inheritance of different coat colours in Newfoundland dogs in Poland. ROCZNIKI NAUKOWE POLSKIEGO TOWARZYSTWA ZOOTECHNICZNEGO 2019. [DOI: 10.5604/01.3001.0013.4539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aim of the study was to present the manner in which coat colour genes are inherited in the Newfoundland dog breed and to estimate the number of dogs with various coat colours in the Polish Newfoundland dog population in 2017. This population numbered 656 dogs, including 248 males and 408 females. The estimated number of dogs of this breed also included all registered puppies, broken down by gender and coat colour. The genes determining coat colour are described, including more precisely the genes responsible for the coat colour of the Newfoundland breed. According to FCI regulations, the coat colours for Newfoundland dogs are black, brown and black-and-white. Other colours, such as brown-and-white or blue, are not recognized for breeding purposes in Europe. The study found that the dominant black coat was predominant in the Polish Newfoundland dog population in 2017. These dogs could be heterozygous at some other loci and have undesirable alleles. The second most common coat colour was chocolate, while the fewest dogs had spotted coats. The group with spotted coats contained more males than females, in contrast to the other two colour variants. There were also individuals with the blue coat colour, which is not accepted for breeding, as the result of mating of parents with proper coat colours. An understanding of how dog coat colours are inherited and the need for tests to determine coat colour genotypes would make it possible to foresee the occurrence of incorrect colours in subsequent generations, which is crucial for Newfoundland dog breeders, whose goal is to obtain dogs whose coat colour is in line with the FCI standard.
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Affiliation(s)
- Maciej Ziółkowski
- University of Agriculture in Krakow Faculty of Animal Sciences, Department of Genetics and Animal Breeding
| | - Agnieszka Redlarska
- University of Agriculture in Krakow Faculty of Animal Sciences Department of Genetics and Animal Breeding
| | - Katarzyna Adamus-Fiszer
- University of Agriculture in Krakow Faculty of Animal Sciences Department of Genetics and Animal Breeding
| | - Joanna Kania-Gierdziewicz
- University of Agriculture in Krakow Faculty of Animal Sciences Department of Genetics and Animal Breeding
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Korec E, Hančl M, Bydžovská M, Chalupa O, Korcová J. Inheritance of coat colour in the cane Corso Italiano dog. BMC Genet 2019; 20:24. [PMID: 30832561 PMCID: PMC6398231 DOI: 10.1186/s12863-019-0731-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/21/2019] [Indexed: 11/15/2022] Open
Abstract
Background The inheritance of different coat colours in the Cane Corso Italiano dog has not been described thus far. We analysed data from 23,271 dogs and bitches using the Cane Corso Italiano Pedigree Database. We are describing for the first time the coat colour segregation ratios in Cane Corso Italiano offspring arising from crosses between parents of all possible coat colour combinations. Results Segregation ratios that do not follow a Mendelian pattern suggest that additional genes are active in the determination of coat colour. Segregation ratios of offspring produced by parental crossing (male colour A x female colour B) were compared with the ratios of offspring produced by reciprocal crossing (male colour B x female colour A) in all possible coat colour combinations. Most of the segregation ratios were the same, but some segregation ratios in reciprocal crosses differed. This result suggests that at least one gene responsible for coat colour is located on a sex chromosome. The sex ratio was analysed in the offspring of all colour groups. A ratio of 1:1 was not confirmed in 8 colour groups by the chi-square test. Conclusions We described for the first time coat colour segregation ratios in Cane Corso Italiano dogs. Furthermore, we present the hypothesis that at least one gene responsible for coat colour is located on a sex chromosome.
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Affiliation(s)
- Evžen Korec
- Department of Genetics, ZOO Tábor, Dukelských hrdinů 19, 17000, Prague 7, Czech Republic.
| | - Matyáš Hančl
- Department of Genetics, ZOO Tábor, Dukelských hrdinů 19, 17000, Prague 7, Czech Republic
| | - Marie Bydžovská
- Department of Genetics, ZOO Tábor, Dukelských hrdinů 19, 17000, Prague 7, Czech Republic
| | - Ondřej Chalupa
- Department of Genetics, ZOO Tábor, Dukelských hrdinů 19, 17000, Prague 7, Czech Republic
| | - Jana Korcová
- Department of Genetics, ZOO Tábor, Dukelských hrdinů 19, 17000, Prague 7, Czech Republic
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Caduff M, Bauer A, Jagannathan V, Leeb T. A single base deletion in the SLC45A2 gene in a Bullmastiff with oculocutaneous albinism. Anim Genet 2017; 48:619-621. [PMID: 28737247 DOI: 10.1111/age.12582] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2017] [Indexed: 11/29/2022]
Abstract
Oculocutaneous albinism type 4 (OCA4) in humans and similar phenotypes in many animal species are caused by variants in the SLC45A2 gene, encoding a putative sugar transporter. In dog, two independent SLC45A2 variants are known that cause oculocutaneous albinism in Doberman Pinschers and several small dog breeds respectively. For the present study, we investigated a Bullmastiff with oculocutaneous albinism. The affected dog was highly inbred and resulted from the mating of a sire to its own grandmother. We obtained whole genome sequence data from the affected dog and searched specifically for variants in candidate genes known to cause albinism. We detected a single base deletion in exon 6 of the SLC45A2 gene (NM_001037947.1:c.1287delC) that has not been reported thus far. This deletion is predicted to result in an early premature stop codon. It was confirmed by Sanger sequencing and perfectly co-segregated with the phenotype in the available family members. We genotyped 174 unrelated dogs from diverse breeds, all of which were homozygous wildtype. We therefore suggest that SLC45A2:c.1287delC causes the observed oculocutaneous albinism in the affected Bullmastiff.
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Affiliation(s)
- M Caduff
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - A Bauer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
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Peters L, Humble E, Kröcker N, Fuchs B, Forcada J, Hoffman JI. Born blonde: a recessive loss-of-function mutation in the melanocortin 1 receptor is associated with cream coat coloration in Antarctic fur seals. Ecol Evol 2016; 6:5705-17. [PMID: 27547348 PMCID: PMC4983585 DOI: 10.1002/ece3.2290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 02/03/2023] Open
Abstract
Although the genetic basis of color variation has been extensively studied in humans and domestic animals, the genetic polymorphisms responsible for different color morphs remain to be elucidated in many wild vertebrate species. For example, hypopigmentation has been observed in numerous marine mammal species but the underlying mutations have not been identified. A particularly compelling candidate gene for explaining color polymorphism is the melanocortin 1 receptor (MC1R), which plays a key role in the regulation of pigment production. We therefore used Antarctic fur seals (Arctocephalus gazella) as a highly tractable marine mammal system with which to test for an association between nucleotide variation at the MC1R and melanin‐based coat color phenotypes. By sequencing 70 wild‐type individuals with dark‐colored coats and 26 hypopigmented individuals with cream‐colored coats, we identified a nonsynonymous mutation that results in the substitution of serine with phenylalanine at an evolutionarily highly conserved structural domain. All of the hypopigmented individuals were homozygous for the allele coding for phenylalanine, consistent with a recessive loss‐of‐function allele. In order to test for cryptic population structure, which can generate artefactual associations, and to evaluate whether homozygosity at the MC1R could be indicative of low genome‐wide heterozygosity, we also genotyped all of the individuals at 50 polymorphic microsatellite loci. We were unable to detect any population structure and also found that wild‐type and hypopigmented individuals did not differ significantly in their standardized multilocus heterozygosity. Such a lack of association implies that hypopigmented individuals are unlikely to suffer disproportionately from inbreeding depression, and hence, we have no reason to believe that they are at a selective disadvantage in the wider population.
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Affiliation(s)
- Lucy Peters
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany; College of Medical, Veterinary & Life Sciences University of Glasgow Graham Kerr Building Glasgow G12 8QQ UK
| | - Emily Humble
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany; British Antarctic Survey High Cross, Madingley Road Cambridge CB3 OET UK
| | - Nicole Kröcker
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany
| | - Birgit Fuchs
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany
| | - Jaume Forcada
- British Antarctic Survey High Cross, Madingley Road Cambridge CB3 OET UK
| | - Joseph I Hoffman
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany
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Wijesena HR, Schmutz SM. A Missense Mutation in SLC45A2 Is Associated with Albinism in Several Small Long Haired Dog Breeds. J Hered 2015; 106:285-8. [DOI: 10.1093/jhered/esv008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/02/2015] [Indexed: 11/13/2022] Open
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12
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Zouganelis GD, Ogden R, Nahar N, Runfola V, Bonab M, Ardalan A, Radford D, Barnett R, Larson G, Hildred A, Jones M, Scarlett G. An old dog and new tricks: Genetic analysis of a Tudor dog recovered from the Mary Rose wreck. Forensic Sci Int 2014; 245:51-7. [DOI: 10.1016/j.forsciint.2014.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/23/2014] [Accepted: 10/04/2014] [Indexed: 11/25/2022]
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13
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Winkler PA, Gornik KR, Ramsey DT, Dubielzig RR, Venta PJ, Petersen-Jones SM, Bartoe JT. A partial gene deletion of SLC45A2 causes oculocutaneous albinism in Doberman pinscher dogs. PLoS One 2014; 9:e92127. [PMID: 24647637 PMCID: PMC3960214 DOI: 10.1371/journal.pone.0092127] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/17/2014] [Indexed: 02/04/2023] Open
Abstract
The first white Doberman pinscher (WDP) dog was registered by the American Kennel Club in 1976. The novelty of the white coat color resulted in extensive line breeding of this dog and her offspring. The WDP phenotype closely resembles human oculocutaneous albinism (OCA) and clinicians noticed a seemingly high prevalence of pigmented masses on these dogs. This study had three specific aims: (1) produce a detailed description of the ocular phenotype of WDPs, (2) objectively determine if an increased prevalence of ocular and cutaneous melanocytic tumors was present in WDPs, and (3) determine if a genetic mutation in any of the genes known to cause human OCA is causal for the WDP phenotype. WDPs have a consistent ocular phenotype of photophobia, hypopigmented adnexal structures, blue irides with a tan periphery and hypopigmented retinal pigment epithelium and choroid. WDPs have a higher prevalence of cutaneous melanocytic neoplasms compared with control standard color Doberman pinschers (SDPs); cutaneous tumors were noted in 12/20 WDP (<5 years of age: 4/12; >5 years of age: 8/8) and 1/20 SDPs (p<0.00001). Using exclusion analysis, four OCA causative genes were investigated for their association with WDP phenotype; TYR, OCA2, TYRP1 and SLC45A2. SLC45A2 was found to be linked to the phenotype and gene sequencing revealed a 4,081 base pair deletion resulting in loss of the terminus of exon seven of SLC45A2 (chr4∶77,062,968–77,067,051). This mutation is highly likely to be the cause of the WDP phenotype and is supported by a lack of detectable SLC45A2 transcript levels by reverse transcriptase PCR. The WDP provides a valuable model for studying OCA4 visual disturbances and melanocytic neoplasms in a large animal model.
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Affiliation(s)
- Paige A. Winkler
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, United States of America
- Genetics Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Kara R. Gornik
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - David T. Ramsey
- The Animal Ophthalmology Center, Williamston, Michigan, United States of America
| | - Richard R. Dubielzig
- Comparative Ocular Pathology Laboratory of Wisconsin, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Patrick J. Venta
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, United States of America
- Genetics Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Simon M. Petersen-Jones
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, United States of America
- Genetics Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Joshua T. Bartoe
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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14
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Abstract
Color variation in companion animals has long been of interest to the breeding and scientific communities. Simple traits, like black versus brown or yellow versus black, have helped to explain principles of transmission genetics and continue to serve as models for studying gene action and interaction. We present a molecular genetic review of pigmentary variation in dogs and cats using a nomenclature and logical framework established by early leaders in the field. For most loci in which molecular variants have been identified (nine in dogs and seven in cats), homologous mutations exist in laboratory mice and/or humans. Exceptions include the K locus in dogs and the Tabby locus in cats, which give rise to alternating stripes or marks of different color, and which illustrate the continued potential of coat color genetics to provide insight into areas that transcend pigment cell biology.
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Affiliation(s)
- Christopher B. Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 and Department of Genetics, Stanford University, Stanford, California 94305;,
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 and Department of Genetics, Stanford University, Stanford, California 94305;,
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15
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Schmutz SM, Melekhovets Y. Coat color DNA testing in dogs: Theory meets practice. Mol Cell Probes 2012; 26:238-42. [DOI: 10.1016/j.mcp.2012.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 03/21/2012] [Accepted: 03/27/2012] [Indexed: 10/28/2022]
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16
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Tsai KL, Noorai RE, Starr-Moss AN, Quignon P, Rinz CJ, Ostrander EA, Steiner JM, Murphy KE, Clark LA. Genome-wide association studies for multiple diseases of the German Shepherd Dog. Mamm Genome 2012; 23:203-11. [PMID: 22105877 PMCID: PMC3509149 DOI: 10.1007/s00335-011-9376-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 10/18/2011] [Indexed: 01/02/2023]
Abstract
The German Shepherd Dog (GSD) is a popular working and companion breed for which over 50 hereditary diseases have been documented. Herein, SNP profiles for 197 GSDs were generated using the Affymetrix v2 canine SNP array for a genome-wide association study to identify loci associated with four diseases: pituitary dwarfism, degenerative myelopathy (DM), congenital megaesophagus (ME), and pancreatic acinar atrophy (PAA). A locus on Chr 9 is strongly associated with pituitary dwarfism and is proximal to a plausible candidate gene, LHX3. Results for DM confirm a major locus encompassing SOD1, in which an associated point mutation was previously identified, but do not suggest modifier loci. Several SNPs on Chr 12 are associated with ME and a 4.7 Mb haplotype block is present in affected dogs. Analysis of additional ME cases for a SNP within the haplotype provides further support for this association. Results for PAA indicate more complex genetic underpinnings. Several regions on multiple chromosomes reach genome-wide significance. However, no major locus is apparent and only two associated haplotype blocks, on Chrs 7 and 12 are observed. These data suggest that PAA may be governed by multiple loci with small effects, or it may be a heterogeneous disorder.
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Affiliation(s)
- Kate L. Tsai
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Rooksana E. Noorai
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Alison N. Starr-Moss
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Pascale Quignon
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. Institut de Génétique et Développement de Rennes, CNRS-UMR6061, Université de Rennes 1, 2 avenue Prof. Léon Bernard, CS34317, Rennes Cedex 35043, France
| | - Caitlin J. Rinz
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Elaine A. Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jörg M. Steiner
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Keith E. Murphy
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Leigh Anne Clark
- Department of Genetics and Biochemistry, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
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17
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Conant EK, Juras R, Cothran EG. Incidence of the mask phenotype M264V mutation in Labrador Retrievers. Res Vet Sci 2011; 91:e98-9. [PMID: 21353269 DOI: 10.1016/j.rvsc.2011.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 01/26/2011] [Accepted: 02/01/2011] [Indexed: 11/19/2022]
Abstract
The introduction of SNP (Single Nucleotide Polymorphism) chips allows for the rapid typing of multiple markers for many individuals at one time. Our lab routinely types dogs using a custom designed combined panel of SNPs for parentage verification and a number of genes for diagnostic tests using an OpenArray platform manufactured by BioTrove (Woburn, MA, USA). By utilizing the same SNP panel across a wide array of canine breeds it is possible to detect trait-associated SNPs in breeds not thought to carry those traits. We genotyped 245 Labrador Retrievers on the canine SNP chip and found 13 animals heterozygous for the M264V mutation associated with autosomal dominant mask trait, and one animal homozygous for this trait. The color genotypes for these animals were further examined. In standard colored Labradors (black, chocolate, and yellow), the mask phenotype would never be distinguishable. As illustrated by this example, we feel this SNP panel is a valuable method for discovering traits not known to exist in a breed.
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Affiliation(s)
- E K Conant
- Texas A&M University, Department of Veterinary Integrative Biosciences, CVM, TAMU 4458, College Station, TX 77843-4458, USA.
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18
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Oguro-Okano M, Honda M, Yamazaki K, Okano K. Mutations in the melanocortin 1 receptor, β-defensin103 and agouti signaling protein genes, and their association with coat color phenotypes in Akita-inu dogs. J Vet Med Sci 2011; 73:853-8. [PMID: 21321476 DOI: 10.1292/jvms.10-0439] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
To identify factors that control coat color in Akita-inu dogs, we sequenced all the exons of the melanocortin 1 receptor (MC1R), β-defensin103 (CBD103) and agouti signaling protein (ASIP) genes of dogs with four distinct coat colors, namely, brindle, sesame, red and white. Then we examined correlations among specific alleles and coat color. In the case of the MC1R gene, all white dogs were homozygous for a nonsense mutation, R306ter, while brindle, sesame, and red dogs had at least one R306 allele. In the case of the CBD103 gene, all brindle dogs were heterozygous for the G23del mutation (deletion of codon 23, encoding glycine), while all sesame and red dogs were homozygous for G23. In the case of the ASIP gene, all dogs, regardless of coat color, had at least one S82 H83 allele. A missense mutation in the ASIP gene, P87L, was identified for the first time in some Akita-inu dogs but was not associated with any specific coloration. Our results indicate that the 2 key mutations, R306ter in the MC1R gene and G23del in the CBD103 gene, are associated with the phenotypic discriminations among brindle, red/sesame, and white coats, while no mutation that might potentially be associated with the discrimination of a sesame coat from a red coat is present in the coding sequences of these three genes.
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Affiliation(s)
- Mieko Oguro-Okano
- Department of Animal Health Technology, Yamazaki Gakuen University, Tokyo, Japan.
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Tsuboi K, Hayashi Y, Jogahara T, Ogura G, Murata Y, Oda SI. Oculocutaneous albinism in Suncus murinus: establishment of a strain and identification of its responsible gene. Exp Anim 2009; 58:31-40. [PMID: 19151509 DOI: 10.1538/expanim.58.31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The house musk shrew Suncus murinus (Insectivora, Soricidae) is referred to as suncus in a laboratory context. Although the capture of albino-like shrews (wild suncus) has been reported previously, albino-like strains have never been established, and the molecular basis of the character has remained elusive. We have established an OCAO mutant strain (oculocutaneous albinism Okinawa), from a wild suncus with a white coat and red eyes, which was captured in 2002. During the course of establishing the strain, it was revealed that the albino-like phenotype was inherited in an autosomal recessive manner. To elucidate the molecular basis of this phenotype, we cloned the suncus cDNAs for tyrosinase (Tyr), pink-eyed dilution (p), and solute carrier family 45, member 2 (Slc45a2), since these genes are involved in oculocutaneous albinism in various species, including humans. Several polymorphisms were identified in these genes; however, linkage analysis excluded the involvement of Tyr and p. On the other hand, two amino acid substitutions (V240A and G366E) were identified in Slc45a2 that cosegregated with the phenotype in the OCAO mutant strain. While V240A was also present in colored suncus collected from Okinawa, G366E was unique to the albino-like suncus and heterozygous carriers. Thus, we conclude that a mutation in Slc45a2 (G366E) is responsible for an albino-like phenotype in Suncus murinus.
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Affiliation(s)
- Kie Tsuboi
- Laboratory of Animal Management and Resources, Graduate School of Bio-Agricultural Sciences, Nagoya University, Japan
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20
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Abstract
Tremendous progress has been made in identifying genes involved in pigmentation in dogs in the past few years. Comparative genomics has both aided and benefited from these findings. Seven genes that cause specific coat colours and/or patterns in dogs have been identified: melanocortin 1 receptor, tyrosinase related protein 1, agouti signal peptide, melanophilin, SILV (formerly PMEL17), microphthalmia-associated transcription factor and beta-defensin 103. Although not all alleles have been yet identified at each locus, DNA tests are available for many. The identification of these alleles has provided information on interactions in this complex set of genes involved in both pigmentation and neurological development. The review also discusses pleiotropic effects of some coat colour genes as they relate to disease. The alleles found in various breeds have shed light on some potential breed development histories and phylogenetic relationships. The information is of value to dog breeders who have selected for and against specific colours since breed standards and dog showing began in the late 1800s. Because coat colour is such a visible trait, this information will also be a valuable teaching resource.
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Affiliation(s)
- S M Schmutz
- Department of Animal and Poultry Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, Canada S7N 5A8.
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