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Maclary ET, Wauer R, Phillips B, Brown A, Boer EF, Samani AM, Shapiro MD. An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon. PLoS Genet 2023; 19:e1010880. [PMID: 37862332 PMCID: PMC10588866 DOI: 10.1371/journal.pgen.1010880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/25/2023] [Indexed: 10/22/2023] Open
Abstract
Variation in pigment patterns within and among vertebrate species reflects underlying changes in cell migration and function that can impact health, reproductive success, and survival. The domestic pigeon (Columba livia) is an exceptional model for understanding the genetic changes that give rise to diverse pigment patterns, as selective breeding has given rise to hundreds of breeds with extensive variation in plumage color and pattern. Here, we map the genetic architecture of a suite of pigmentation phenotypes known as piebalding. Piebalding is characterized by patches of pigmented and non-pigmented feathers, and these plumage patterns are often breed-specific and stable across generations. Using a combination of quantitative trait locus mapping in F2 laboratory crosses and genome-wide association analysis, we identify a locus associated with piebalding across many pigeon breeds. This shared locus harbors a candidate gene, EDNRB2, that is a known regulator of pigment cell migration, proliferation, and survival. We discover multiple distinct haplotypes at the EDNRB2 locus in piebald pigeons, which include a mix of protein-coding, noncoding, and structural variants that are associated with depigmentation in specific plumage regions. These results identify a role for EDNRB2 in pigment patterning in the domestic pigeon, and highlight how repeated selection at a single locus can generate a diverse array of stable and heritable pigment patterns.
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Affiliation(s)
- Emily T. Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Ryan Wauer
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Bridget Phillips
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Audrey Brown
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Elena F. Boer
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Atoosa M. Samani
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
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2
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Maclary ET, Wauer R, Phillips B, Brown A, Boer EF, Samani AM, Shapiro MD. An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550625. [PMID: 37546953 PMCID: PMC10402103 DOI: 10.1101/2023.07.26.550625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Variation in pigment patterns within and among vertebrate species reflects underlying changes in cell migration and function that can impact health, reproductive success, and survival. The domestic pigeon (Columba livia) is an exceptional model for understanding the genetic changes that give rise to diverse pigment patterns, as selective breeding has given rise to hundreds of breeds with extensive variation in plumage color and pattern. Here, we map the genetic architecture of a suite of pigmentation phenotypes known as piebalding. Piebalding is characterized by patches of pigmented and non-pigmented feathers, and these plumage patterns are often breed-specific and stable across generations. Using a combination of quantitative trait locus mapping in F2 laboratory crosses and genome-wide association analysis, we identify a locus associated with piebalding across many pigeon breeds. This shared locus harbors a candidate gene, EDNRB2, that is a known regulator of pigment cell migration, proliferation, and survival. We discover multiple distinct haplotypes at the EDNRB2 locus in piebald pigeons, which include a mix of protein-coding, noncoding, and structural variants that are associated with depigmentation in specific plumage regions. These results identify a role for EDNRB2 in pigment patterning in the domestic pigeon, and highlight how repeated selection at a single locus can generate a diverse array of stable and heritable pigment patterns.
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Affiliation(s)
- Emily T. Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Ryan Wauer
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Bridget Phillips
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Audrey Brown
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Elena F. Boer
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Atoosa M. Samani
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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Heinrich J, Berger C, Berger B, Hecht W, Phillips C, Parson W. The LASSIE MPS panel: Predicting externally visible traits in dogs for forensic purposes. Forensic Sci Int Genet 2023; 66:102893. [PMID: 37290253 DOI: 10.1016/j.fsigen.2023.102893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/28/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Predicting the outward appearance of dogs via their DNA, also known as Canine DNA Phenotyping, is a young, emerging field of research in forensic genetics. The few previous studies published in this respect were restricted to the consecutive analysis of single DNA markers, a process that is time- and sample-consuming and therefore not a viable option for limited forensic specimens. Here, we report on the development and evaluation of a Massively Parallel Sequencing (MPS) based molecular genetic assay, the LASSIE MPS Panel. This panel aims to predict externally visible as well as skeletal traits, which include coat color, coat pattern, coat structure, tail morphology, skull shape, ear shape, eye color and body size from DNA using 44 genetic markers in a single molecular genetic assay. A biostatistical naïve Bayes classification approach was applied to identify the most informative marker combinations for predicting phenotypes. Overall, the predictive performance was characterized by a very high classification success for some of the trait categories, and high to moderate success for others. The performance of the developed predictive framework was further evaluated using blind samples from three randomly selected dog individuals, whose appearance was well predicted.
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Affiliation(s)
- Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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4
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Haase B, Willet CE, Chew T, Samaha G, Child G, Wade CM. De-novo and genome-wide meta-analyses identify a risk haplotype for congenital sensorineural deafness in Dalmatian dogs. Sci Rep 2022; 12:15439. [PMID: 36104420 PMCID: PMC9474838 DOI: 10.1038/s41598-022-19535-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/30/2022] [Indexed: 11/29/2022] Open
Abstract
Congenital sensorineural deafness (CSD) has been reported to affect up to 30% of Dalmatian dogs world-wide and while unilaterally deaf dogs can live a close to normal life, dogs suffering bilateral deafness are frequently euthanized. Extreme-white coat patterning as encoded by the gene Melanocyte Inducing Transcription Factor (MITF) has long been postulated as the major risk factor for CSD in the Dalmatian breed. While attempts to identify causative risk variants associated with CSD have been numerous, no genome-wide association study has positively identified MITF as a risk locus for either bilateral or unilateral deafness in the Dalmatian breed to date. In this study, we identified an association with CSD on CFA20 in the vicinity of MITF within Australian Dalmatian dogs. Although not genome-wide significant, the association signal was validated by reanalysing publicly available data and merging the wider data resource with the local data to improve statistical power. The merged data, representing three major global populations of Dalmatian dogs, enabled us to identify a single, well-defined genome-wide significant risk haplotype for CSD. The haplotype was formed by three genome-wide significant associated markers (BICF2G630233852T>C, BICF2G630233861T>C, BICF2G630233888G>A) on CFA20 with 62% of bilaterally deaf dogs homozygous for the risk haplotype (CCA), while 30% of bilaterally deaf and 45% of hearing dogs carried one copy of the risk haplotype. Animals homozygous or heterozygous for the low-risk haplotype were less likely to be unilaterally deaf. While the association between the risk haplotype and deafness is incomplete, animals homozygous for the risk haplotype were 10-times more likely to be bilaterally deaf. Although the underlying causative variants are yet to be discovered, results from this study can now assist with reducing deafness in Dalmatian dogs.
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Ouhrouch A, Boitard S, Boyer F, Servin B, Da Silva A, Pompanon F, Haddioui A, Benjelloun B. Genomic Uniqueness of Local Sheep Breeds From Morocco. Front Genet 2021; 12:723599. [PMID: 34925440 PMCID: PMC8675355 DOI: 10.3389/fgene.2021.723599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/09/2021] [Indexed: 01/17/2023] Open
Abstract
Sheep farming is a major source of meat in Morocco and plays a key role in the country's agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.
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Affiliation(s)
- Abdessamad Ouhrouch
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco.,Biotechnologies and Valorization of Plant-Genetic Resources Laboratory, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Simon Boitard
- CBGP, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie MT-Blanc, CNRS, LECA, Grenoble, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet-Tolosan, France
| | - Anne Da Silva
- PEREINE/E2LIM, Faculty of Science and Technics, Limoges, France
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie MT-Blanc, CNRS, LECA, Grenoble, France
| | - Abdelmajid Haddioui
- Biotechnologies and Valorization of Plant-Genetic Resources Laboratory, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Badr Benjelloun
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
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Seddon JM, Fortes M, Kelly-Smith M, Sommerlad SF, Hayward JJ, Burmeister L, De Risio L, Mellersh C, Freeman J, Strain GM. Deafness in Australian Cattle Dogs associated to QTL on chromosome 20 in genome-wide association study analyses. Anim Genet 2021; 52:694-702. [PMID: 34318504 DOI: 10.1111/age.13115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 11/29/2022]
Abstract
Pigment-associated deafness is a common hereditary condition in a range of dog breeds. The aim of this study was to perform a genome-wide association analysis to investigate the genetic architecture of deafness in Australian Cattle Dogs. Genotypes for 104 757 polymorphisms in 216 dogs were available for analyses after quality control. A genomic relationship matrix was used in the mixed model analyses to account for polygenic effects, as we tested each polymorphism for its association with deafness, in a case/control experimental design. Three approaches were used to code the genotypes and test for additive, recessive and dominant SNP effects. The genome-wide association study analyses identified a clear association peak on CFA20, with the most significant SNPs on this chromosome (1.29 × 10-4 ) in the vicinity of MITF. Variants in MITF have been associated with white pigmentation in dogs and with deafness in humans and other species, supporting the premise that canine deafness is associated with variants in or near this gene. A recessive inheritance for the peak in CFA20 is possible given the significant results in the recessive model; however, the estimated heritability was low (4.54 × 10-5 ). Further validation, identification of variants and testing in other dog breeds are needed.
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Affiliation(s)
- J M Seddon
- School of Veterinary Science, The University of Queensland, Gatton, Qld, 4343, Australia
| | - M Fortes
- School of Chemistry and Molecular Biosciences, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Qld, 4072, Australia
| | - M Kelly-Smith
- Comparative Biomedical Sciences, Louisiana State University, School of Veterinary Medicine, Baton Rouge, LA, 70803, USA
| | - S F Sommerlad
- School of Veterinary Science, The University of Queensland, Gatton, Qld, 4343, Australia
| | - J J Hayward
- Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - L Burmeister
- Animal Health Trust, Newmarket, Suffolk, CB8 7UU, UK
| | - L De Risio
- Animal Health Trust, Newmarket, Suffolk, CB8 7UU, UK
| | - C Mellersh
- Animal Health Trust, Newmarket, Suffolk, CB8 7UU, UK
| | - J Freeman
- Animal Health Trust, Newmarket, Suffolk, CB8 7UU, UK
| | - G M Strain
- Comparative Biomedical Sciences, Louisiana State University, School of Veterinary Medicine, Baton Rouge, LA, 70803, 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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8
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Brancalion L, Haase B, Mazrier H, Willet CE, Lindblad-Toh K, Lingaas F, Wade CM. Roan, ticked and clear coat patterns in the canine are associated with three haplotypes near usherin on CFA38. Anim Genet 2021; 52:198-207. [PMID: 33539602 PMCID: PMC7986734 DOI: 10.1111/age.13040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 12/19/2022]
Abstract
White coat patterning is a feature of many dog breeds and is known to be coded primarily by the gene micropthalmia‐associated transcription factor (MITF). This patterning in the coat can be modified by other factors to produce the attractive phenotypes termed ‘ticked’ and ‘roan’ that describe the presence of flecks of color that vary in distribution and intensity within otherwise ‘clear’ white markings. The appearance of the pigment in the white patterning caused by ticking and roaning intensifies in the weeks after birth. We applied genome‐wide association to compare English Cocker Spaniels of roan phenotype (N = 34) with parti‐color (non‐roan) English Cocker Spaniels (N = 9) and identified an associated locus on CFA 38, CFA38:11 057 040 (Praw = 8.9 × 10−10, Pgenome = 2.7 × 10−5). A local case–control association in English Springer Spaniels comparing 11 ticked and six clear dogs identified indicative association with a different haplotype, CFA38:11 122 467G>T (Praw = 1.7 × 10−5) and CFA38:11 124 294A>C (Praw = 1.7 × 10−5). We characterize three haplotypes in Spaniels according to their putative functional variant profiles at CFA38:11 111 286C>T (missense), CFA38:11 131 841–11 143 239DUP.insTTAA (using strongly linked marker CFA38:11 143 243C>T) and CFA38:11 156 425T>C (splice site). In Spaniels, the haplotypes work as an allelic series including alleles (t, recessive clear; T, dominant ticked/parti‐color; and TR, incomplete dominant roan) to control the appearance of pigmented spots or flecks in otherwise white areas of the canine coat. In Spaniels the associated haplotypes are t (CCT), T (TCC) and TR (TTT) for SNP markers on CFA38 at 11 111 286C>T, 11 143 243C>T and 11 156 425T>C respectively. It is likely that other alleles exist in this series and together the haplotypes result in a complex range of patterning that is only visible when dogs have white patterning resulting from the epistatic gene Micropthalmia‐associated transcription factor (the S‐locus).
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Affiliation(s)
- L Brancalion
- Faculty of Science, University of Sydney, Camperdown, 2006, NSW, Australia
| | - B Haase
- Faculty of Science, University of Sydney, Camperdown, 2006, NSW, Australia
| | - H Mazrier
- Faculty of Science, University of Sydney, Camperdown, 2006, NSW, Australia
| | - C E Willet
- Sydney Informatics Hub, University of Sydney, Camperdown, 2006, NSW, Australia
| | - K Lindblad-Toh
- The Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 75123, Sweden
| | - F Lingaas
- Section of Medical Genetics, Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, Oslo, N-0102, Norway
| | - C M Wade
- Faculty of Science, University of Sydney, Camperdown, 2006, NSW, Australia
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Hayward JJ, Kelly-Smith M, Boyko AR, Burmeister L, De Risio L, Mellersh C, Freeman J, Strain GM. A genome-wide association study of deafness in three canine breeds. PLoS One 2020; 15:e0232900. [PMID: 32413090 PMCID: PMC7228063 DOI: 10.1371/journal.pone.0232900] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/23/2020] [Indexed: 12/17/2022] Open
Abstract
Congenital deafness in the domestic dog is usually related to the presence of white pigmentation, which is controlled primarily by the piebald locus on chromosome 20 and also by merle on chromosome 10. Pigment-associated deafness is also seen in other species, including cats, mice, sheep, alpacas, horses, cows, pigs, and humans, but the genetic factors determining why some piebald or merle dogs develop deafness while others do not have yet to be determined. Here we perform a genome-wide association study (GWAS) to identify regions of the canine genome significantly associated with deafness in three dog breeds carrying piebald: Dalmatian, Australian cattle dog, and English setter. We include bilaterally deaf, unilaterally deaf, and matched control dogs from the same litter, phenotyped using the brainstem auditory evoked response (BAER) hearing test. Principal component analysis showed that we have different distributions of cases and controls in genetically distinct Dalmatian populations, therefore GWAS was performed separately for North American and UK samples. We identified one genome-wide significant association and 14 suggestive (chromosome-wide) associations using the GWAS design of bilaterally deaf vs. control Australian cattle dogs. However, these associations were not located on the same chromosome as the piebald locus, indicating the complexity of the genetics underlying this disease in the domestic dog. Because of this apparent complex genetic architecture, larger sample sizes may be needed to detect the genetic loci modulating risk in piebald dogs.
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Affiliation(s)
- Jessica J. Hayward
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Maria Kelly-Smith
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Adam R. Boyko
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | | | - Luisa De Risio
- Animal Health Trust, Newmarket, Suffolk, England, United Kingdom
| | - Cathryn Mellersh
- Animal Health Trust, Newmarket, Suffolk, England, United Kingdom
| | - Julia Freeman
- Animal Health Trust, Newmarket, Suffolk, England, United Kingdom
| | - George M. Strain
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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10
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Kelly-Smith M, Strain GM. STRING data mining of GWAS data in canine hereditary pigment-associated deafness. Vet Anim Sci 2020; 9:100118. [PMID: 32734119 PMCID: PMC7386748 DOI: 10.1016/j.vas.2020.100118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies may fail to identify significant associations between a disorder and causative genes in complex hereditary disorders. STRING software is a bioinformatics data mining tool that identifies known and predicted physical and functional relationship networks among the proteins of candidate genes. STRING analysis provides a mechanism to identify gene-gene interactions that might not otherwise have been recognized. Relationships identified from STRING analysis can uncover function-based gene-gene relationships that may not be easily extracted from literature, thereby providing genes for pursuit as a cause of a complex hereditary disorder. In this study STRING analysis was applied to identification of candidate genes to pursue as the cause of pigment-associated hereditary deafness in dogs.
Most canine deafness is linked to white pigmentation caused by the piebald locus, shown to be the gene MITF (melanocyte inducing transcription factor), but studies have failed to identify a deafness cause. The coding regions of MITF have not been shown to be mutated in deaf dogs, leading us to pursue genes acting on or controlled by MITF. We have genotyped DNA from 502 deaf and hearing Australian cattle dogs, Dalmatians, and English setters, breeds with a high deafness prevalence. Genome-wide significance was not attained in any of our analyses, but we did identify several suggestive associations. Genome-wide association studies (GWAS) in complex hereditary disorders frequently fail to identify causative gene variants, so advanced bioinformatics data mining techniques are needed to extract information to guide future studies. STRING diagrams are graphical representations of known and predicted networks of protein-protein interactions, identifying documented relationships between gene proteins based on the scientific literature, to identify functional gene groupings to pursue for further scrutiny. The STRING program predicts associations at a preset confidence level and suggests biological functions based on the identified genes. Starting with (1) genes within 500 kb of GWAS-suggested SNPs, (2) known pigmentation genes, (3) known human deafness genes, and (4) genes identified from proteomic analysis of the cochlea, we generated STRING diagrams that included these genes. We then reduced the number of genes by excluding genes with no relationship to auditory function, pigmentation, or relevant structures, and identified clusters of genes that warrant further investigation.
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Affiliation(s)
- Maria Kelly-Smith
- Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803 USA
| | - George M Strain
- Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803 USA
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11
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Vasiliadis D, Metzger J, Distl O. Demographic assessment of the Dalmatian dog - effective population size, linkage disequilibrium and inbreeding coefficients. Canine Med Genet 2020; 7:3. [PMID: 32835229 PMCID: PMC7371805 DOI: 10.1186/s40575-020-00082-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/17/2020] [Indexed: 01/08/2023] Open
Abstract
Background The calculation of demographic measures is a useful tool for evaluating the genomic architecture of dog breeds and enables ranking dog breeds in terms of genetic diversity. To achieve this for the German Dalmatian dog population, 307 purebred animals of this breed were genotyped on the Illumina Canine high density BeadChip. The analysis of pedigree-based inbreeding was performed based on a pedigree with 25,761 dogs including the genotyped dogs. Results The effective population size derived from squared correlation coefficients between SNP alleles (r2) was 69. The maximum value of r2 was 0.56, resulting in a 50% decay value of 0.28 at a marker distance of 37.5 kb. The effective population size calculated from pedigree data using individual increase in inbreeding over equivalent generations was 116. The pedigree inbreeding coefficient was 0.026. The genomic inbreeding coefficient based on the length of runs of homozygosity (ROH) was calculated for seven length categories of ROHs, and ranged from 0.08 to 0.28. The fixation coefficients FIS_PED and FIS_GENO were at 0.017 and 0.004. PANTHER statistical overrepresentation analysis of genes located in consensus ROHs revealed highly underrepresented biological processes in 50% of the investigated dogs. One of those is the 0.28 fold enriched “immune response”, which might be associated to the high prevalence of allergic dermatitis in the breed. Candidate genes for congenital sensorineural deafness (CCSD, a highly prevalent disease in the Dalmatian) were discovered in consensus ROHs. Conclusions The fast decay of r2 and the moderate inbreeding coefficients indicate that the German Dalmatian dog population is rather diverse. Pedigree- and genomic-based inbreeding measures were highly correlated and therefore prove good reliability for the given population. Analyses of consensus ROHs with genes coding for deafness and other breed-defining traits, such as hyperuricosuria, indicate that those ROH became fixed in the Dalmatian population about 500 years ago. In case of the Dalmatian dog, a ROH of 40 SNPs length is enough to investigate signatures of selection (e.g. the ROH with the fixed hyperuricosuria mutation) as far back as the breed formation point approximately 500 years ago.
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Affiliation(s)
- Danae Vasiliadis
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Julia Metzger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Ottmar Distl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
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12
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Hai T, Guo W, Yao J, Cao C, Luo A, Qi M, Wang X, Wang X, Huang J, Zhang Y, Zhang H, Wang D, Shang H, Hong Q, Zhang R, Jia Q, Zheng Q, Qin G, Li Y, Zhang T, Jin W, Chen ZY, Wang H, Zhou Q, Meng A, Wei H, Yang S, Zhao J. Creation of miniature pig model of human Waardenburg syndrome type 2A by ENU mutagenesis. Hum Genet 2017; 136:1463-1475. [PMID: 29094203 DOI: 10.1007/s00439-017-1851-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/22/2017] [Indexed: 02/08/2023]
Abstract
Human Waardenburg syndrome 2A (WS2A) is a dominant hearing loss (HL) syndrome caused by mutations in the microphthalmia-associated transcription factor (MITF) gene. In mouse models with MITF mutations, WS2A is transmitted in a recessive pattern, which limits the study of hearing loss (HL) pathology. In the current study, we performed ENU (ethylnitrosourea) mutagenesis that resulted in substituting a conserved lysine with a serine (p. L247S) in the DNA-binding domain of the MITF gene to generate a novel miniature pig model of WS2A. The heterozygous mutant pig (MITF +/L247S) exhibits a dominant form of profound HL and hypopigmentation in skin, hair, and iris, accompanied by degeneration of stria vascularis (SV), fused hair cells, and the absence of endocochlear potential, which indicate the pathology of human WS2A. Besides hypopigmentation and bilateral HL, the homozygous mutant pig (MITF L247S/L247S) and CRISPR/Cas9-mediated MITF bi-allelic knockout pigs both exhibited anophthalmia. Three WS2 patients carrying MITF mutations adjacent to the corresponding region were also identified. The pig models resemble the clinical symptom and molecular pathology of human WS2A patients perfectly, which will provide new clues for better understanding the etiology and development of novel treatment strategies for human HL.
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Affiliation(s)
- Tang Hai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Weiwei Guo
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jing Yao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Chunwei Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Ailing Luo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Meng Qi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xianlong Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Jiaojiao Huang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Hongyong Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Dayu Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Haitao Shang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, 400038, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qianlong Hong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Rui Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qitao Jia
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qiantao Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Guosong Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Yongshun Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Tao Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Weiwu Jin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Zheng-Yi Chen
- Department of Otolaryngology, Harvard Medical School and Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA, 02114, USA
| | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Anming Meng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, 400038, China. .,Chinese Swine Mutagenesis Consortium, Beijing, China.
| | - Shiming Yang
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Jianguo Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,Chinese Swine Mutagenesis Consortium, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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13
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Volpato G, Dioli M, Di Nardo A. Piebald Camels. PASTORALISM : RESEARCH, POLICY AND PRACTICE 2017; 7:3. [PMID: 32269746 PMCID: PMC7114962 DOI: 10.1186/s13570-017-0075-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/14/2017] [Indexed: 06/11/2023]
Abstract
Animal breeds are the diverse outcome of the thousands-year-long process of livestock domestication. Many of these breeds are piebald, resulting from the artificial selection by pastoralists of animals bearing a genetic condition known as leucism, and selected for their productive, behavioural, or aesthetical traits. Piebald dromedary camels have not been studied or discussed before, and their same existence is often overlooked. Based on fieldwork in Western Sahara, direct observations across Northern and East Africa and the Middle East, and a literature review, we address the morphological and behavioural traits, geographical distribution, taxonomy, and material and cultural importance of piebald (painted) camels. They are a hundreds-year-old camel breed used for caravans, as mounts, and for aesthetical and cultural reasons across Sudan, Niger, Mali, Mauritania, Western Sahara, and Morocco. While they are increasingly bred out of a pastoral context for tourism and entertainment in the Canary Islands, mainland Europe, and the USA, in part of their original African range, piebald camels are under threat due to wars, droughts, and demise of pastoral livelihoods. More research is needed about these 'beautiful and dignified' animals.
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Affiliation(s)
- Gabriele Volpato
- Center for Integrative Conservation Research, University of Georgia, Athens, GA USA
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14
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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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15
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van Steenbeek FG, Hytönen MK, Leegwater PAJ, Lohi H. The canine era: the rise of a biomedical model. Anim Genet 2016; 47:519-27. [PMID: 27324307 DOI: 10.1111/age.12460] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2016] [Indexed: 12/29/2022]
Abstract
Since the annotation of its genome a decade ago, the dog has proven to be an excellent model for the study of inherited diseases. A large variety of spontaneous simple and complex phenotypes occur in dogs, providing physiologically relevant models to corresponding human conditions. In addition, gene discovery is facilitated in clinically less heterogeneous purebred dogs with closed population structures because smaller study cohorts and fewer markers are often sufficient to expose causal variants. Here, we review the development of genomic resources from microsatellites to whole-genome sequencing and give examples of successful findings that have followed the technological progress. The increasing amount of whole-genome sequence data warrants better functional annotation of the canine genome to more effectively utilise this unique model to understand genetic contributions in morphological, behavioural and other complex traits.
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Affiliation(s)
- F G van Steenbeek
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3508 TD, Utrecht, the Netherlands.
| | - M K Hytönen
- Research Programs Unit, Molecular Neurology, Department of Veterinary Biosciences 00014, Folkhälsan Research Center, University of Helsinki, Helsinki, Finland
| | - P A J Leegwater
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3508 TD, Utrecht, the Netherlands
| | - H Lohi
- Research Programs Unit, Molecular Neurology, Department of Veterinary Biosciences 00014, Folkhälsan Research Center, University of Helsinki, Helsinki, Finland
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16
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Abstract
Although deafness can be acquired throughout an animal's life from a variety of causes, hereditary deafness, especially congenital hereditary deafness, is a significant problem in several species. Extensive reviews exist of the genetics of deafness in humans and mice, but not for deafness in domestic animals. Hereditary deafness in many species and breeds is associated with loci for white pigmentation, where the cochlear pathology is cochleo-saccular. In other cases, there is no pigmentation association and the cochlear pathology is neuroepithelial. Late onset hereditary deafness has recently been identified in dogs and may be present but not yet recognized in other species. Few genes responsible for deafness have been identified in animals, but progress has been made for identifying genes responsible for the associated pigmentation phenotypes. Across species, the genes identified with deafness or white pigmentation patterns include MITF, PMEL, KIT, EDNRB, CDH23, TYR, and TRPM1 in dog, cat, horse, cow, pig, sheep, ferret, mink, camelid, and rabbit. Multiple causative genes are present in some species. Significant work remains in many cases to identify specific chromosomal deafness genes so that DNA testing can be used to identify carriers of the mutated genes and thereby reduce deafness prevalence.
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Affiliation(s)
- George M. Strain
- Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
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17
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Markakis MN, Soedring VE, Dantzer V, Christensen K, Anistoroaei R. Association of MITF gene with hearing and pigmentation phenotype in Hedlund white American mink (Neovison vison). J Genet 2015; 93:477-81. [PMID: 25189243 DOI: 10.1007/s12041-014-0370-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marios N Markakis
- Department of Biology, Plant Growth and Development, University of Antwerp, 2020 Antwerp, Belgium.
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18
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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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19
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Kluth S, Distl O. Congenital sensorineural deafness in dalmatian dogs associated with quantitative trait loci. PLoS One 2013; 8:e80642. [PMID: 24324618 PMCID: PMC3851758 DOI: 10.1371/journal.pone.0080642] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 10/14/2013] [Indexed: 12/13/2022] Open
Abstract
A genome-wide association study (GWAS) was performed for 235 Dalmatian dogs using the canine Illumina high density bead chip to identify quantitative trait loci (QTL) associated with canine congenital sensorineural deafness (CCSD). Data analysis was performed for all Dalmatian dogs and in addition, separately for brown-eyed and blue-eyed dogs because of the significant influence of eye colour on CCSD in Dalmatian dogs. Mixed linear model analysis (MLM) revealed seven QTL with experiment-wide significant associations (-log10P>5.0) for CCSD in all Dalmatian dogs. Six QTL with experiment-wide significant associations for CCSD were found in brown-eyed Dalmatian dogs and in blue-eyed Dalmatian dogs, four experiment-wide significant QTL were detected. The experiment-wide CCSD-associated SNPs explained 82% of the phenotypic variance of CCSD. Five CCSD-loci on dog chromosomes (CFA) 6, 14, 27, 29 and 31 were in close vicinity of genes shown as causative for hearing loss in human and/or mouse.
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Affiliation(s)
- Susanne Kluth
- Institute for Animal Breeding and Genetics, 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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20
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Reissmann M, Ludwig A. Pleiotropic effects of coat colour-associated mutations in humans, mice and other mammals. Semin Cell Dev Biol 2013; 24:576-86. [PMID: 23583561 DOI: 10.1016/j.semcdb.2013.03.014] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 12/20/2022]
Abstract
The characterisation of the pleiotropic effects of coat colour-associated mutations in mammals illustrates that sensory organs and nerves are particularly affected by disorders because of the shared origin of melanocytes and neurocytes in the neural crest; e.g. the eye-colour is a valuable indicator of disorders in pigment production and eye dysfunctions. Disorders related to coat colour-associated alleles also occur in the skin (melanoma), reproductive tract and immune system. Additionally, the coat colour phenotype of an individual influences its general behaviour and fitness. Mutations in the same genes often produce similar coat colours and pleiotropic effects in different species (e.g., KIT [reproductive disorders, lethality], EDNRB [megacolon] and LYST [CHS]). Whereas similar disorders and similar-looking coat colour phenotypes sometimes have a different genetic background (e.g., deafness [EDN3/EDNRB, MITF, PAX and SNAI2] and visual diseases [OCA2, RAB38, SLC24A5, SLC45A2, TRPM1 and TYR]). The human predilection for fancy phenotypes that ignore disorders and genetic defects is a major driving force for the increase of pleiotropic effects in domestic species and laboratory subjects since domestication has commenced approximately 18,000 years ago.
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Key Words
- AS
- ASIP
- ATRN
- Agouti signalling protein
- Albino
- Angelman syndrome
- Attractin (mahogany)
- BLOC
- Biogenesis of lysosomal organelles complex
- CCSD
- CHS
- CSD
- CSNB
- Canine congenital sensorineural deafness
- Chediak-Higashi syndrome
- Coat colour gene
- Congenital sensorineural deafness
- Congenital stationary night blindness
- Disorder
- EDN3
- EDNRB
- Endothelin 3
- Endothelin receptor type B
- Epistasis
- Fitness
- GS
- Griscelli syndrome (type 1 or 2)
- HPS
- HSCR
- Hermansky-Pudlak syndrome with different types
- Hirschsprung disease
- IPE
- Iris pigment epithelium
- KIT
- KIT ligand (steel factor)
- KITLG
- LFS
- LYST
- Lavender foal syndrome
- Lethal
- Leucism
- Lysosomal trafficking regulator
- MC1R
- MCOA
- MCOLN3
- MGRN1
- MITF
- MYO5A
- Mahogunin ring finger 1 (E3 ubiquitin protein ligase)
- Melanocortin 1 receptor
- Melanoma
- Microphthalmia-associated transcription factor
- Mucolipin 3 (TRPML3)
- Multiple congenital ocular anomalies
- Myosin VA (heavy chain 12, myoxin)
- OA
- OCA
- OCA2
- OLWS
- OSTM1
- Ocular albinism
- Oculocutaneous albinism II (pink-eye dilution homolog)
- Oculocutaneous albinism type 1–4
- Osteopetrosis associated transmembrane protein 1 (Grey lethal osteopetrosis)
- Overo lethal white syndrome
- PAX3
- PMEL
- PWS
- Paired box 3
- Pleiotropy
- Prader-Willi syndrome
- Premelanosome protein (Pmel17, SILV)
- RAB27A
- RAB27A member RAS oncogene family
- RAB38
- RAB38 member RAS oncogene family
- RPE
- Reproduction
- Retinal pigmented epithelium
- SLC24A5
- SLC2A9
- SLC45A2
- SNAI2
- STX17
- Snail homolog 2 (Drosophila), (SLUG), SOX10, SRY (sex determining region Y)-box 10
- Solute carrier family 2 (facilitated glucose transporter), member 9
- Solute carrier family 24, member 5
- Solute carrier family 45, member 2, MATP
- Syntaxin 17
- TRPM1
- TYR
- Tameness
- Transient receptor potential cation channel, subfamily M, member 1 (melastatin-1)
- Tyrosinase, TYRP1, Tyrosinase-related protein 1
- V-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog, tyrosine kinase receptor (c-kit)
- WS
- Waardenburg syndrome (type 1, type 2 combined with Tietz syndrome type 3 Klein-Waardenburg syndrome, type 4 Waardenburg-Shah syndrome)
- alpha-melanocyte-stimulating hormone
- αMSH
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Affiliation(s)
- Monika Reissmann
- Humboldt University Berlin, Department for Crop and Animal Sciences, Berlin, Germany.
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Sommerlad SF, Morton JM, Haile-Mariam M, Johnstone I, Seddon JM, O'Leary CA. Prevalence of congenital hereditary sensorineural deafness in Australian Cattle Dogs and associations with coat characteristics and sex. BMC Vet Res 2012; 8:202. [PMID: 23107143 PMCID: PMC3489614 DOI: 10.1186/1746-6148-8-202] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 10/23/2012] [Indexed: 11/11/2022] Open
Abstract
Background Congenital hereditary sensorineural deafness (CHSD) occurs in many dog breeds, including Australian Cattle Dogs. In some breeds, CHSD is associated with a lack of cochlear melanocytes in the stria vascularis, certain coat characteristics, and potentially, abnormalities in neuroepithelial pigment production. This study investigates phenotypic markers for CHSD in 899 Australian Cattle Dogs. Results Auditory function was tested in 899 Australian Cattle Dogs in family groups using brainstem auditory evoked response testing. Coat colour and patterns, facial and body markings, gender and parental hearing status were recorded. Deafness prevalence among all 899 dogs was 10.8% with 7.5% unilaterally deaf, and 3.3% bilaterally deaf, and amongst pups from completely tested litters (n = 696) was 11.1%, with 7.5% unilaterally deaf, and 3.6% bilaterally deaf. Univariable and multivariable analyses revealed a negative association between deafness and bilateral facial masks (odds ratio 0.2; P ≤ 0.001). Using multivariable logistic animal modelling, the risk of deafness was lower in dogs with pigmented body spots (odds ratio 0.4; P = 0.050). No significant associations were found between deafness and coat colour. Within unilaterally deaf dogs with unilateral facial masks, no association was observed between the side of deafness and side of mask. The side of unilateral deafness was not significantly clustered amongst unilaterally deaf dogs from the same litter. Females were at increased risk of deafness (odds ratio from a logistic animal model 1.9; P = 0.034) after adjusting for any confounding by mask type and pigmented body spots. Conclusions Australian Cattle Dogs suffer from CHSD, and this disease is more common in dogs with mask-free faces, and in those without pigmented body patches. In unilaterally deaf dogs with unilateral masks, the lack of observed association between side of deafness and side of mask suggests that if CHSD is due to defects in molecular pigment pathways, the molecular control of embryonic melanoblast migration from ectoderm to skin differs from control of migration from ectoderm to cochlea. In Australian Cattle Dogs, CHSD may be more common in females.
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Affiliation(s)
- Susan F Sommerlad
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, 4343, Australia.
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22
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Comito B, Knowles KE, Strain GM. Congenital deafness in Jack Russell terriers: prevalence and association with phenotype. Vet J 2012; 193:404-7. [PMID: 22456033 DOI: 10.1016/j.tvjl.2012.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 01/03/2012] [Accepted: 02/26/2012] [Indexed: 11/25/2022]
Abstract
Congenital hereditary sensorineural deafness is the most common form of deafness in dogs. The objectives of this study were to determine a reliable measure of the prevalence of deafness in Jack Russell terriers, an affected breed, and associations between deafness and phenotypic characteristics. Brainstem auditory evoked response recordings and phenotypic parameters (coat color, coat texture, sex, eye color, sire and dam hearing status) were recorded for 1009 Jack Russell terriers. The prevalence of unilateral and bilateral deafness was 3.57% and 0.50%, respectively, lower by a factor of three to four than in earlier reports based on smaller and closely related kindreds. Significant association with deafness was identified with white coat color and parental hearing status, but not with sex or coat type. Lack of significant sex or coat type associations and the significant association with white coat color are consistent with previous reports. In conclusion the prevalence of deafness in Jack Russell terriers is lower than initially reported. Deafness was associated with white coat color and parental hearing status. The association with parental hearing status supports this form of deafness being a heritable trait in the breed and the association with white coat color supports an inheritance linked to pigmentation genes.
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Affiliation(s)
- B Comito
- Veterinary Neurological Center, 4202 E. Raymond St., Phoenix, AZ 85040, USA
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23
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Abstract
During the last decade, coat colouration in mammals has been investigated in numerous studies. Most of these studies addressing the genetics of coat colouration were on domesticated animals. In contrast to their wild ancestors, domesticated species are often characterized by a huge allelic variability of coat-colour-associated genes. This variability results from artificial selection accepting negative pleiotropic effects linked with certain coat-colour variants. Recent studies demonstrate that this selection for coat-colour phenotypes started at the beginning of domestication. Although to date more than 300 genetic loci and more than 150 identified coat-colour-associated genes have been discovered, which influence pigmentation in various ways, the genetic pathways influencing coat colouration are still only poorly described. On the one hand, similar coat colourations observed in different species can be the product of a few conserved genes. On the other hand, different genes can be responsible for highly similar coat colourations in different individuals of a species or in different species. Therefore, any phenotypic classification of coat colouration blurs underlying differences in the genetic basis of colour variants. In this review we focus on (i) the underlying causes that have resulted in the observed increase of colour variation in domesticated animals compared to their wild ancestors, and (ii) the current state of knowledge with regard to the molecular mechanisms of colouration, with a special emphasis on when and where the different coat-colour-associated genes act.
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Affiliation(s)
- Michael Cieslak
- Leibniz Institute for Zoo and Wildlife Research, Research Group of Evolutionary Genetics, Berlin, Germany
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24
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Sommerlad S, McRae AF, McDonald B, Johnstone I, Cuttell L, Seddon JM, O'Leary CA. Congenital sensorineural deafness in Australian stumpy-tail cattle dogs is an autosomal recessive trait that maps to CFA10. PLoS One 2010; 5:e13364. [PMID: 20967282 PMCID: PMC2953516 DOI: 10.1371/journal.pone.0013364] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 09/14/2010] [Indexed: 11/18/2022] Open
Abstract
Background Congenital sensorineural deafness is an inherited condition found in many dog breeds, including Australian Stumpy-tail Cattle Dogs (ASCD). This deafness is evident in young pups and may affect one ear (unilateral) or both ears (bilateral). The genetic locus/loci involved is unknown for all dog breeds. The aims of this study were to determine incidence, inheritance mechanism, and possible association of congenital sensorineural deafness with coat colour in ASCD and to identify the genetic locus underpinning this disease. Methodology/Principal Findings A total of 315 ASCD were tested for sensorineural deafness using the brain stem auditory evoked response (BAER) test. Disease penetrance was estimated directly, using the ratio of unilaterally to bilaterally deaf dogs, and segregation analysis was performed using Mendel. A complete genome screen was undertaken using 325 microsatellites spread throughout the genome, on a pedigree of 50 BAER tested ASCD in which deafness was segregating. Fifty-six dogs (17.8%) were deaf, with 17 bilaterally and 39 unilaterally deaf. Unilaterally deaf dogs showed no significant left/right bias (p = 0.19) and no significant difference was observed in frequencies between the sexes (p = 0.18). Penetrance of deafness was estimated as 0.72. Testing the association of red/blue coat colour and deafness without accounting for pedigree structure showed that red dogs were 1.8 times more likely to be deaf (p = 0.045). The within family association between red/blue coat colour and deafness was strongly significant (p = 0.00036), with red coat colour segregating more frequently with deafness (COR = 0.48). The relationship between deafness and coat speckling approached significance (p = 0.07), with the lack of statistical significance possibly due to only four families co-segregating for both deafness and speckling. The deafness phenotype was mapped to CFA10 (maximum linkage peak on CFA10 −log10 p-value = 3.64), as was both coat colour and speckling. Fine mapping was then performed on 45 of these 50 dogs and a further 48 dogs (n = 93). Sequencing candidate gene Sox10 in 6 hearing ASCD, 2 unilaterally deaf ASCD and 2 bilaterally deaf ASCD did not reveal any disease-associated mutations. Conclusions Deafness in ASCD is an incompletely penetrant autosomal recessive inherited disease that maps to CFA10.
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Affiliation(s)
- Susan Sommerlad
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Allan F. McRae
- Queensland Statistical Genetics, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Brenda McDonald
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Isobel Johnstone
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Leigh Cuttell
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Jennifer M. Seddon
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Caroline A. O'Leary
- Centre for Companion Animal Health, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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Bellone RR, Forsyth G, Leeb T, Archer S, Sigurdsson S, Imsland F, Mauceli E, Engensteiner M, Bailey E, Sandmeyer L, Grahn B, Lindblad-Toh K, Wade CM. Fine-mapping and mutation analysis of TRPM1: a candidate gene for leopard complex (LP) spotting and congenital stationary night blindness in horses. Brief Funct Genomics 2010; 9:193-207. [PMID: 20353955 DOI: 10.1093/bfgp/elq002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Leopard Complex spotting occurs in several breeds of horses and is caused by an incompletely dominant allele (LP). Homozygosity for LP is also associated with congenital stationary night blindness (CSNB) in Appaloosa horses. Previously, LP was mapped to a 6 cm region on ECA1 containing the candidate gene TRPM1 (Transient Receptor Potential Cation Channel, Subfamily M, Member 1) and decreased expression of this gene, measured by qRT-PCR, was identified as the likely cause of both spotting and ocular phenotypes. This study describes investigations for a mutation causing or associated with the Leopard Complex and CSNB phenotype in horses. Re-sequencing of the gene and associated splice sites within the 105 624 bp genomic region of TRPM1 led to the discovery of 18 SNPs. Most of the SNPs did not have a predictive value for the presence of LP. However, one SNP (ECA1:108,249,293 C>T) found within intron 11 had a strong (P < 0.0005), but not complete, association with LP and CSNB and thus is a good marker but unlikely to be causative. To further localize the association, 70 SNPs spanning over two Mb including the TRPM1 gene were genotyped in 192 horses from three different breeds segregating for LP. A single 173 kb haplotype associated with LP and CSNB (ECA1: 108,197,355- 108,370,150) was identified. Illumina sequencing of 300 kb surrounding this haplotype revealed 57 SNP variants. Based on their localization within expressed sequences or regions of high sequence conservation across mammals, six of these SNPs were considered to be the most likely candidate mutations. While the precise function of TRPM1 remains to be elucidated, this work solidifies its functional role in both pigmentation and night vision. Further, this work has identified several potential regulatory elements of the TRPM1 gene that should be investigated further in this and other species.
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