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Li R, Li D, Xu S, Zhang P, Zhang Z, He F, Li W, Sun G, Jiang R, Li Z, Tian Y, Liu X, Kang X. Whole-transcriptome sequencing reveals a melanin-related ceRNA regulatory network in the breast muscle of Xichuan black-bone chicken. Poult Sci 2024; 103:103539. [PMID: 38382189 PMCID: PMC10900940 DOI: 10.1016/j.psj.2024.103539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
The economic losses incurred due to reduced muscle pigmentation highlight the crucial role of melanin-based coloration in the meat of black-bone chickens. Melanogenesis in the breast muscle of black-bone chickens is currently poorly understood in terms of molecular mechanisms. This study employed whole-transcriptome sequencing to analyze black and white breast muscle samples from black-bone chickens, leading to the identification of 367 differentially expressed (DE) mRNAs, 48 DElncRNAs, 104 DEcircRNAs, and 112 DEmiRNAs involved in melanin deposition. Based on these findings, a competitive endogenous RNA (ceRNA) network was developed to better understand the complex mechanisms of melanin deposition. Furthermore, our analysis revealed key DEmRNAs (TYR, DCT, EDNRB, MLPH and OCA2) regulated by DEmiRNAs (gga-miR-140-5p, gga-miR-1682, gga-miR-3529, gga-miR-499-3p, novel-m0012-3p, gga-miR-200b-5p, gga-miR-203a, gga-miR-6651-5p, gga-miR-7455-3p, gga-miR-31-5p, miR-140-x, miR-455-x, novel-m0065-3p, gga-miR-29b-1-5p, miR-455-y, novel-m0085-3p, and gga-miR-196-1-3p). These DEmiRNAs competitively interacted with DElncRNAs including MSTRG.2609.2, MSTRG.4185.1, LOC112530666, LOC112533366, LOC771030, LOC107054724, LOC121107411, LOC100859072, LOC101750037, LOC121108550, LOC121109224, LOC121110876, and LOC101749016, as well as DEcircRNAs, such as novel_circ_000158, novel_circ_000623, novel_001518, and novel_circ_003596. The findings from this study provide insight into the mechanisms that regulate lncRNA, circRNA, miRNA, and mRNA expression in chicken melanin deposition.
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Affiliation(s)
- Ruiting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - DongHua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China.
| | - Shuohui Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Pengwei Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Zhiyuan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Fumin He
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China; The Shennong Laboratory, Zhengzhou, 450046, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China; The Shennong Laboratory, Zhengzhou, 450046, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China; The Shennong Laboratory, Zhengzhou, 450046, China
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Genes of Congenital Dermatologic Disorders in Dogs—A Review. FOLIA VETERINARIA 2021. [DOI: 10.2478/fv-2021-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
This article presents an overview of up-to-date identified genes responsible for congenital canine skin diseases of dogs and the characteristics of these diseases. Congenital skin diseases constitute a specific group of dermatologic disorders that plays an important role in breeding of purebred dogs. They include primary seborrhoea, ichthyosis, hereditary nasal parakeratosis, dermatomyositis, colour dilution alopecia, skin mucinosis, dermoid sinus, lethal acrodermatitis, acral mutilation syndrome, keratoconjunctivitis sicca, ichthyosiform dermatosis, bullous epidermolysis, exfoliative dermal lupus erythematosus, congenital footpad hyperkeratosis and sebaceous adenitis. In the majority of cases, their occurrence is linked to particular breeds. In more than half of these diseases a specific defective gene variant responsible for the disease has been identified. Genetic tests for identification of the relevant defective genes serve as an important tool in the diagnostics of diseases in veterinary practice and in breeding of purebred dogs.
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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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Caramalac SM, Caramalac SM, Babo-Terra VJ, Ramos CAN, Palumbo MIP. PCR-RFLP molecular confirmation of color dilution alopecia in dogs in Brazil. J Vet Diagn Invest 2021; 33:984-986. [PMID: 34088257 PMCID: PMC8366239 DOI: 10.1177/10406387211022309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Color dilution alopecia (CDA) is a dermatopathy observed exclusively in animals having a diluted coat color. In dogs, color dilution occurs as a result of a single-nucleotide variation (SNV) c.-22G > A in the melanophilin gene. We standardized a PCR-restriction-fragment length polymorphism (PCR-RFLP) technique to identify this mutation and determine its frequency in dogs in Brazil. The standardized PCR-RFLP technique could efficiently identify the SNV c.-22G > A in the melanophilin gene, with mutated allele frequencies of 0.1, 0.1, and 0.0875 in Dachshund, Miniature Pinscher, and Yorkshire Terrier breeds, respectively, with no statistical difference among the breeds (p = 0.252). The mutation was identified in 2 homozygous Dachshund dogs with alopecia, confirming the clinical characteristic of CDA. The standardization of a simpler and more accessible molecular technique for recognition of the SNV c.-22G > A in the melanophilin gene allows identification of heterozygous (phenotypically normal) dogs that can be excluded from reproduction, to avoid the birth of dogs with diluted coat color and consequently CDA.
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Affiliation(s)
- Silvana M. Caramalac
- Faculty of Veterinary Medicine and Animal Science, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Simone M. Caramalac
- Faculty of Veterinary Medicine and Animal Science, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Veronica J. Babo-Terra
- Faculty of Veterinary Medicine and Animal Science, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Carlos A. N. Ramos
- Faculty of Veterinary Medicine and Animal Science, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Mariana I. P. Palumbo
- Faculty of Veterinary Medicine and Animal Science, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
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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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Chen Y, Hu S, Liu M, Zhao B, Yang N, Li J, Chen Q, Zhou J, Bao G, Wu X. Analysis of Genome DNA Methylation at Inherited Coat Color Dilutions of Rex Rabbits. Front Genet 2021; 11:603528. [PMID: 33552123 PMCID: PMC7859435 DOI: 10.3389/fgene.2020.603528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/15/2020] [Indexed: 12/02/2022] Open
Abstract
Background: The dilution of color in rabbits is associated with many different genetic mechanisms that form different color groups. A number of previous studies have revealed potential regulatory mechanisms by which epigenetics regulate pigmentation. However, the genome-wide DNA methylation involved in animal coat color dilution remains unknown. Results: We compared genome-wide DNA methylation profiles in Rex rabbit hair follicles in a Chinchilla group (Ch) and a diluted Chinchilla group (DCh) through whole-genome bisulfite sequencing (WGBS). Approximately 3.5% of the cytosine sites were methylated in both groups, of which the CG methylation type was in greatest abundance. In total, we identified 126,405 differentially methylated regions (DMRs) between the two groups, corresponding to 11,459 DMR-associated genes (DMGs). Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that these DMGs were principally involved in developmental pigmentation and Wnt signaling pathways. In addition, two DMRs were randomly selected to verify that the WGBS data were reliable using bisulfite sequencing PCR, and seven DMGs were analyzed to establish the relationship between the level of DNA methylation and mRNA expression using qRT-PCR. Due to the limitation of small sample size, replication of the results with a larger sample size would be important in future studies. Conclusion: These findings provide evidence that there is an association between inherited color dilution and DNA methylation alterations in hair follicles, greatly contributing to our understanding of the epigenetic regulation of rabbit pigmentation.
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Affiliation(s)
- Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Shuaishuai Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ming Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Naisu Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qiuran Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Juan Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guolian Bao
- Animal Husbandry and Veterinary Research Institute Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, China
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Being Merle: The Molecular Genetic Background of the Canine Merle Mutation. Genes (Basel) 2020; 11:genes11060660. [PMID: 32560567 PMCID: PMC7349775 DOI: 10.3390/genes11060660] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
The intensity of the merle pattern is determined by the length of the poly(A) tail of a repeat element which has been inserted into the boundary of intron 10 and exon 11 of the PMEL17 locus in reverse orientation. This poly(A) tail behaves as a microsatellite, and due to replication slippage, longer and shorter alleles of it might be generated during cell divisions. The length of the poly(A) tail regulates the splicing mechanism. In the case of shorter tails, the removal of intron 10 takes place at the original splicing, resulting in a normal premelanosome protein (PMEL). Longer tails generate larger insertions, forcing splicing to a cryptic splice site, thereby coding for an abnormal PMEL protein, which is unable to form the normal fibrillar matrix of the eumelanosomes. Thus, eumelanin deposition ensuring the dark color formation is reduced. In summary, the longer the poly(A) tail, the lighter the coat color intensity of the melanocytes. These mutations can occur in the somatic cells and the resulting cell clones will shape the merle pattern of the coat. When they take place in the germ line, they occasionally produce offspring with unexpected color variations which are different from those of their parents.
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8
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Posbergh CJ, Staiger EA, Huson HJ. A Stop-Gain Mutation within MLPH Is Responsible for the Lilac Dilution Observed in Jacob Sheep. Genes (Basel) 2020; 11:genes11060618. [PMID: 32512769 PMCID: PMC7349772 DOI: 10.3390/genes11060618] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 11/16/2022] Open
Abstract
A coat color dilution, called lilac, was observed within the Jacob sheep breed. This dilution results in sheep appearing gray, where black would normally occur. Pedigree analysis suggested an autosomal recessive inheritance. Whole-genome sequencing of a dilute case, a known carrier, and sixteen non-dilute sheep was used to identify the molecular variant responsible for the coat color change. Through investigation of the genes MLPH, MYO5A, and RAB27A, we discovered a nonsynonymous mutation within MLPH, which appeared to match the reported autosomal recessive nature of the lilac dilution. This mutation (NC_019458.2:g.3451931C>A) results in a premature stop codon being introduced early in the protein (NP_001139743.1:p.Glu14*), likely losing its function. Validation testing of additional lilac Jacob sheep and known carriers, unrelated to the original case, showed a complete concordance between the mutation and the dilution. This stop-gain mutation is likely the causative mutation for dilution within Jacob sheep.
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Affiliation(s)
- Christian J. Posbergh
- Department of Animal Science, Cornell University, Ithaca, NY 14853, USA;
- Correspondence: (C.J.P.); (H.J.H.)
| | - Elizabeth A. Staiger
- Department of Animal Science, Cornell University, Ithaca, NY 14853, USA;
- Department of Animal Sciences, Auburn University, Auburn, AL 36849, USA
| | - Heather J. Huson
- Department of Animal Science, Cornell University, Ithaca, NY 14853, USA;
- Correspondence: (C.J.P.); (H.J.H.)
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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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Li J, Chen Y, Liu M, Chen Q, Zhou J, Bao G, Wu X. Association of Melanophilin (MLPH) gene polymorphism with coat colour in Rex rabbits. WORLD RABBIT SCIENCE 2020. [DOI: 10.4995/wrs.2020.12082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Rex rabbit, with multiple phenotypes and colourful fur, is an interesting model for assessing the effect of coat colour gene mutations on characteristic pigmentation phenotype. Based on previous study, the <em>melanophilin</em> (<em>MLPH</em>) gene is a positional candidate gene related coat colour dilution. The fur colours are a lighter shade, e.g. grey instead of black. We sequenced 1689 base pairs of the <em>MLPH</em> gene in Chinchilla and black Rex rabbit. A total of 13 polymorphisms were identified, including seven missense mutations. The rabbit <em>MLPH</em> gene has a very high GC content and the protein shows 64.87% identity to the orthologous human protein (lack of homologous amino acids encoded by human MLPH exon 9). Hardy-Weinberg test showed that, except for the g.606C>A single nucleotid polymorphism (SNP), all other SNPs were in Hardy-Weinberg equilibrium. Haplotype analysis revealed that the seven missense mutation SNPs of two strains of Rex rabbits formed 10 haplotypes, but there were only seven major types of haplotypes (haplotype frequency <em>P</em>>0.05). The major haplotypes of the Chinchilla and black Rex rabbits were H1/H2/H3/H4/H5 and H1/H2/H3/H6/H8, respectively. The special haplotypes of Chinchilla Rex rabbit (H4, H5, H7) were consistently associated with the Chinchilla phenotype. This study provides evidence that different coat colour formation may be caused by one or more mutations within <em>MLPH</em> gene in several Rex rabbit strains. The data on polymorphisms that are associated with the Chinchilla phenotype facilitate the breeding of rabbits with defined coat colours.
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Weich K, Affolter V, York D, Rebhun R, Grahn R, Kallenberg A, Bannasch D. Pigment Intensity in Dogs is Associated with a Copy Number Variant Upstream of KITLG. Genes (Basel) 2020; 11:genes11010075. [PMID: 31936656 PMCID: PMC7017362 DOI: 10.3390/genes11010075] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 01/14/2023] Open
Abstract
Dogs exhibit a wide variety of coat color types, and many genes have been identified that control pigment production, appearance, and distribution. Some breeds, such as the Nova Scotia Duck Tolling Retriever (NSDTR), exhibit variation in pheomelanin pigment intensity that is not explained by known genetic variants. A genome-wide association study comparing light red to dark red in the NSDTR identified a significantly associated region on canine chromosome 15 (CFA 15:23 Mb–38 Mb). Coverage analysis of whole genome sequence data from eight dogs identified a 6 kb copy number variant (CNV) 152 kb upstream of KITLG. Genotyping with digital droplet PCR (ddPCR) confirmed a significant association between an increased copy number with the dark-red coat color in NSDTR (p = 6.1 × 10−7). The copy number of the CNV was also significantly associated with coat color variation in both eumelanin and pheomelanin-based Poodles (p = 1.5 × 10−8, 4.0 × 10−9) and across other breeds. Moreover, the copy number correlated with pigment intensity along the hair shaft in both pheomelanin and eumelanin coats. KITLG plays an important role in melanogenesis, and variants upstream of KITLG have been associated with coat color variation in mice as well as hair color in humans consistent with its role in the domestic dog.
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Affiliation(s)
- Kalie Weich
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616, USA;
| | - Verena Affolter
- Department of Pathology, Microbiology, and Immunology, University of California-Davis, Davis, CA 95616, USA;
| | - Daniel York
- Department of Surgical and Radiological Sciences, University of California-Davis, Davis, CA 95616, USA; (D.Y.); (R.R.)
| | - Robert Rebhun
- Department of Surgical and Radiological Sciences, University of California-Davis, Davis, CA 95616, USA; (D.Y.); (R.R.)
| | - Robert Grahn
- Veterinary Genetics Laboratory, University of California-Davis, Davis, CA 95616, USA; (R.G.); (A.K.)
| | - Angelica Kallenberg
- Veterinary Genetics Laboratory, University of California-Davis, Davis, CA 95616, USA; (R.G.); (A.K.)
| | - Danika Bannasch
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616, USA;
- Correspondence: ; Tel.: +1-530-754-8728
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Genomic Characterization of External Morphology Traits in Kelpies Does Not Support Common Ancestry with the Australian Dingo. Genes (Basel) 2019; 10:genes10050337. [PMID: 31058880 PMCID: PMC6563003 DOI: 10.3390/genes10050337] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 01/06/2023] Open
Abstract
The Kelpie is a breed developed in Australia for use as a livestock herding dog. It has been proposed that the development of the breed included gene flow from the Australian Dingo (Canis dingo), a canid species present on the Australian continent for around 4000 years. The Kelpie breed is split between working and conformation types that have readily recognizable differences in external morphology. We characterize known gene variants relating to external morphology in sequenced representatives of both Kelpie types (Australian Kelpie—conformation; Australian Working Kelpie—herding) and compare the variants present with those in sequenced Australian Dingoes, including 25 canids with locus-constrained data and one with a whole genome sequence. Variants assessed include identified coat color and ear morphology variants. We describe a new variant site in the transcribed region of methionine sulfoxide reductase 3 that may relate to ear phenotype. None of the morphology variants analyzed offer support for co-ancestry of the Kelpie breed with the Australian Dingo.
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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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14
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Langevin M, Synkova H, Jancuskova T, Pekova S. Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh. PLoS One 2018; 13:e0198536. [PMID: 30235206 PMCID: PMC6147463 DOI: 10.1371/journal.pone.0198536] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/09/2018] [Indexed: 12/25/2022] Open
Abstract
It has been recognized that the Merle coat pattern in dogs is not only a visually interesting feature, but it also exerts an important biological role, in terms of hearing and vision impairments. In 2006, the Merle (M) locus was mapped to the SILV gene (aka PMEL) with a SINE element in it, and the inserted retroelement was proven causative to the Merle phenotype. Mapping of the M locus was a genetic breakthrough and many breeders started implementing SILV SINE testing in their breeding programs. Unfortunately, the situation turned out complicated as genotypes of Merle tested individuals did not always correspond to expected phenotypes, sometimes with undesired health consequences in the offspring. Two variants of SILV SINE, allelic to the wild type sequence, have been described so far–Mc and M. Here we report a significantly larger portfolio of existing Merle alleles (Mc, Mc+, Ma, Ma+, M, Mh) in Merle dogs, which are associated with unique coat color features and stratified health impairment risk. The refinement of allelic identification was made possible by systematic, detailed observation of Merle phenotypes in a cohort of 181 dogs from known Merle breeds, by many breeders worldwide, and the use of advanced molecular technology enabling the discrimination of individual Merle alleles with significantly higher precision than previously available. We also show that mosaicism of Merle alleles is an unexpectedly frequent phenomenon, which was identified in 30 out of 181 (16.6%) dogs in our study group. Importantly, not only major alleles, but also minor Merle alleles can be inherited by the offspring. Thus, mosaic findings cannot be neglected and must be reported to the breeder in their whole extent. Most importantly, sperm cells seem to be a significant source of germline Merle allelic variants which can be passed to the offspring on Mendelian basis and explain unusual genotype / phenotype findings in the offspring. In light of negative health consequences that may be attributed to certain Merle breeding strategies, we strongly advocate implementation of the refined Merle allele testing for all dogs of Merle breeds to help the breeders in selection of suitable mating partners and production of healthy offspring.
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Affiliation(s)
- Mary Langevin
- Cat´s Cradle Catahoulas, Oro Medonte, Ontario, Canada
| | - Helena Synkova
- European Association of Louisiana Catahoulas, Ceske Budejovice, Czech Republic
| | - Tereza Jancuskova
- Vemodia a.s., Laboratory for veterinary Molecular Diagnostics, Prague, Czech Republic
| | - Sona Pekova
- Vemodia a.s., Laboratory for veterinary Molecular Diagnostics, Prague, Czech Republic
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15
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Demars J, Iannuccelli N, Utzeri VJ, Auvinet G, Riquet J, Fontanesi L, Allain D. New Insights into the Melanophilin ( MLPH) Gene Affecting Coat Color Dilution in Rabbits. Genes (Basel) 2018; 9:genes9090430. [PMID: 30142960 PMCID: PMC6162760 DOI: 10.3390/genes9090430] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/06/2018] [Accepted: 08/13/2018] [Indexed: 11/16/2022] Open
Abstract
Coat color dilution corresponds to a specific pigmentation phenotype that leads to a dilution of wild type pigments. It affects both eumelanin and pheomelanin containing melanosomes. The mode of inheritance of the dilution phenotype is autosomal recessive. Candidate gene approaches focused on the melanophilin (MLPH) gene highlighted two variants associated with the dilution phenotype in rabbits: The c.111-5C>A variant that is located in an acceptor splice site or the c.585delG variant, a frameshift mutation. On the transcript level, the skipping of two exons has been reported as the molecular mechanism responsible for the coat color dilution. To clarify, which of the two variants represents the causal variant, (i) we analyzed their allelic segregation by genotyping Castor and Chinchilla populations, and (ii) we evaluated their functional effects on the stability of MLPH transcripts in skin samples of animals with diluted or wild type coat color. Firstly, we showed that the c.585delG variant showed perfect association with the dilution phenotype in contrast to the intronic c.111-5C>A variant. Secondly, we identified three different MLPH isoforms including the wild type isoform, the exon-skipping isoform and a retained intron isoform. Thirdly, we observed a drastic and significant decrease of MLPH transcript levels in rabbits with a coat color dilution (p-values ranging from 10−03 to 10−06). Together, our results bring new insights into the coat color dilution trait.
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Affiliation(s)
- Julie Demars
- GenPhySE, INRA Animal Genetics, Toulouse Veterinary School (ENVT), Université de Toulouse, 31326 Castanet Tolosan, France.
| | - Nathalie Iannuccelli
- GenPhySE, INRA Animal Genetics, Toulouse Veterinary School (ENVT), Université de Toulouse, 31326 Castanet Tolosan, France.
| | - Valerio Joe Utzeri
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy.
| | | | - Juliette Riquet
- GenPhySE, INRA Animal Genetics, Toulouse Veterinary School (ENVT), Université de Toulouse, 31326 Castanet Tolosan, France.
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy.
| | - Daniel Allain
- GenPhySE, INRA Animal Genetics, Toulouse Veterinary School (ENVT), Université de Toulouse, 31326 Castanet Tolosan, France.
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16
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Bauer A, Kehl A, Jagannathan V, Leeb T. A novel MLPH variant in dogs with coat colour dilution. Anim Genet 2018; 49:94-97. [PMID: 29349785 DOI: 10.1111/age.12632] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 11/28/2022]
Abstract
Coat colour dilution may be the result of altered melanosome transport in melanocytes. Loss-of-function variants in the melanophilin gene (MLPH) cause a recessively inherited form of coat colour dilution in many mammalian and avian species including the dog. MLPH corresponds to the D locus in many domestic animals, and recessive alleles at this locus are frequently denoted with d. In this study, we investigated dilute coloured Chow Chows whose coat colour could not be explained by their genotype at the previously known MLPH:c.-22G>A variant. Whole genome sequencing of such a dilute Chow Chow revealed another variant in the MLPH gene: MLPH:c.705G>C. We propose to designate the corresponding mutant alleles at these two variants d1 and d2 . We performed an association study in a cohort of 15 dilute and 28 non-dilute Chow Chows. The dilute dogs were all either compound heterozygous d1 /d2 or homozygous d2 /d2 , whereas the non-dilute dogs carried at least one wildtype allele D. The d2 allele did not occur in 417 dogs from diverse other breeds. However, when we genotyped a Sloughi family, in which a dilute coloured puppy had been born out of non-dilute parents, we again observed perfect co-segregation of the newly discovered d2 allele with coat colour dilution. Finally, we identified a blue Thai Ridgeback with the d1 /d2 genotype. Thus, our data identify the MLPH:c.705G>C as a variant explaining a second canine dilution allele. Although relatively rare overall, this d2 allele is segregating in at least three dog breeds, Chow Chows, Sloughis and Thai Ridgebacks.
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Affiliation(s)
- A Bauer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - A Kehl
- Laboklin, 97688, Bad Kissingen, Germany
| | - 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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17
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Peng Y, Liu X, Geng L, Ma R, Li L, Li J, Zhang C, Liu Z, Gong Y, Li X. Illumina-sequencing based transcriptome study of coat color phenotypes in domestic goats. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0543-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Taye M, Lee W, Caetano-Anolles K, Dessie T, Hanotte O, Mwai OA, Kemp S, Cho S, Oh SJ, Lee HK, Kim H. Whole genome detection of signature of positive selection in African cattle reveals selection for thermotolerance. Anim Sci J 2017; 88:1889-1901. [PMID: 28748670 DOI: 10.1111/asj.12851] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/20/2017] [Indexed: 12/11/2022]
Abstract
As African indigenous cattle evolved in a hot tropical climate, they have developed an inherent thermotolerance; survival mechanisms include a light-colored and shiny coat, increased sweating, and cellular and molecular mechanisms to cope with high environmental temperature. Here, we report the positive selection signature of genes in African cattle breeds which contribute for their heat tolerance mechanisms. We compared the genomes of five indigenous African cattle breeds with the genomes of four commercial cattle breeds using cross-population composite likelihood ratio (XP-CLR) and cross-population extended haplotype homozygosity (XP-EHH) statistical methods. We identified 296 (XP-EHH) and 327 (XP-CLR) positively selected genes. Gene ontology analysis resulted in 41 biological process terms and six Kyoto Encyclopedia of Genes and Genomes pathways. Several genes and pathways were found to be involved in oxidative stress response, osmotic stress response, heat shock response, hair and skin properties, sweat gland development and sweating, feed intake and metabolism, and reproduction functions. The genes and pathways identified directly or indirectly contribute to the superior heat tolerance mechanisms in African cattle populations. The result will improve our understanding of the biological mechanisms of heat tolerance in African cattle breeds and opens an avenue for further study.
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Affiliation(s)
- Mengistie Taye
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.,College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Wonseok Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Kelsey Caetano-Anolles
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.,The University of Nottingham, School of Life Sciences, Nottingham, UK
| | - Okeyo Ally Mwai
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Stephen Kemp
- The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, The University of Edinburgh, Midlothian, UK.,International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Seoae Cho
- C&K genomics, Seoul National University, Seoul, Korea
| | - Sung Jong Oh
- National Institute of Animal Science, RDA, Wanju, Korea
| | - Hak-Kyo Lee
- Department of Animal Biotechnology, The Animal Molecular Genetics & Breeding Center, Chonbuk National University, Jeonju, Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.,C&K genomics, Seoul National University, Seoul, Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.,Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
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19
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Genome sequence, population history, and pelage genetics of the endangered African wild dog (Lycaon pictus). BMC Genomics 2016; 17:1013. [PMID: 27938335 PMCID: PMC5148847 DOI: 10.1186/s12864-016-3368-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 12/02/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The African wild dog (Lycaon pictus) is an endangered African canid threatened by severe habitat fragmentation, human-wildlife conflict, and infectious disease. A highly specialized carnivore, it is distinguished by its social structure, dental morphology, absence of dewclaws, and colorful pelage. RESULTS We sequenced the genomes of two individuals from populations representing two distinct ecological histories (Laikipia County, Kenya and KwaZulu-Natal Province, South Africa). We reconstructed population demographic histories for the two individuals and scanned the genomes for evidence of selection. CONCLUSIONS We show that the African wild dog has undergone at least two effective population size reductions in the last 1,000,000 years. We found evidence of Lycaon individual-specific regions of low diversity, suggestive of inbreeding or population-specific selection. Further research is needed to clarify whether these population reductions and low diversity regions are characteristic of the species as a whole. We documented positive selection on the Lycaon mitochondrial genome. Finally, we identified several candidate genes (ASIP, MITF, MLPH, PMEL) that may play a role in the characteristic Lycaon pelage.
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20
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Kulikov AV, Bazhenova EY, Kulikova EA, Fursenko DV, Trapezova LI, Terenina EE, Mormede P, Popova NK, Trapezov OV. Interplay between aggression, brain monoamines and fur color mutation in the American mink. GENES BRAIN AND BEHAVIOR 2016; 15:733-740. [PMID: 27489198 DOI: 10.1111/gbb.12313] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/15/2016] [Accepted: 07/28/2016] [Indexed: 12/01/2022]
Abstract
Domestication of wild animals alters the aggression towards humans, brain monoamines and coat pigmentation. Our aim is the interplay between aggression, brain monoamines and depigmentation. The Hedlund white mutation in the American mink is an extreme case of depigmentation observed in domesticated animals. The aggressive (-2.06 ± 0.03) and tame (+3.5 ± 0.1) populations of wild-type dark brown color (standard) minks were bred during 17 successive generations for aggressive or tame reaction towards humans, respectively. The Hedlund mutation was transferred to the aggressive and tame backgrounds to generate aggressive (-1.2 ± 0.1) and tame (+3.0 ± 0.2) Hedlund minks. Four groups of 10 males with equal expression of aggressive (-2) or tame (+5) behavior, standard or with the Hedlund mutation, were selected to study biogenic amines in the brain. Decreased levels of noradrenaline in the hypothalamus, but increased concentrations of the serotonin metabolite, 5-hydroxyindoleacetic acid and dopamine metabolite, homovanillic acid, in the striatum were measured in the tame compared with the aggressive standard minks. The Hedlund mutation increased noradrenaline level in the hypothalamus and substantia nigra, serotonin level in the substantia nigra and striatum and decreased dopamine concentration in the hypothalamus and striatum. Significant interaction effects were found between the Hedlund mutation and aggressive behavior on serotonin metabolism in the substantia nigra (P < 0.001), dopamine level in the midbrain (P < 0.01) and its metabolism in the striatum (P < 0.05). These results provide the first experimental evidence of the interplay between aggression, brain monoamines and the Hedlund mutation in the American minks.
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Affiliation(s)
- A V Kulikov
- Department of Genetic Models of Neuropathologies, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E Y Bazhenova
- Department of Genetic Models of Neuropathologies, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E A Kulikova
- Department of Behavioral Neurogenomics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D V Fursenko
- Department of Genetic Models of Neuropathologies, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - L I Trapezova
- Department of Genetics and Selection of Fur and Farm Animals, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E E Terenina
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - P Mormede
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - N K Popova
- Department of Behavioral Neurogenomics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O V Trapezov
- Department of Genetics and Selection of Fur and Farm Animals, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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21
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Li W, Sartelet A, Tamma N, Coppieters W, Georges M, Charlier C. Reverse genetic screen for loss-of-function mutations uncovers a frameshifting deletion in the melanophilin gene accountable for a distinctive coat color in Belgian Blue cattle. Anim Genet 2015; 47:110-3. [PMID: 26582259 DOI: 10.1111/age.12383] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2015] [Indexed: 11/30/2022]
Abstract
In the course of a reverse genetic screen in the Belgian Blue cattle breed, we uncovered a 10-bp deletion (c.87_96del) in the first coding exon of the melanophilin gene (MLPH), which introduces a premature stop codon (p.Glu32Aspfs*1) in the same exon, truncating 94% of the protein. Recessive damaging mutations in the MLPH gene are well known to cause skin, hair, coat or plumage color dilution phenotypes in numerous species, including human, mice, dog, cat, mink, rabbit, chicken and quail. Large-scale array genotyping undertaken to identify p.Glu32Aspfs*1 homozygous mutant animals revealed a mutation frequency of 5% in the breed and allowed for the identification of 10 homozygous mutants. As expression of a colored coat requires at least one wild-type allele at the co-dominant Roan locus encoded by the KIT ligand gene (KITLG), homozygous mutants for p.Ala227Asp corresponding with the missense mutation were excluded. The six remaining colored calves displayed a distinctive dilution phenotype as anticipated. This new coat color was named 'cool gray'. It is the first damaging mutation in the MLPH gene described in cattle and extends the already long list of species with diluted color due to recessive mutations in MLPH and broadens the color palette of gray in this breed.
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Affiliation(s)
- Wanbo Li
- GIGA-R and Faculty of Veterinary Medicine, University of Liège, 1 avenue de l'hôpital, 4000 Liège, Belgium
| | - Arnaud Sartelet
- Bovine Clinic, FARAH and Faculty of Veterinary Medicine, University of Liège, 20 boulevard de Colonster 4000 Liège, Belgium
| | - Nico Tamma
- GIGA-R and Faculty of Veterinary Medicine, University of Liège, 1 avenue de l'hôpital, 4000 Liège, Belgium
| | - Wouter Coppieters
- GIGA-R and Faculty of Veterinary Medicine, University of Liège, 1 avenue de l'hôpital, 4000 Liège, Belgium.,GIGA-Genomics platform, University of Liège, 1 avenue de l'hôpital, 4000 Liège, Belgium
| | - Michel Georges
- GIGA-R and Faculty of Veterinary Medicine, University of Liège, 1 avenue de l'hôpital, 4000 Liège, Belgium
| | - Carole Charlier
- GIGA-R and Faculty of Veterinary Medicine, University of Liège, 1 avenue de l'hôpital, 4000 Liège, Belgium
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22
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Duke FD, Teixeira LBC, Galle LE, Green N, Dubielzig RR. Malignant uveal schwannoma with peripheral nerve extension in a 12-week-old color-dilute Labrador Retriever. Vet Pathol 2014; 52:181-5. [PMID: 24513800 DOI: 10.1177/0300985814522811] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The formalin-fixed, amber-colored right globe from a 12-week-old female silver Labrador Retriever dog was submitted to the Comparative Ocular Pathology Laboratory of Wisconsin for light microscopic evaluation. The clinical history described a collapsed anterior chamber and multifocal nodular lesions in the peripheral iris. Histologically, immunohistochemically, and ultrastructurally, the uveal mass was consistent with a malignant schwannoma; there was extension along peripheral nerves within the sclera. The signalment and behavior of the neoplasm distinguish it from the uveal schwannoma of blue-eyed dogs and bear some resemblance to the ocular lesions in human neurofibromatosis. The dilute color mutation may contribute to the cause. Six weeks later, the dog did not develop any additional masses.
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Affiliation(s)
- F D Duke
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - L B C Teixeira
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - L E Galle
- Mississippi Veterinary Ophthalmology Specialists, Ocean Springs, Mississippi, USA
| | - N Green
- Animal Care Center, Mobile, Alabama, USA
| | - R R Dubielzig
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
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23
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Lehner S, Gähle M, Dierks C, Stelter R, Gerber J, Brehm R, Distl O. Two-exon skipping within MLPH is associated with coat color dilution in rabbits. PLoS One 2013; 8:e84525. [PMID: 24376820 PMCID: PMC3869861 DOI: 10.1371/journal.pone.0084525] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 11/15/2013] [Indexed: 11/19/2022] Open
Abstract
Coat color dilution turns black coat color to blue and red color to cream and is a characteristic in many mammalian species. Matings among Netherland Dwarf, Loh, and Lionhead Dwarf rabbits over two generations gave evidence for a monogenic autosomal recessive inheritance of coat colour dilution. Histological analyses showed non-uniformly distributed, large, agglomerating melanin granules in the hair bulbs of coat color diluted rabbits. We sequenced the cDNA of MLPH in two dilute and one black rabbit for polymorphism detection. In both color diluted rabbits, skipping of exons 3 and 4 was present resulting in altered amino acids at p.QGL[37-39]QWA and a premature stop codon at p.K40*. Sequencing of genomic DNA revealed a c.111-5C>A splice acceptor mutation within the polypyrimidine tract of intron 2 within MLPH. This mutation presumably causes skipping of exons 3 and 4. In 14/15 dilute rabbits, the c.111-5C>A mutation was homozygous and in a further dilute rabbit, heterozygous and in combination with a homozygous frame shift mutation within exon 6 (c.585delG). In conclusion, our results demonstrated a colour dilution associated MLPH splice variant causing a strongly truncated protein (p.Q37QfsX4). An involvement of further MLPH-associated mutations needs further investigations.
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Affiliation(s)
- Stefanie Lehner
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Marion Gähle
- Institute for Anatomy, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Claudia Dierks
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ricarda Stelter
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
- Clinic for Pets, Reptiles and Pet and Feral Birds, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Jonathan Gerber
- Institute for Anatomy, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ralph Brehm
- Institute for Anatomy, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
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24
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Fontanesi L, Scotti E, Allain D, Dall'Olio S. A frameshift mutation in themelanophilingene causes the dilute coat colour in rabbit (Oryctolagus cuniculus) breeds. Anim Genet 2013; 45:248-55. [DOI: 10.1111/age.12104] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2013] [Indexed: 11/29/2022]
Affiliation(s)
- L. Fontanesi
- Division of Animal Sciences; Department of Agricultural and Food Sciences (DISTAL); University of Bologna; Viale Fanin 46 40127 Bologna Italy
- Centre for Genome Biology; University of Bologna; 40126 Bologna Italy
| | - E. Scotti
- Division of Animal Sciences; Department of Agricultural and Food Sciences (DISTAL); University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - D. Allain
- INRA; UR631; SAGA; CS52627 31326 Castanet Tolosan France
- INRA; UE 1372; GenESI; Le Magneraud; BP52 17700 Surgères France
| | - S. Dall'Olio
- Division of Animal Sciences; Department of Agricultural and Food Sciences (DISTAL); University of Bologna; Viale Fanin 46 40127 Bologna Italy
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25
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Cirera S, Markakis MN, Christensen K, Anistoroaei R. New insights into the melanophilin (MLPH) gene controlling coat color phenotypes in American mink. Gene 2013; 527:48-54. [PMID: 23747352 DOI: 10.1016/j.gene.2013.05.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 05/21/2013] [Accepted: 05/23/2013] [Indexed: 10/26/2022]
Abstract
The mutation causing the Silverblue color type (pp) is one of the most used recessive mutations within American mink (Neovison vison) fur farming, since it is involved in some of the popular color types such as Violet and Saphire which originate from a combination of recessive mutations. In the present study, the genomic and mRNA sequences of the melanophilin (MLPH) gene were studied in Violet, Silverblue and wild-type (wt) mink animals. Although breeding schemes and previous literature indicates that the Violet (aammpp) phenotype is a triple recessive color type involving the same locus as the Silverblue (pp) color type, our findings indicate different genotypes at the MLPH locus. Upon comparison at genomic level, we identified two deletions of the entire intron 7 and of the 5' end of intron 8 in the sequence of the Silverblue MLPH gene. When investigating the mRNA, the Silverblue animals completely lack exon 8, which encodes 65 residues, of which 47 define the Myosin Va (MYO5A) binding domain. This may cause the incorrect anchoring of the MLPH protein to MYO5A in Silverblue animals, resulting in an improper pigmentation as seen in diluted phenotypes. Additionally, in the MLPH mRNA of wt, Violet and Silverblue phenotypes, part of intron 8 is retained resulting in a truncated MLPH protein, which is 359 residues long in wt and Violet and 284 residues long in Silverblue. Subsequently, our findings point out that the missing actin-binding domain, in neither of the 3 analyzed phenotypes affects the transport of melanosomes or the consequent final pigmentation. Moreover, the loss of the major part of the MYO5A domain in the Silverblue MLPH protein seems to be the responsible for the dilute phenotype. Based on our genomic DNA data, genetic tests for selecting Silverblue and Violet carrier animals can be performed in American mink.
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Affiliation(s)
- Susanna Cirera
- University of Copenhagen, Faculty of Health and Medical Science, Department of Veterinary Clinical and Animal Sciences, Division of Genetics, Bioinformatics and Breeding, 1870 Frederiksberg C, Denmark
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26
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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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Gerding WM, Schreiber S, Dekomien G, Epplen JT. Tracing the origin of 'blue Weimaraner' dogs by molecular genetics. J Anim Breed Genet 2011; 128:153-60. [PMID: 21385230 DOI: 10.1111/j.1439-0388.2010.00888.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Weimaraner dogs are defined by light brown coat colour termed grey including several shadings ranging from silver and deer to mouse grey. In contrast, the so-called blue Weimaraners (BW) with lightened black-pigmented coat have been proposed to represent spontaneous revertants in the Weimaraner breed. In order to investigate the genetic determinants of the characteristic grey coat colour versus those of BW, known variation in coat colour genes including TYRP1 and MLPH were analysed in a number of grey and blue dogs. Variations at the B locus cause grey coat colour in Weimaraners via two non-functional TYRP1 copies (bb) including the b(s), b(d) and b(c) alleles. In all BW, at least one functional TYRP1 allele (Bb or BB genotype) was identified. Defined microsatellite alleles in TYRP1 intron 4 are linked to this functional B allele in BW. These alleles were also detected in various other dog breeds, but not in grey Weimaraners. The combination of a dominant trait for blue versus grey together with a specific TYRP1 haplotype in BW suggests that blue coat colour is not the result of spontaneous (back-) mutation in grey Weimaraners. This inference is even emphasized by the presence of a unique Y-chomosomal haplotype in a male offspring of the supposed ancestor of the BW population which - according to pedigree information - carries a copy of the original Y chromosome. Thus, molecular genetic analyses of coat colours combined with Y-chromosomal haplotypes allow tracing the origin of atypical dogs in respective canine populations.
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Affiliation(s)
- W M Gerding
- Human Genetics, Ruhr-University, Bochum, Germany.
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Parker HG, Shearin AL, Ostrander EA. Man's best friend becomes biology's best in show: genome analyses in the domestic dog. Annu Rev Genet 2011; 44:309-36. [PMID: 21047261 DOI: 10.1146/annurev-genet-102808-115200] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the last five years, canine genetics has gone from map construction to complex disease deconstruction. The availability of a draft canine genome sequence, dense marker chips, and an understanding of the genome architecture has changed the types of studies canine geneticists can undertake. There is now a clear recognition that the dog system offers the opportunity to understand the genetics of both simple and complex traits, including those associated with morphology, disease susceptibility, and behavior. In this review, we summarize recent findings regarding canine domestication and review new information on the organization of the canine genome. We discuss studies aimed at finding genes controlling morphological phenotypes and provide examples of the way such paradigms may be applied to studies of behavior. We also discuss the many ways in which the dog has illuminated our understanding of human disease and conclude with a discussion on where the field is likely headed in the next five years.
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Affiliation(s)
- Heidi G Parker
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Bannasch D, Young A, Myers J, Truvé K, Dickinson P, Gregg J, Davis R, Bongcam-Rudloff E, Webster MT, Lindblad-Toh K, Pedersen N. Localization of canine brachycephaly using an across breed mapping approach. PLoS One 2010; 5:e9632. [PMID: 20224736 PMCID: PMC2835769 DOI: 10.1371/journal.pone.0009632] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 02/19/2010] [Indexed: 12/23/2022] Open
Abstract
The domestic dog, Canis familiaris, exhibits profound phenotypic diversity and is an ideal model organism for the genetic dissection of simple and complex traits. However, some of the most interesting phenotypes are fixed in particular breeds and are therefore less tractable to genetic analysis using classical segregation-based mapping approaches. We implemented an across breed mapping approach using a moderately dense SNP array, a low number of animals and breeds carefully selected for the phenotypes of interest to identify genetic variants responsible for breed-defining characteristics. Using a modest number of affected (10–30) and control (20–60) samples from multiple breeds, the correct chromosomal assignment was identified in a proof of concept experiment using three previously defined loci; hyperuricosuria, white spotting and chondrodysplasia. Genome-wide association was performed in a similar manner for one of the most striking morphological traits in dogs: brachycephalic head type. Although candidate gene approaches based on comparable phenotypes in mice and humans have been utilized for this trait, the causative gene has remained elusive using this method. Samples from nine affected breeds and thirteen control breeds identified strong genome-wide associations for brachycephalic head type on Cfa 1. Two independent datasets identified the same genomic region. Levels of relative heterozygosity in the associated region indicate that it has been subjected to a selective sweep, consistent with it being a breed defining morphological characteristic. Genotyping additional dogs in the region confirmed the association. To date, the genetic structure of dog breeds has primarily been exploited for genome wide association for segregating traits. These results demonstrate that non-segregating traits under strong selection are equally tractable to genetic analysis using small sample numbers.
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Affiliation(s)
- Danika Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America.
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30
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Characterization and SNP Identification of Part of the Goat Melanophilin Gene. Biochem Genet 2009; 47:198-206. [DOI: 10.1007/s10528-008-9217-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2008] [Accepted: 09/15/2008] [Indexed: 10/21/2022]
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31
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Welle M, Philipp U, Rufenacht S, Roosje P, Scharfenstein M, Schutz E, Brenig B, Linek M, Mecklenburg L, Grest P, Drogemuller M, Haase B, Leeb T, Drogemuller C. MLPH Genotype--Melanin Phenotype Correlation in Dilute Dogs. J Hered 2009. [DOI: 10.1093/jhered/esp010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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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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Vaez M, Follett SA, Bed'hom B, Gourichon D, Tixier-Boichard M, Burke T. A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phenotype in the chicken. BMC Genet 2008; 9:7. [PMID: 18197963 PMCID: PMC2253553 DOI: 10.1186/1471-2156-9-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Accepted: 01/15/2008] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The lavender phenotype in the chicken causes the dilution of both black (eumelanin) and red/brown (phaeomelanin) pigments. Defects in three genes involved in intracellular melanosomal transport, previously described in mammals, give rise to similar diluted pigmentation phenotypes as those seen in lavender chickens. RESULTS We have used a candidate-gene approach based on an expectation of homology with mammals to isolate a gene involved in pigmentation in chicken. Comparative sequence analysis of candidate genes in the chicken identified a strong association between a mutation in the MLPH gene and the diluted pigmentation phenotype. This mutation results in the amino acid change R35W, at a site also associated with similar phenotypes in mice, humans and cats. CONCLUSION This is the first time that an avian species with a mutation in the MLPH gene has been reported.
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Affiliation(s)
- Mohsen Vaez
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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Drögemüller C, Philipp U, Haase B, Günzel-Apel AR, Leeb T. A Noncoding Melanophilin Gene (MLPH) SNP at the Splice Donor of Exon 1 Represents a Candidate Causal Mutation for Coat Color Dilution in Dogs. J Hered 2007; 98:468-73. [PMID: 17519392 DOI: 10.1093/jhered/esm021] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Coat color dilution in several breeds of dog is characterized by a specific pigmentation phenotype and sometimes accompanied by hair loss and recurrent skin inflammation, the so-called color dilution alopecia or black hair follicular dysplasia. Coat color dilution (d) is inherited as a Mendelian autosomal recessive trait. In a previous study, MLPH polymorphisms showed perfect cosegregation with the dilute phenotype within breeds. However, different dilute haplotypes were found in different breeds, and no single polymorphism was identified in the coding sequence that was likely to be causative for the dilute phenotype. We resequenced the 5'-region of the canine MLPH gene and identified a strong candidate single nucleotide polymorphism within the nontranslated exon 1, which showed perfect association to the dilute phenotype in 65 dilute dogs from 7 different breeds. The A/G polymorphism is located at the last nucleotide of exon 1 and the mutant A-allele is predicted to reduce splicing efficiency 8-fold. An MLPH mRNA expression study using quantitative reverse transcriptase-polymerase chain reaction confirmed that dd animals had only about approximately 25% of the MLPH transcript compared with DD animals. These results provide preliminary evidence that the reported regulatory MLPH mutation might represent a causal mutation for coat color dilution in dogs.
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Affiliation(s)
- Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Berne, Bremgartenstrasse 109a, 3001 Berne, Switzerland
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Abstract
Alopecia, that is, lack of hair in any quantity, is a frequent complaint of pet owners. Although mostly acquired, rare congenital forms of alopecia exist that are associated with abnormalities in hair follicle morphogenesis. Congenital alopecias can result in changes in quality or quantity of hair follicles and the hair fibres produced by them. They vary in terms of clinical presentation and mode of inheritance. Histopathology is usually needed in order to differentiate between a reduced number of otherwise normal hair follicles and qualitative hair follicle abnormalities. Although our understanding of the molecular mechanisms that drive hair follicle morphogenesis in mice and humans has significantly increased during the last decade, still very little is known about congenital alopecias in domestic animals. Because of their rarity and the general lack of knowledge about their pathophysiology, classification of congenital alopecias in domestic animals is still unsatisfactory. This article reviews hair follicle morphogenesis and its most important molecular mechanisms, and it discusses the various forms of congenital alopecia occurring in domestic animals that have been described in the literature, differentiating between hair follicle aplasia, hair follicle dysplasia (i.e. defects associated with hair follicle development and defects associated with hair shaft formation), and neuroectodermal dysplasias, the latter involving the hair follicle pigmentary system.
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Ishida Y, David VA, Eizirik E, Schäffer AA, Neelam BA, Roelke ME, Hannah SS, O'Brien SJ, Menotti-Raymond M. A homozygous single-base deletion in MLPH causes the dilute coat color phenotype in the domestic cat. Genomics 2006; 88:698-705. [PMID: 16860533 DOI: 10.1016/j.ygeno.2006.06.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 06/09/2006] [Accepted: 06/12/2006] [Indexed: 11/22/2022]
Abstract
Three proteins have been described in humans and mice as being essential for even distribution, transport, and translocation of pigment granules, with defects in these molecules giving rise to lighter skin/coat color. The dilute phenotype in domestic cats affects both eumelanin and phaeomelanin pigment pathways; for example, black pigmentation combined with dilute appears gray and orange pigments appear cream. The dilute pigmentation segregates as a fully penetrant, autosomal recessive trait. We conducted classical linkage mapping with microsatellites in a large multigeneration pedigree of domestic cats and detected tight linkage for dilute on cat chromosome C1 (theta=0.08, LOD=10.81). Fine-mapping identified a genomic region exhibiting conserved synteny to human chromosome 2, which included one of the three dilute candidate genes, melanophilin (MLPH). Sequence analysis in dilute cats identified a single base pair deletion in exon 2 of MLPH transcripts that introduces a stop codon 11 amino acids downstream, resulting in the truncation of the bulk of the MLPH protein. The occurrence of this homozygous variant in 97 unrelated dilute cats representing 26 cat breeds and random-bred cats, along with 89 unrelated wild-type cats representing 29 breeds and random-bred cats, supports the finding that dilute is caused by this single mutation in MLPH (p<0.00001). Single-nucleotide polymorphism analyses in dilute individuals identified a single haplotype in dilute cats, suggesting that a single mutation event in MLPH gave rise to dilute in domestic cats.
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Affiliation(s)
- Yasuko Ishida
- Laboratory of Genomic Diversity, National Cancer Institute, Building 560, Room 11-38, Fort Detrick, Frederick, MD 21702, USA.
| | - Victor A David
- Laboratory of Genomic Diversity, National Cancer Institute, Building 560, Room 11-38, Fort Detrick, Frederick, MD 21702, USA
| | - Eduardo Eizirik
- Centro de Biologia Genômica e Molecular, PUCRS, Porto Alegre, RS 90619-900, Brazil
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
| | - Beena A Neelam
- Advanced Biomedical Computing Center, SAIC-Frederick, National Cancer Institute, Frederick, MD 21702, USA
| | - Melody E Roelke
- Laboratory of Genomic Diversity, SAIC-Frederick, National Cancer Institute, Frederick, MD 21702, USA
| | | | - Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Building 560, Room 11-38, Fort Detrick, Frederick, MD 21702, USA
| | - Marilyn Menotti-Raymond
- Laboratory of Genomic Diversity, National Cancer Institute, Building 560, Room 11-38, Fort Detrick, Frederick, MD 21702, USA.
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von Bomhard W, Mauldin EA, Schmutz SM, Leeb T, Casal ML. Black hair follicular dysplasia in Large Münsterländer dogs: clinical, histological and ultrastructural features. Vet Dermatol 2006; 17:182-8. [PMID: 16674733 PMCID: PMC3330242 DOI: 10.1111/j.1365-3164.2006.00517.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Four Large Münsterländer cross-bred dogs affected with black hair follicular dysplasia (BHFD) and one unaffected control littermate were observed, and skin was sampled weekly over the first 19 weeks of life. Affected dogs were born with silvery grey hair, a consequence of melanin clumping in the hair shafts. Hair bulb melanocytes were densely pigmented, and contained abundant stage IV melanosomes but adjacent matrix keratinocytes lacked melanosomes. Melanin clumping was not prominent in epidermal melanocytes in the haired skin but occurred in the foot pads. Follicular changes progressed from bulbar clumping, clumping in the isthmus/infundibulum and finally to dysplastic hair shafts. Alopecia developed progressively in pigmented areas. Silver-grey hair, melanin clumping, accumulation of stage IV melanosomes within melanocytes and insufficient melanin transfer to adjacent keratinocytes are also classic features of human Griscelli syndrome. The underlying cause in Griscelli syndrome is a defect of melanocytic intracellular transport proteins leading to inadequate and disorganized melanosome transfer to keratinocytes with resultant melanin clumping. In view of the correlation in the phenotype, histology and ultrastructure between both disorders, a defect in intracellular melanosome transport is postulated as the pathogenic mechanism in BHFD.
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Affiliation(s)
- Wolf von Bomhard
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, 19104, USA
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Hédan B, Corre S, Hitte C, Dréano S, Vilboux T, Derrien T, Denis B, Galibert F, Galibert MD, André C. Coat colour in dogs: identification of the merle locus in the Australian shepherd breed. BMC Vet Res 2006; 2:9. [PMID: 16504149 PMCID: PMC1431520 DOI: 10.1186/1746-6148-2-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Accepted: 02/27/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coat colours in canines have many natural phenotypic variants. Some of the genes and alleles involved also cause genetic developmental defects, which are also observed in humans and mice. We studied the genetic bases of the merle phenotype in dogs to shed light on the pigmentation mechanisms and to identify genes involved in these complex pathways. The merle phenotype includes a lack of eumelanic pigmentation and developmental defects, hearing impairments and microphthalmia. It is similar to that observed in microphthalmia mouse mutants. RESULTS Taking advantage of the dog as a powerful genetic model and using recently available genomic resources, we investigated the segregation of the merle phenotype in a five-generation pedigree, comprising 96 sampled Australian shepherd dogs. Genetic linkage analysis allowed us to identify a locus for the merle phenotype, spanning 5.5 megabases, at the centromeric tip of canine chromosome 10 (CFA10). This locus was supported by a Lod score of 15.65 at a recombination fraction theta = 0. Linkage analysis in three other breeds revealed that the same region is linked to the merle phenotype. This region, which is orthologous to human chromosome 12 (HSA12 q13-q14), belongs to a conserved ordered segment in the human and mouse genome and comprises several genes potentially involved in pigmentation and development. CONCLUSION This study has identified the locus for the merle coat colour in dogs to be at the centromeric end of CFA10. Genetic studies on other breeds segregating the merle phenotype should allow the locus to be defined more accurately with the aim of identifying the gene. This work shows the power of the canine system to search for the genetic bases of mammalian pigmentation and developmental pathways.
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Affiliation(s)
- Benoit Hédan
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Sébastien Corre
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Christophe Hitte
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Stéphane Dréano
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Thierry Vilboux
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Thomas Derrien
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | | | - Francis Galibert
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Marie-Dominique Galibert
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Catherine André
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
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Abstract
The dog has emerged as a premier species for the study of morphology, behavior, and disease. The recent availability of a high-quality draft sequence lifts the dog system to a new threshold. We provide a primer to use the dog genome by first focusing on its evolutionary history. We overview the relationship of dogs to wild canids and discuss their origin and domestication. Dogs clearly originated from a substantial number of gray wolves and dog breeds define distinct genetic units that can be divided into at least four hierarchical groupings. We review evidence showing that dogs have high levels of linkage disequilibrium. Consequently, given that dog breeds express specific phenotypic traits and vary in behavior and the incidence of genetic disease, genomic-wide scans for linkage disequilibrium may allow the discovery of genes influencing breed-specific characteristics. Finally, we review studies that have utilized the dog to understand the genetic underpinning of several traits, and we summarize genomic resources that can be used to advance such studies. We suggest that given these resources and the unique characteristics of breeds, that the dog is a uniquely valuable resource for studying the genetic basis of complex traits.
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Affiliation(s)
- Elaine A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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