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McFadden A, Vierra M, Martin K, Brooks SA, Everts RE, Lafayette C. Spotting the Pattern: A Review on White Coat Color in the Domestic Horse. Animals (Basel) 2024; 14:451. [PMID: 38338094 PMCID: PMC10854722 DOI: 10.3390/ani14030451] [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: 12/25/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Traits such as shape, size, and color often influence the economic and sentimental value of a horse. Around the world, horses are bred and prized for the colors and markings that make their unique coat patterns stand out from the crowd. The underlying genetic mechanisms determining the color of a horse's coat can vary greatly in their complexity. For example, only two genetic markers are used to determine a horse's base coat color, whereas over 50 genetic variations have been discovered to cause white patterning in horses. Some of these white-causing mutations are benign and beautiful, while others have a notable impact on horse health. Negative effects range from slightly more innocuous defects, like deafness, to more pernicious defects, such as the lethal developmental defect incurred when a horse inherits two copies of the Lethal White Overo allele. In this review, we explore, in detail, the etiology of white spotting and its overall effect on the domestic horse to Spot the Pattern of these beautiful (and sometimes dangerous) white mutations.
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Affiliation(s)
- Aiden McFadden
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
| | - Micaela Vierra
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
| | - Katie Martin
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
| | - Samantha A. Brooks
- Department of Animal Sciences, UF Genetics Institute, University of Florida, Gainesville, FL 32611, USA;
| | - Robin E. Everts
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
| | - Christa Lafayette
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
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2
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Bellone RR, Tanaka J, Esdaile E, Sutton RB, Payette F, Leduc L, Till BJ, Abdel-Ghaffar AK, Hammond M, Magdesian KG. A de novo 2.3 kb structural variant in MITF explains a novel splashed white phenotype in a Thoroughbred family. Anim Genet 2023; 54:752-762. [PMID: 37697831 DOI: 10.1111/age.13352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/12/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023]
Abstract
Splashed white in horses is characterized by extensive white patterning on the legs, face and abdomen and may be accompanied by deafness. To date, seven variants in microphthalmia-associated transcription factor (MITF) and two variants in Paired Box 3 (PAX3) have been identified to explain this phenotype. A splashed white Thoroughbred stallion, whose sire and dam were not patterned, was hypothesized to have a de novo variant leading to his white coat pattern. A whole-genome sequencing candidate gene approach identified two single nucleotide variants (SNVs) in SOX10, four SNVs in MITF and a 2.3 kb deletion in MITF with the alternative allele present in this stallion but absent in the other 18 horses analyzed. All six SNVs were annotated as modifiers and were not further considered. The deletion in MITF (NC_009159.3:g.21555811_21558139delinsAAAT) encompasses exon 9 encoding a part of the helix-loop-helix domain required for DNA binding. Sanger sequencing and parentage testing confirmed that this deletion was a de novo mutation of maternal origin. Consistent with the published nomenclature, we denote this likely causal variant as SW8. Genotyping three of this stallion's offspring identified SW8 only in the nearly all-white foal that was confirmed deaf by brainstem auditory evoked response testing. This foal was also a compound heterozygote for dominant white variants (W20/W22), but to date, W variants alone have not been connected to deafness. SW8 marks the fourth de novo MITF variant in horses reported to cause white patterning. The link between deafness and all MITF variants with and without other variants impacting melanocyte development and function needs to be further explored.
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Affiliation(s)
- R R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - J Tanaka
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - E Esdaile
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - R B Sutton
- Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - F Payette
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, University School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania, USA
| | - L Leduc
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, University School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania, USA
| | - B J Till
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - A K Abdel-Ghaffar
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - M Hammond
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - K G Magdesian
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
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3
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Gossett CL, Guyer D, Hein J, Brooks SA. Digital Phenotyping Reveals Phenotype Diversity and Epistasis among White Spotting Alleles in the American Paint Horse. Genes (Basel) 2023; 14:2011. [PMID: 38002953 PMCID: PMC10671537 DOI: 10.3390/genes14112011] [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: 09/01/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/26/2023] Open
Abstract
White spotting is an iconic feature of the American Paint Horse. The American Paint Horse Association (APHA) is dedicated to recording pedigree and performance of this stock-type breed, while preserving its distinctive coat color and conformation. Here, the depigmented proportion of the coat (% white coat) was measured using digital photograph analysis of 1195 registered American Paint Horses. Genotypes for nine white-spotting polymorphisms commonly found in Paint Horses, and two pigment-producing loci MCIR and ASIP genes, were also provided by the APHA. White-coat percent significantly increased in horses with more white-spotting alleles present, regardless of the number of loci bearing those alleles, likely due to a strong additive genetic effect at each white-spotting locus, as well as an additive epistatic effect among white spotting loci. Paint Horses with a chestnut base coat color (genotype e/e at MC1R) possessed a significantly higher white coat percentage, suggesting confirming an epistatic interaction between pigmentation signaling genes and loci for white spotting. The APHA registry categories of Regular versus Solid Paint-Bred also differed in their median white coat percentage (p < 0.0001), but not in the overall ranges of this phenotype, reenforcing the importance of the regional patterns of the depigmentation in the definition of the desired APHA phenotype. Multi-locus phenotype prediction models for white-coat percentage performed only moderately well, and improvements in the sample size and the number of loci genotyped will likely be needed before such an approach could be used practically by APHA breeders. In the future, models that enable phenotype prediction based on genotypes, and automated phenotype assessment could increase the production of valuable visual traits in the American Paint Horse population and improve the APHA member experience during the registration process.
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Affiliation(s)
- Chelby Lynn Gossett
- UF Genetics Institute, University of Florida Department of Animal Sciences, Gainesville, FL 32611-0910, USA
| | - Danielle Guyer
- UF Genetics Institute, University of Florida Department of Animal Sciences, Gainesville, FL 32611-0910, USA
| | - Jessica Hein
- American Paint Horse Association, Fort Worth, TX 76161-0023, USA
| | - Samantha A. Brooks
- UF Genetics Institute, University of Florida Department of Animal Sciences, Gainesville, FL 32611-0910, USA
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4
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Elkin J, Martin A, Courtier-Orgogozo V, Santos ME. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol Rev Camb Philos Soc 2023; 98:1250-1277. [PMID: 37017088 DOI: 10.1111/brv.12952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
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Affiliation(s)
- Joel Elkin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington, DC, 20052, USA
| | | | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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5
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McFadden A, Martin K, Foster G, Vierra M, Lundquist EW, Everts RE, Martin E, Volz E, McLoone K, Brooks SA, Lafayette C. 5'UTR Variant in KIT Associated with White Spotting in Horses. J Equine Vet Sci 2023:104563. [PMID: 37182614 DOI: 10.1016/j.jevs.2023.104563] [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: 03/09/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/16/2023]
Abstract
Mutations in KIT, a gene that influences melanoblast migration and pigmentation, often result in mammalian white spotting. As of February 2023, over 30 KIT variants associated with white spotting were documented in Equus caballus (horse). Here we report an association of increased white spotting on the skin and coat with a variant in the 5'UTR of KIT (rs1149701677: g.79,618,649A>C). Horses possessing at least one alternate allele demonstrate phenotypic characteristics similar to other KIT mutations: clear borders around unpigmented regions on the body, face, and limbs. Using a quantitative measure of depigmentation, we observed an average white score of 10.70 among individuals with rs1149701677, while the average score of the control, homozygous reference sample was 2.23 (p=1.892e-11, n=109, t-test). The rs1149701677 site has a cross-species conservation score of 3.4, one of the highest scores across the KIT 5'UTR, implying regulatory importance for this site. Ensembl also predicted a "moderately impactful" functional effect for the rs1149701677 variant. We propose that this single nucleotide variant likely alters the regulation of KIT, which in turn may disrupt melanoblast migration causing an increase in white spotting on the coat. Alternatively, the rs1149701677 variant may be in linkage with another nearby variant with an as-yet-undiscovered functional impact. We propose to term this new allele "Holiday White" or W35 based on conventional nomenclature.
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Affiliation(s)
| | | | | | | | | | | | | | - Erin Volz
- Etalon Inc, Menlo Park, CA 94025, USA
| | | | - Samantha A Brooks
- Department of Animal Sciences, UF Genetics Institute University of Florida, Gainesville, FL 32611-0910, USA
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6
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Breed Distribution and Allele Frequencies of Base Coat Color, Dilution, and White Patterning Variants across 28 Horse Breeds. Genes (Basel) 2022; 13:genes13091641. [PMID: 36140807 PMCID: PMC9498372 DOI: 10.3390/genes13091641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Since domestication, horses have been selectively bred for various coat colors and white spotting patterns. To investigate breed distribution, allele frequencies, and potential lethal variants for recommendations on genetic testing, 29 variants within 14 genes were investigated in 11,281 horses from 28 breeds. The recessive chestnut ea allele in melanocortin 1 receptor (MC1R) (p.D84N) was identified in four breeds: Knabstrupper, Paint Horse, Percheron, and Quarter Horse. After filtering for relatedness, ea allele frequency in Knabstruppers was estimated at 0.035, thus illustrating the importance of testing for mate selection for base coat color. The Rocky Mountain Horse breed had the highest allele frequency for two of the dilution variants under investigation (Za.f. = 0.32 and Cha.f. = 0.026); marker-assisted selection in this breed could aid in the production of horses with desirable dilute coats with less severe ocular anomalies caused by the silver (Z) allele. With regard to white patterning, nine horses homozygous for the paired box 3 (PAX3) splashed white 2 (SW2) allele (p.C70Y) and six horses homozygous for the KIT proto-oncogene, receptor tyrosine kinase (KIT) sabino 1 (SB1) allele (ECA3g.79544206A>T) were identified, thus determining they are rare and confirming that homozygosity for SW2 is not embryonic lethal. The KIT dominant white 20 (W20) allele (p.R682H) was identified in all but three breeds: Arabian (n = 151), Icelandic Horse (n = 66), and Norwegian Fjord Horse (n = 90). The role of W20 in pigmentation across breeds is not well understood; given the different selection regimes of the breeds investigated, these data provide justification for further evaluating the functional role of this allele in pigmentation. Here, we present the largest dataset reported for coat color variants in horses to date, and these data highlight the importance of breed-specific studies to inform on the proper use of marker-assisted selection and to develop hypotheses related to pigmentation for further testing in horses.
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7
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Patterson Rosa L, Martin K, Vierra M, Lundquist E, Foster G, Brooks SA, Lafayette C. A KIT Variant Associated with Increased White Spotting Epistatic to MC1R Genotype in Horses ( Equus caballus). Animals (Basel) 2022; 12:ani12151958. [PMID: 35953947 PMCID: PMC9367399 DOI: 10.3390/ani12151958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Over 40 identified genetic variants contribute to white spotting in the horse. White markings and spotting are under selection for their impact on the economic value of an equine, yet many phenotypes have an unknown genetic basis. Previous studies also demonstrate an interaction between MC1R and ASIP pigmentation loci and white spotting associated with KIT and MITF. We investigated two stallions presenting with a white spotting phenotype of unknown cause. Exon sequencing of the KIT and MITF candidate genes identified a missense variant in KIT (rs1140732842, NC_009146.3:g.79566881T>C, p.T391A) predicted by SIFT and PROVEAN as not tolerated/deleterious. Three independent observers generated an Average Grade of White (AGW) phenotype score for 147 individuals based on photographs. The KIT variant demonstrates a significant QTL association to AGW (p = 3.3 × 10−12). Association with the MC1R Extension locus demonstrated that, although not in LD, MC1R e/e (chestnut) individuals had higher AGW scores than MC1R E/- individuals (p = 3.09 × 10−17). We also report complete linkage of the previously reported KIT W19 allele to this missense variant. We propose to term this variant W34, following the standardized nomenclature for white spotting variants within the equine KIT gene, and report its epistatic interaction with MC1R.
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Affiliation(s)
- Laura Patterson Rosa
- Etalon, Inc., Menlo Park, CA 94025, USA; (K.M.); (M.V.); (E.L.); (G.F.)
- Correspondence: (L.P.R.); (C.L.); Tel.: +1-650-380-2995 (C.L.)
| | - Katie Martin
- Etalon, Inc., Menlo Park, CA 94025, USA; (K.M.); (M.V.); (E.L.); (G.F.)
| | - Micaela Vierra
- Etalon, Inc., Menlo Park, CA 94025, USA; (K.M.); (M.V.); (E.L.); (G.F.)
| | - Erica Lundquist
- Etalon, Inc., Menlo Park, CA 94025, USA; (K.M.); (M.V.); (E.L.); (G.F.)
| | - Gabriel Foster
- Etalon, Inc., Menlo Park, CA 94025, USA; (K.M.); (M.V.); (E.L.); (G.F.)
| | - Samantha A. Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA;
| | - Christa Lafayette
- Etalon, Inc., Menlo Park, CA 94025, USA; (K.M.); (M.V.); (E.L.); (G.F.)
- Correspondence: (L.P.R.); (C.L.); Tel.: +1-650-380-2995 (C.L.)
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8
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Patterson Rosa L, Martin K, Vierra M, Foster G, Brooks SA, Lafayette C. Non-frameshift deletion on MITF is associated with a novel splashed white spotting pattern in horses (Equus caballus). Anim Genet 2022; 53:538-540. [PMID: 35672910 DOI: 10.1111/age.13225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | - Samantha A Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
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9
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Esdaile E, Till B, Kallenberg A, Fremeux M, Bickel L, Bellone RR. A de novo missense mutation in KIT is responsible for dominant white spotting phenotype in a Standardbred horse. Anim Genet 2022; 53:534-537. [PMID: 35641888 DOI: 10.1111/age.13222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/04/2022] [Indexed: 12/31/2022]
Affiliation(s)
- Elizabeth Esdaile
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Brad Till
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Angelica Kallenberg
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Michelle Fremeux
- InfogeneNZ, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Leslie Bickel
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
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10
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Manakhov AD, Mintseva MY, Andreeva TV, Trapezov OV, Rogaev EI. Shadow coat colour in American mink associated with a missense mutation in the KIT gene. Anim Genet 2022; 53:522-525. [PMID: 35481560 DOI: 10.1111/age.13202] [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: 11/01/2021] [Revised: 03/21/2022] [Accepted: 04/04/2022] [Indexed: 11/26/2022]
Abstract
The classical genetic analysis describes more 35 mutations that are involved in the formation of the American mink (Neovison vison) fur colour phenotype. To date, only eight of these mutations have been linked to specific genes. Shadow is a member of the commercially valuable Black cross colour family. Here, we performed whole-genome sequencing of the American mink with a Shadow Silverblue (Sh /+ p/p) phenotype. We identified a missense mutation (c.2374 G>T) in the gene encoding the KIT proto-oncogene, receptor tyrosine kinase gene (KIT), which plays a critical role in melanogenesis as well as in the survival, growth and development of other cell types. The reported mutation results in amino acid substitution p.Asp792Tyr in a highly conserved catalytic loop of the KIT protein.
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Affiliation(s)
- Andrey D Manakhov
- Centre for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Yu Mintseva
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V Andreeva
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Oleg V Trapezov
- Department of Animals and Human Genetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Evgeny I Rogaev
- Centre for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Psychiatry, UMass Chan Medical School, Worcester, Massachusetts, USA
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11
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Identification of W13 in the American Miniature Horse and Shetland Pony Populations. Genes (Basel) 2021; 12:genes12121985. [PMID: 34946933 PMCID: PMC8702037 DOI: 10.3390/genes12121985] [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: 11/25/2021] [Revised: 12/07/2021] [Accepted: 12/11/2021] [Indexed: 11/16/2022] Open
Abstract
Coat color is a trait of economic significance in horses. Variants in seven genes have been documented to cause white patterning in horses. Of the 34 variants that have been identified in KIT proto-oncogene, receptor tyrosine kinase (KIT), 27 have only been reported in a single individual or family and thus not all are routinely offered for genetic testing. Therefore, to enable proper use of marker-assisted selection, determining breed specificity for these alleles is warranted. Screening 19 unregistered all-white Shetland ponies for 16 white patterning markers identified 14 individuals whose phenotype could not be explained by testing results. In evaluating other known dominant white variants, 14 horses were heterozygous for W13. W13 was previously only reported in two quarter horses and a family of Australian miniature horses. Genotyping known white spotting variants in 30 owner-reported white animals (25 Miniature Horses and five Shetland ponies) identified two additional W13/N American Miniature Horses. The estimated allele frequency of W13 in the American Miniature Horse was 0.0063 (79 N/N, 1 W13/N) and the allele was not detected in a random sample (n = 59) of Shetland ponies. No homozygous W13 individuals were identified and W13/N ponies had a similar all-white coat with pink skin phenotype, regardless of the other white spotting variants present, demonstrating that W13 results in a Mendelian inherited dominant white phenotype and homozygosity is likely lethal. These findings document the presence of W13 in the American Miniature Horse and Shetland pony populations at a low frequency and illustrate the importance of testing for this variant in additional breeds.
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12
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Patterson Rosa L, Martin K, Vierra M, Foster G, Lundquist E, Brooks SA, Lafayette C. Two Variants of KIT Causing White Patterning in Stock-Type Horses. J Hered 2021; 112:447-451. [PMID: 34223905 DOI: 10.1093/jhered/esab033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
Over 30 polymorphisms in the KIT Proto-Oncogene Receptor Tyrosine Kinase (KIT) gene have been implicated in white spotting patterns ranging from small areas to full dermal depigmentation in the horse. We performed a candidate-gene exon sequencing approach on KIT and MITF, 2 known causatives of white spotting patterns, within 2 families of horses of unknown white spotting. Family 1 (Fam1, N = 5) consisted of a Quarter Horse stallion and 4 offspring with white spotting pattern ranging from legs, lower ventral, and head regions with jagged borders, to almost complete white. The second family (Fam2, N = 7) consisted of 6 half-sibling American Paint Horse/Quarter Horse and their dam, demonstrating unpigmented limbs with belly spots and an extensive white patterning on the face. This approach resulted in 2 variants significantly associated with familial phenotypes, where Fam1 variant is an indel leading to a frameshift mutation, and Fam2 a non-synonymous SNP. We validated the variants within an unrelated population of horses (Fam2 variant, P = 0.00271944) as well as for protein functional impact with ExPASy, Protter, Phyre2, SMART, PROVEAN, SIFT, and I-TASSER, confirming the reported associations. Fam1 associated variant, deemed W31, alters the protein sequence, leading to an early stop codon truncating the normal amino acid sequence from 972 to just 115 amino acids. Fam2 associated variant, deemed W32, may have a subtle impact on receptor function or could be in linkage with a non-coding or regulatory change creating the mild spotting pattern observed in this family.
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Affiliation(s)
| | | | | | | | | | - Samantha A Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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13
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Magdesian KG, Tanaka J, Bellone RR. A De Novo MITF Deletion Explains a Novel Splashed White Phenotype in an American Paint Horse. J Hered 2021; 111:287-293. [PMID: 32242630 PMCID: PMC7238438 DOI: 10.1093/jhered/esaa009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/01/2020] [Indexed: 11/14/2022] Open
Abstract
Splashed white is a coat color pattern in horses characterized by extensive white patterning on the legs, belly, and face often accompanied by blue eyes and deafness. Three mutations in microphthalmia-associated transcription factor (MITF) and two mutations in Paired Box 3 (PAX3) have been identified that explain splashed white patterns (SW1-SW5). An American Paint Horse stallion with a splashed white phenotype and blue eyes, whose parents were not white patterned, was negative for the 5 known splashed white variants and other known white spotting alleles. This novel splashed white phenotype (SW6) was hypothesized to be caused by a de novo mutation in MITF or PAX3. Analysis of whole-genome sequencing using the EquCab3.0 reference genome for comparison identified an 8.7 kb deletion in MITF on ECA16 (NC_009159.3:g.21551060-21559770del). The deletion encompassed part of intron 7 through the 3' UTR of exon 9 of MITF, including the helix-loop-helix DNA-binding domain (ENSECAT00000006375.3). This variant is predicted to truncate protein and impair binding to DNA. Sanger sequencing confirmed the stallion was heterozygous for the MITF deletion. No single nucleotide polymorphisms (SNPs) or structural variants were identified in PAX3 or any of the other candidate genes that were unique to the stallion or predicted to affect protein function. Genotyping five of the stallion's splashed white offspring, including one all white foal, found that they were also heterozygous for the deletion. Given the role of MITF in producing white pattern phenotypes, and the predicted deleterious effect of this mutation, this 8.7 kb deletion is the likely causal variant for SW6.
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Affiliation(s)
- K Gary Magdesian
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, CA
| | - Jocelyn Tanaka
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA
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14
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Munds RA, Titus CL, Moreira LAA, Eggert LS, Blomquist GE. Examining the molecular basis of coat color in a nocturnal primate family (Lorisidae). Ecol Evol 2021; 11:4442-4459. [PMID: 33976821 PMCID: PMC8093732 DOI: 10.1002/ece3.7338] [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] [Received: 05/16/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 02/03/2023] Open
Abstract
Organisms use color for camouflage, sexual signaling, or as a warning sign of danger. Primates are one of the most vibrantly colored Orders of mammals. However, the genetics underlying their coat color are poorly known, limiting our ability to study molecular aspects of its evolution. The role of the melanocortin 1 receptor (MC1R) in color evolution has been implicated in studies on rocket pocket mice (Chaetodipus intermediusi), toucans (Ramphastidae), and many domesticated animals. From these studies, we know that changes in MC1R result in a yellow/red or a brown/black morphology. Here, we investigate the evolution of MC1R in Lorisidae, a monophyletic nocturnal primate family, with some genera displaying high contrast variation in color patterns and other genera being monochromatic. Even more unique, the Lorisidae family has the only venomous primate: the slow loris (Nycticebus). Research has suggested that the contrasting coat patterns of slow lorises are aposematic signals for their venom. If so, we predict the MC1R in slow lorises will be under positive selection. In our study, we found that Lorisidae MC1R is under purifying selection (ω = 0.0912). In Lorisidae MC1R, there were a total of 75 variable nucleotides, 18 of which were nonsynonymous. Six of these nonsynonymous substitutions were found on the Perodicticus branch, which our reconstructions found to be the only member of Lorisidae that has predominantly lighter coat color; no substitutions were associated with Nycticebus. Our findings generate new insight into the genetics of pelage color and evolution among a unique group of nocturnal mammals and suggest putative underpinnings of monochromatic color evolution in the Perodicticus lineage.
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Affiliation(s)
- Rachel A. Munds
- Department of Anthropology & ArchaeologyUniversity of CalgaryCalgaryABCanada
- Nocturnal Primate Research GroupOxford Brookes UniversityOxfordUK
| | - Chelsea L. Titus
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Lais A. A. Moreira
- Department of Anthropology & ArchaeologyUniversity of CalgaryCalgaryABCanada
| | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
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15
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Wen J, Shao P, Chen Y, Wang L, Lv X, Yang W, Jia Y, Jiang Z, Zhu B, Qu L. Genomic scan revealed KIT gene underlying white/gray plumage color in Chinese domestic geese. Anim Genet 2021; 52:356-360. [PMID: 33644907 DOI: 10.1111/age.13050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2021] [Indexed: 01/17/2023]
Abstract
Goose is an important type of domesticated poultry. The wild geese that are regarded as the ancestors of modern domestic geese present gray plumage. Domesticated, geese have both white and gray feathers. To elucidate the genetic mechanisms underlying the formation of white and gray plumage in geese, we resequenced the whole genome of 18 geese from six populations including white and gray goose breeds. The average sequencing depth per individual was 9.81× and the average genome coverage was 96.8%. A total of 346 genes were detected in the top 1% of FST scores of gray- and white-feathered geese, and a significant FST site was located in the intron region within the KIT gene, the 18 bp deletion in KIT having the strongest potential association with white feathers. It has been reported that a number of genes are associated with plumage colors in birds. However, no studies have identified the relationship between KIT and plumage color in birds at present, although the white coat can be attributed to mutations in KIT in some mammals. Our study showed that that KIT is a plausible candidate gene for white/gray plumage color in Chinese domestic geese.
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Affiliation(s)
- J Wen
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100094, China
| | - P Shao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100094, China
| | - Y Chen
- Beijing Animal Husbandry and Veterinary Station, Beijing, 100107, China
| | - L Wang
- Beijing Animal Husbandry and Veterinary Station, Beijing, 100107, China
| | - X Lv
- Beijing Animal Husbandry and Veterinary Station, Beijing, 100107, China
| | - W Yang
- Beijing Animal Husbandry and Veterinary Station, Beijing, 100107, China
| | - Y Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Z Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, 99164, USA
| | - B Zhu
- Zhuozhou Animal Health Supervision Station, Hebei, 072750, China
| | - L Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100094, China
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16
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Xu J, Fu Y, Hu Y, Yin L, Tang Z, Yin D, Zhu M, Yu M, Li X, Zhou Y, Zhao S, Liu X. Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features. J Anim Sci Biotechnol 2020; 11:115. [PMID: 33292532 PMCID: PMC7713148 DOI: 10.1186/s40104-020-00520-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/19/2020] [Indexed: 01/15/2023] Open
Abstract
Background A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds. Results In this study, we performed GWAS using a standard mixed linear model with three types of genome variants (SNP, InDel, and CNV) that were identified from public, whole-genome, sequencing data sets. We used 469 pigs of 57 breeds, and we identified and analyzed approximately 19 million SNPs, 1.8 million InDels, and 18,016 CNVs. We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes, which included coat color, ear shape, gradient zone, body weight, body length, and body height. A total of 37 candidate genes was identified, which included 27 that were reported previously (e.g., PLAG1 for body weight), but the other 10 were newly detected candidate genes (e.g., ADAMTS9 for coat color). Conclusion Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits. Supplementary Information Supplementary information accompanies this paper at 10.1186/s40104-020-00520-8.
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Affiliation(s)
- Jingya Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Yuhua Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Lilin Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Zhenshuang Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Dong Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
| | - Xiaolei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
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17
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Kvist L, Honka J, Niskanen M, Liedes O, Aspi J. Selection in the Finnhorse, a native all-around horse breed. J Anim Breed Genet 2020; 138:188-203. [PMID: 33226152 PMCID: PMC7894145 DOI: 10.1111/jbg.12524] [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: 08/24/2020] [Revised: 10/20/2020] [Accepted: 11/01/2020] [Indexed: 12/19/2022]
Abstract
Selection by breeders modifies the morphology, behaviour and performance of domesticated species. Here, we examined signs of selection in Finnhorse, the only native horse breed in Finland. We first searched divergent genomic regions between Finnhorses and other breeds, as well as between different breeding sections of the Finnhorse with data from Illumina Equine SNP70 BeadChip, and then studied several of the detected regions in more detail. We found altogether 35 common outlier SNPs between Finnhorses and other breeds using two different selection tests. Many of the SNPs were located close to genes affecting coat colour, performance, size, sugar metabolism, immune response and olfaction. We selected genes affecting coat colour (KIT, MITF, PMEL), performance (MSTN) and locomotion (DMRT3) for a more detailed examination. In addition, we looked for, and found, associations with height at withers and SNPs located close to gene LCORL. Among the four breeding sections of Finnhorses (harness trotters, riding horses, draught horses and pony‐sized horses), a single SNP located close to the DMRT3 gene was significantly differentiated and only between harness trotters and pony‐sized horses.
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Affiliation(s)
- Laura Kvist
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Johanna Honka
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Markku Niskanen
- Research Unit of History, Culture and Communications, University of Oulu, Oulu, Finland
| | - Oona Liedes
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Jouni Aspi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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18
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He Z, Dai X, Beaumont M, Yu F. Detecting and Quantifying Natural Selection at Two Linked Loci from Time Series Data of Allele Frequencies with Forward-in-Time Simulations. Genetics 2020; 216:521-541. [PMID: 32826299 PMCID: PMC7536848 DOI: 10.1534/genetics.120.303463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 08/15/2020] [Indexed: 12/16/2022] Open
Abstract
Recent advances in DNA sequencing techniques have made it possible to monitor genomes in great detail over time. This improvement provides an opportunity for us to study natural selection based on time serial samples of genomes while accounting for genetic recombination effect and local linkage information. Such time series genomic data allow for more accurate estimation of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel Bayesian statistical framework for inferring natural selection at a pair of linked loci by capitalising on the temporal aspect of DNA data with the additional flexibility of modeling the sampled chromosomes that contain unknown alleles. Our approach is built on a hidden Markov model where the underlying process is a two-locus Wright-Fisher diffusion with selection, which enables us to explicitly model genetic recombination and local linkage. The posterior probability distribution for selection coefficients is computed by applying the particle marginal Metropolis-Hastings algorithm, which allows us to efficiently calculate the likelihood. We evaluate the performance of our Bayesian inference procedure through extensive simulations, showing that our approach can deliver accurate estimates of selection coefficients, and the addition of genetic recombination and local linkage brings about significant improvement in the inference of natural selection. We also illustrate the utility of our method on real data with an application to ancient DNA data associated with white spotting patterns in horses.
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Affiliation(s)
- Zhangyi He
- School of Mathematics, University of Bristol, BS8 1UG, United Kingdom
| | - Xiaoyang Dai
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Feng Yu
- School of Mathematics, University of Bristol, BS8 1UG, United Kingdom
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19
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Brooks SA, Palermo KM, Kahn A, Hein J. Impact of white‐spotting alleles, including
W20
, on phenotype in the American Paint Horse. Anim Genet 2020; 51:707-715. [DOI: 10.1111/age.12960] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2020] [Indexed: 01/09/2023]
Affiliation(s)
- S. A. Brooks
- Department of Animal Sciences UF Genetics Institute University of Florida Gainesville FL 32611‐0910 USA
| | - K. M. Palermo
- Department of Animal Sciences UF Genetics Institute University of Florida Gainesville FL 32611‐0910 USA
| | - A. Kahn
- Department of Animal Sciences UF Genetics Institute University of Florida Gainesville FL 32611‐0910 USA
| | - J. Hein
- American Paint Horse Association Fort Worth TX 76161‐0023 USA
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20
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Coat Color Roan Shows Association with KIT Variants and No Evidence of Lethality in Icelandic Horses. Genes (Basel) 2020; 11:genes11060680. [PMID: 32580410 PMCID: PMC7348759 DOI: 10.3390/genes11060680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 11/26/2022] Open
Abstract
Roan (Rn) horses show a typical seasonal change of color. Their body is covered with colored and white hair. We performed a descriptive statistical analysis of breeding records of Icelandic horses to challenge the hypothesis of roan being lethal in utero under homozygous condition. The roan to non-roan ratio of foals from roan × roan matings revealed homozygous roan Icelandic horses to be viable. Even though roan is known to be inherited in a dominant mode and epistatic to other coat colors, the causative mutation is still unknown. Nevertheless, an association between roan phenotype and the KIT gene was shown for different horse breeds. In the present study, we identified KIT variants by Sanger sequencing, and show that KIT is also associated with roan in the Icelandic horse breed.
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21
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Abstract
Genetic testing in horses began in the 1960s, when parentage testing using blood group markers became the standard. In the 1990s, parentage testing shifted from evaluating blood groups to DNA testing. The development of genetics and genomics in both human and veterinarian medicine, along with continued technological advances in the last 2 decades, has helped unravel the causal variants for many horse traits. Genetic testing is also now possible for a variety of phenotypic and disease traits and is used to assist in breeding and clinical management decisions. This article describes the genetic tests that are currently available for horses.
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Affiliation(s)
- Rebecca R Bellone
- Department of Population Health and Reproduction Davis, CA 95616, USA; Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA.
| | - Felipe Avila
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
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22
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Tang Z, Fu Y, Xu J, Zhu M, Li X, Yu M, Zhao S, Liu X. Discovery of selection-driven genetic differences of Duroc, Landrace, and Yorkshire pig breeds by EigenGWAS and F st analyses. Anim Genet 2020; 51:531-540. [PMID: 32400898 DOI: 10.1111/age.12946] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2020] [Indexed: 01/08/2023]
Abstract
Pigs are one of the earliest domesticated animals and multiple breeds have been developed to meet the various demands of consumers. EigenGWAS is a novel strategy to identify candidate genes that underlying population genetic differences and to infer candidate regions under selection as well. In this study, EigenGWAS and Fst analyses were performed using the public re-sequencing data of three typical commercial pig breeds, Duroc, Landrace and Yorkshire. The intersection of genome-wide significant SNPs detected by EigenGWAS and top-ranked 1% SNPs of Fst results were treated as signals under selection. Using the data of all three breeds, 3062 signals under selection were detected and the nearby genomic regions within 300 kb upstream and downstream covered 6.54% of whole genome. Pairs of breeds were analysed along with the pathway analysis. The gene function enrichment results indicated that many candidate genes located in the genomic regions of the signals under selection were associated with biological processes related to growth, metabolism, reproduction, sensory perception, etc. Among the candidate genes, the FSHB, AHR, PTHLH, KDR and FST genes were reported to be associated with reproductive performance; the KIT, KITLG, MITF, MC1R and EDNRB genes were previously identified to affect coat colour; the RETREG1, TXNIP, BMP5, PPARD and RBP4 genes were reported to be associated with lipid metabolism and growth traits. The identified genetic differences across the three commercial breeds will advance understanding of the artificial selection history of pigs and the signals under selection will suggest potential uses in pig genomic breeding programmes.
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Affiliation(s)
- Z Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Y Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - J Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - M Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - X Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - M Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - S Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - X Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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23
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Grilz-Seger G, Reiter S, Neuditschko M, Wallner B, Rieder S, Leeb T, Jagannathan V, Mesarič M, Cotman M, Pausch H, Lindgren G, Velie B, Horna M, Brem G, Druml T. A Genome-Wide Association Analysis in Noriker Horses Identifies a SNP Associated With Roan Coat Color. J Equine Vet Sci 2020; 88:102950. [PMID: 32303326 DOI: 10.1016/j.jevs.2020.102950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 01/20/2023]
Abstract
The roan coat color in horses is characterized by dispersed white hair and dark points. This phenotype segregates in a broad range of horse breeds, while the underlying genetic background is still unknown. Previous studies mapped the roan locus to the KIT gene on equine chromosome 3 (ECA3). However, this association could not be validated across different horse breeds. Performing a genome-wide association analysis (GWAS) in Noriker horses, we identified a single nucleotide polymorphism (SNP) (ECA3:g.79,543.439 A > G) in the intron 17 of the KIT gene. The G -allele of the top associated SNP was present in other roan horses, namely Quarter Horse, Murgese, Slovenian, and Belgian draught horse, while it was absent in a panel of 15 breeds, including 657 non-roan horses. In further 379 gray Lipizzan horses, eight animals exhibited a heterozygous genotype (A/G). Comparative whole-genome sequence analysis of the KIT region revealed two deletions in the downstream region (ECA3:79,533,217_79,533,224delTCGTCTTC; ECA3:79,533,282_79,533,285delTTCT) and a 3 bp deletion combined with 17 bp insertion in intron 20 of KIT (ECA3:79,588,128_79,588,130delinsTTATCTCTATAGTAGTT). Within the Noriker sample, these loci were in complete linkage disequilibrium (LD) with the identified top SNP. Based upon pedigree information and historical records, we were able to trace back the genetic origin of roan coat color to a baroque gene pool. Furthermore, our data suggest allelic heterogeneity and the existence of additional roan alleles in ponies and breeds related to the English Thoroughbred. In order to study the roan phenotype segregating in those breeds, further association and verification studies are required.
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Affiliation(s)
- Gertrud Grilz-Seger
- Department of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria.
| | - Simone Reiter
- Department of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria
| | | | - Barbara Wallner
- Department of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria
| | | | - Tosso Leeb
- Department of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Department of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Matjaz Mesarič
- Clinic for Reproduction and Large Animals, University of Ljubljana, Veterinary Faculty, Ljubljana, Slovenia
| | - Markus Cotman
- Department for Preclinical Sciences, University of Ljubljana, Veterinary Faculty, Ljubljana, Slovenia
| | | | - Gabriella Lindgren
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Brandon Velie
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Michaela Horna
- Department of Animal Husbandry, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Gottfried Brem
- Department of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria
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24
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Genetic heterogeneity of white markings in Quarter Horses. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.103935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Jivanji S, Worth G, Lopdell TJ, Yeates A, Couldrey C, Reynolds E, Tiplady K, McNaughton L, Johnson TJJ, Davis SR, Harris B, Spelman R, Snell RG, Garrick D, Littlejohn MD. Genome-wide association analysis reveals QTL and candidate mutations involved in white spotting in cattle. Genet Sel Evol 2019; 51:62. [PMID: 31703548 PMCID: PMC6839108 DOI: 10.1186/s12711-019-0506-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 10/25/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND White spotting of the coat is a characteristic trait of various domestic species including cattle and other mammals. It is a hallmark of Holstein-Friesian cattle, and several previous studies have detected genetic loci with major effects for white spotting in animals with Holstein-Friesian ancestry. Here, our aim was to better understand the underlying genetic and molecular mechanisms of white spotting, by conducting the largest mapping study for this trait in cattle, to date. RESULTS Using imputed whole-genome sequence data, we conducted a genome-wide association analysis in 2973 mixed-breed cows and bulls. Highly significant quantitative trait loci (QTL) were found on chromosomes 6 and 22, highlighting the well-established coat color genes KIT and MITF as likely responsible for these effects. These results are in broad agreement with previous studies, although we also report a third significant QTL on chromosome 2 that appears to be novel. This signal maps immediately adjacent to the PAX3 gene, which encodes a known transcription factor that controls MITF expression and is the causal locus for white spotting in horses. More detailed examination of these loci revealed a candidate causal mutation in PAX3 (p.Thr424Met), and another candidate mutation (rs209784468) within a conserved element in intron 2 of MITF transcripts expressed in the skin. These analyses also revealed a mechanistic ambiguity at the chromosome 6 locus, where highly dispersed association signals suggested multiple or multiallelic QTL involving KIT and/or other genes in this region. CONCLUSIONS Our findings extend those of previous studies that reported KIT as a likely causal gene for white spotting, and report novel associations between candidate causal mutations in both the MITF and PAX3 genes. The sizes of the effects of these QTL are substantial, and could be used to select animals with darker, or conversely whiter, coats depending on the desired characteristics.
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Affiliation(s)
- Swati Jivanji
- Massey University Manawatu, Private Bag 11 222, Palmerston North, 4442 New Zealand
| | - Gemma Worth
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Thomas J. Lopdell
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Anna Yeates
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Christine Couldrey
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Edwardo Reynolds
- Massey University Manawatu, Private Bag 11 222, Palmerston North, 4442 New Zealand
| | - Kathryn Tiplady
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Lorna McNaughton
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Thomas J. J. Johnson
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Stephen R. Davis
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Bevin Harris
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Richard Spelman
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
| | - Russell G. Snell
- The University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Dorian Garrick
- Massey University Manawatu, Private Bag 11 222, Palmerston North, 4442 New Zealand
| | - Mathew D. Littlejohn
- Livestock Improvement Corporation (LIC), 605 Ruakura Rd, Newstead, 3286 New Zealand
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26
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Talenti A, Bertolini F, Williams J, Moaeen-Ud-Din M, Frattini S, Coizet B, Pagnacco G, Reecy J, Rothschild MF, Crepaldi P. Genomic Analysis Suggests KITLG is Responsible for a Roan Pattern in two Pakistani Goat Breeds. J Hered 2019; 109:315-319. [PMID: 29099936 DOI: 10.1093/jhered/esx093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/25/2017] [Indexed: 11/12/2022] Open
Abstract
The roan coat color pattern is described as the presence of white hairs intermixed with pigmented hairs. This kind of pigmentation pattern has been observed in many domestic species, including the goat. The molecular mechanisms and inheritance that underlie this pattern are known for some species and the KITLG gene has been shown associated with this phenotype. To date, no research effort has been carried out to find the gene(s) that control(s) roan coat color pattern in goats. In the present study, after genotyping with the GoatSNP50 BeadChip, 35 goats that showed a roan pattern and that belonged to two Pakistan breeds (Group A) were analyzed and then compared to 740 goats of 39 Italian and Pakistan goat breeds that did not have the same coat color pattern (Group B). Runs of homozygosity-based and XP-EHH analyses were used to identify unique genomic regions potentially associated with the roan pattern. A total of 3 regions on chromosomes 5, 6, and 12 were considered unique among the group A versus group B comparisons. The A region > 1.7 Mb on chromosome 5 was the most divergent between the two groups. This region contains six genes, including the KITLG gene. Our findings support the hypothesis that the KITLG gene may be associated with the roan phenotype in goats.
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Affiliation(s)
- Andrea Talenti
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | | | - Jamie Williams
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
| | - Muhammad Moaeen-Ud-Din
- Laboratories of Animal Breeding & Genetics, PMAS-Arid Agriculture University, Rawalpindi, Pakistan
| | - Stefano Frattini
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Beatrice Coizet
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Giulio Pagnacco
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, Iowa, USA
| | - Paola Crepaldi
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
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27
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Hug P, Jude R, Henkel J, Jagannathan V, Leeb T. A novel
KIT
deletion variant in a German Riding Pony with white‐spotting coat colour phenotype. Anim Genet 2019; 50:761-763. [DOI: 10.1111/age.12840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2019] [Indexed: 11/28/2022]
Affiliation(s)
- P. Hug
- Institute of Genetics, Vetsuisse Faculty University of Bern Bern 3001 Switzerland
- DermFocus University of Bern Bern 3001 Switzerland
| | - R. Jude
- RJC Weilerswist 53919 Germany
| | - J. Henkel
- Institute of Genetics, Vetsuisse Faculty University of Bern Bern 3001 Switzerland
- DermFocus University of Bern Bern 3001 Switzerland
| | - V. Jagannathan
- Institute of Genetics, Vetsuisse Faculty University of Bern Bern 3001 Switzerland
- DermFocus University of Bern Bern 3001 Switzerland
| | - T. Leeb
- Institute of Genetics, Vetsuisse Faculty University of Bern Bern 3001 Switzerland
- DermFocus University of Bern Bern 3001 Switzerland
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28
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Grilz-Seger G, Neuditschko M, Ricard A, Velie B, Lindgren G, Mesarič M, Cotman M, Horna M, Dobretsberger M, Brem G, Druml T. Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and Near Eastern Horse Breeds. Genes (Basel) 2019; 10:genes10070491. [PMID: 31261764 PMCID: PMC6679042 DOI: 10.3390/genes10070491] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/18/2019] [Accepted: 06/26/2019] [Indexed: 01/10/2023] Open
Abstract
Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine selection signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total of 1476 horses originating from 12 breeds for the loss of genetic diversity by runs of homozygosity (ROH) utilizing a 670,000 single nucleotide polymorphism (SNP) genotyping array. Overlapping homozygous regions (ROH islands) indicating signatures of selection were identified by breed and similarities/dissimilarities between populations were evaluated. In the entire dataset, 180 ROH islands were identified, whilst 100 islands were breed specific, all other overlapped in 36 genomic regions with at least one ROH island of another breed. Furthermore, two ROH hot spots were determined at horse chromosome 3 (ECA3) and ECA11. Besides the confirmation of previously documented target genes involved in selection for coat color (MC1R, STX17, ASIP), body size (LCORL/NCAPG, ZFAT, LASP1, HMGA2), racing ability (PPARGC1A), behavioral traits (GRIN2B, NTM/OPCML) and gait patterns (DMRT3), several putative target genes related to embryonic morphogenesis (HOXB), energy metabolism (IGFBP-1, IGFBP-3), hair follicle morphogenesis (KRT25, KRT27, INTU) and autophagy (RALB) were highlighted. Furthermore, genes were pinpointed which might be involved in environmental adaptation of specific habitats (UVSSA, STXBP4, COX11, HLF, MMD).
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Affiliation(s)
- Gertrud Grilz-Seger
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
| | - Markus Neuditschko
- Agroscope, Swiss National Stud Farm, Les Longs Prés, CH-1580 Avenches, Switzerland.
| | - Anne Ricard
- UMR 1313 Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, Domaine de Vilvert, Bat 211, 78352 Jouy-en-Josas, France.
| | - Brandon Velie
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Ulls väg 26, 750 07 Uppsala, Sweden.
- School of Life and Environmental Sciences, University of Sydney, Eastern Ave, 2006 NSW Sydney, Australia.
| | - Gabriella Lindgren
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Ulls väg 26, 750 07 Uppsala, Sweden.
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium.
| | - Matjaz Mesarič
- Clinic for Reproduction and Large Animals, University of Ljubljana, Veterinary, Faculty, Cesta v Mestni log 47, 1000 Ljubljana, Slovenia.
| | - Marko Cotman
- Institute for Preclinical Sciences, University of Ljubljana, Veterinary Faculty, Gerbičeva 60, 1000 Ljubljana, Slovenia.
| | - Michaela Horna
- Department of Animal Husbandry, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia.
| | - Max Dobretsberger
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
| | - Thomas Druml
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
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29
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Knickelbein KE, Lassaline ME, Singer-Berk M, Reilly CM, Clode AB, Famula TR, Michau TM, Bellone RR. A missense mutation in damage-specific DNA binding protein 2 is a genetic risk factor for ocular squamous cell carcinoma in Belgian horses. Equine Vet J 2019; 52:34-40. [PMID: 30903710 DOI: 10.1111/evj.13116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 03/15/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND Belgian horses are commonly affected with ocular squamous cell carcinoma (SCC), the most common cancer of the equine eye. A missense mutation in damage-specific DNA binding protein 2 (DDB2 c.1013C>T, p.Thr338Met) has been established as a recessive genetic risk factor for ocular SCC in the Haflinger breed. A sample of Belgian horses with unknown SCC phenotype was shown to possess this variant at a similar frequency to the Haflinger breed. Retrospective studies indicate that chestnut coat colour may predispose to the development of SCC. OBJECTIVES To determine if DDB2 c.1013C>T is a risk factor for ocular SCC in a strictly phenotyped sample of Belgian horses. To investigate associations between coat colour loci genotypes and ocular SCC. STUDY DESIGN Retrospective and prospective case identification, genetic investigation. METHODS Genomic DNA was isolated from blood, hair or formalin-fixed paraffin-embedded tissue from 25 Belgian horses with histologically confirmed ocular SCC and 18 unaffected Belgian horses. Association testing of 34 single nucleotide variants from 11 genomic loci and genotyping for DDB2 c.1013C>T and coat colour alleles were performed. Exons of DDB2 were sequenced in four cases and two controls. Associations were analysed by Chi-square or Fisher's exact tests and relative risk was calculated. RESULTS Homozygosity for DDB2 c.1013C>T was significantly associated with ocular SCC (P = 7.4 × 10-7 ). Seventy-six per cent of affected horses were homozygous for the variant. Relative risk for homozygous horses developing SCC was 4.0 (P = 1.0 × 10-4 ). Sequencing DDB2 did not identify a variant more concordant with disease phenotype. An association between disease and coat colour loci was not identified. MAIN LIMITATIONS Phenotyping was determined at a single timepoint. Each included horse genotyped as chestnut, so association with this MC1R variant could not be investigated. CONCLUSIONS A missense variant, DDB2 c.1013C>T, p.Thr338Met, is a risk factor for ocular SCC in Belgian horses. A genetic risk test is commercially available.
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Affiliation(s)
- K E Knickelbein
- Veterinary Medical Teaching Hospital, University of California-Davis, Davis, California, USA.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - M E Lassaline
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - M Singer-Berk
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - C M Reilly
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - A B Clode
- New England Equine Medical & Surgical Center, PLLC, Dover, New Hampshire, USA
| | - T R Famula
- Department of Animal Science, University of California-Davis, Davis, California, USA
| | - T M Michau
- Blue Pearl Specialty and Emergency Pet Hospital, Tampa, Florida, USA
| | - R R Bellone
- Veterinary Medical Teaching Hospital, University of California-Davis, Davis, California, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
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30
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Henkel J, Lafayette C, Brooks SA, Martin K, Patterson-Rosa L, Cook D, Jagannathan V, Leeb T. Whole-genome sequencing reveals a large deletion in the MITF gene in horses with white spotted coat colour and increased risk of deafness. Anim Genet 2019; 50:172-174. [PMID: 30644113 DOI: 10.1111/age.12762] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2018] [Indexed: 01/18/2023]
Abstract
White spotting phenotypes in horses are highly valued in some breeds. They are quite variable and may range from the common white markings up to completely white horses. EDNRB, KIT, MITF, PAX3 and TRPM1 represent known candidate genes for white spotting phenotypes in horses. For the present study, we investigated an American Paint Horse family segregating a phenotype involving white spotting and blue eyes. Six of eight horses with the white-spotting phenotype were deaf. We obtained whole-genome sequence data from an affected horse and specifically searched for structural variants in the known candidate genes. This analysis revealed a heterozygous ~63-kb deletion spanning exons 6-9 of the MITF gene (chr16:21 503 211-21 566 617). We confirmed the breakpoints of the deletion by PCR and Sanger sequencing. PCR-based genotyping revealed that all eight available affected horses from the family carried the deletion. The finding of an MITF variant fits well with the syndromic phenotype involving both depigmentation and an increased risk for deafness and corresponds to human Waardenburg syndrome type 2A. Our findings will enable more precise genetic testing for depigmentation phenotypes in horses.
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Affiliation(s)
- J Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | | | - S A Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA
| | - K Martin
- Etalon Inc., Menlo Park, CA, 94025, USA
| | - L Patterson-Rosa
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA
| | - D Cook
- Etalon Inc., Menlo Park, CA, 94025, USA
| | - 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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31
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Validation of high-resolution melting analysis as a diagnostic tool for endothelin receptor B mutation in American Paint horses and allele frequency estimation. Mol Cell Probes 2018; 41:52-56. [PMID: 30096357 DOI: 10.1016/j.mcp.2018.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/17/2018] [Accepted: 08/07/2018] [Indexed: 11/21/2022]
Abstract
Overo lethal white foal syndrome (OLWFS) is a genetic disorder caused by a dinucleotide mutation in the endothelin receptor type B (EDNRB) gene leading to the death of affected foals shortly after birth. The use of rapid and reliable genetic testing is imperative for the early diagnosis of the mutation avoiding, therefore, either additional suffering or the production of affected animals. In the present study, we developed and validated a high-resolution melting (HRM) genotyping assay to detect the OLWFS causative mutation, and we also determined the frequency of heterozygotes among American Paint horses in Brazil. The HRM genotyping assay resulted in a high sensitivity, specificity, and positive and negative predictive values. The overall estimated frequency of heterozygotes was 21.6%; however, this frequency increased to 89.5% when considering only overo horses. The HRM assay optimized here was a reliable and suitable method for the detection of the dinucleotide mutation observed in the EDNRB gene resulting in a fast, accurate, and precise diagnostic tool. The causative gene mutation of OLWFS is present in heterozygosity in the American Paint Horse population in Brazil and is highly frequent among overo horses.
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32
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Druml T, Grilz-Seger G, Neuditschko M, Horna M, Ricard A, Pausch H, Brem G. Novel insights into Sabino1 and splashed white coat color patterns in horses. Anim Genet 2018; 49:249-253. [PMID: 29635692 PMCID: PMC6001536 DOI: 10.1111/age.12657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2018] [Indexed: 11/27/2022]
Abstract
Within the framework of genome‐wide analyses using the novel Axiom® genotyping array, we investigated the distribution of two previously described coat color patterns, namely sabino1 (SBI), associated with the KIT gene (KI16+1037A), and splashed white, associated with the PAX3 gene (ECA6:g.11429753C>T; PAX3C70Y), including a total of 899 horses originating from eight different breeds (Achal Theke, Purebred Arabian, Partbred Arabian, Anglo‐Arabian, Shagya Arabian, Haflinger, Lipizzan and Noriker). Based on the data we collected we were able to demonstrate that, besides Quarter horses, the PAX3C70Y allele is also present in Noriker (seven out of 189) and Lipizzan (three out of 329) horses. The SB1 allele was present in three breeds (Haflinger, 14 out of 98; Noriker, four out of 189; Lipizzan one out of 329). Furthermore, we examined the phenotypes of SB1‐ and PAX3C70Y‐carrier horses for their characteristic white spotting patterns. None of the SB1/sb1‐carrier horses met the criteria defining the Sabino1 pattern according to current applied protocols. From 10 heterozygous PAX3C70Y‐carrier horses, two had nearly a splashed white phenotype. The results of this large‐scale experiment on the genetic association of white spotting patterns in horses underline the influence of gene interactions and population differences on complex traits such as Sabino1 and splashed white.
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Affiliation(s)
- T Druml
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, A-1210, Vienna, Austria
| | | | - M Neuditschko
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, A-1210, Vienna, Austria.,Agroscope, Swiss National Stud Farm, Les Longs Prés, CH-1580, Avenches, Switzerland
| | - M Horna
- Department of Animal Husbandry, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76, Nitra, Slovak Republic
| | - A Ricard
- UMR 1313 Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, Domaine de Vilvert, Bat 211, 78352, Jouy-en-Josas, France.,Institut Français du Cheval et de l'Equitation, Recherche et Innovation, La Jumenterie du Pin, 61310, Exmes, France
| | - H Pausch
- Animal Genomics, ETH Zürich, CH-8092, Zürich, Switzerland
| | - G Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, A-1210, Vienna, Austria
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33
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Gaunitz C, Fages A, Hanghøj K, Albrechtsen A, Khan N, Schubert M, Seguin-Orlando A, Owens IJ, Felkel S, Bignon-Lau O, de Barros Damgaard P, Mittnik A, Mohaseb AF, Davoudi H, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Crubézy E, Benecke N, Olsen S, Brown D, Anthony D, Massy K, Pitulko V, Kasparov A, Brem G, Hofreiter M, Mukhtarova G, Baimukhanov N, Lõugas L, Onar V, Stockhammer PW, Krause J, Boldgiv B, Undrakhbold S, Erdenebaatar D, Lepetz S, Mashkour M, Ludwig A, Wallner B, Merz V, Merz I, Zaibert V, Willerslev E, Librado P, Outram AK, Orlando L. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science 2018; 360:111-114. [DOI: 10.1126/science.aao3297] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/31/2018] [Indexed: 12/28/2022]
Abstract
The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski’s horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.
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34
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Horecká E, Horecký Č, Knoll A. Standardization of Methodology for Polymorphism Detection in ASIP, MC1R and MATP Genes in Relation to Colour in Horses. ACTA UNIVERSITATIS AGRICULTURAE ET SILVICULTURAE MENDELIANAE BRUNENSIS 2017. [DOI: 10.11118/actaun201765041161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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35
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Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L. Ancient genomic changes associated with domestication of the horse. Science 2017; 356:442-445. [DOI: 10.1126/science.aam5298] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Ancient genomics of horse domesticationThe domestication of the horse was a seminal event in human cultural evolution. Libradoet al.obtained genome sequences from 14 horses from the Bronze and Iron Ages, about 2000 to 4000 years ago, soon after domestication. They identified variants determining coat color and genes selected during the domestication process. They could also see evidence of admixture with archaic horses and the demography of the domestication process, which included the accumulation of deleterious variants. The horse appears to have undergone a different type of domestication process than animals that were domesticated simply for food.Science, this issue p.442
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Affiliation(s)
- Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Charleen Gaunitz
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Mélanie Pruvost
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris Diderot, 75205 Paris cedex 13, France
| | - Anders Albrechtsen
- Bioinformatics Center, Department of Biology, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Antoine Fages
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Naveed Khan
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | | | - Aitor Serres-Armero
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Lukas F. K. Kuderna
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Inna S. Povolotskaya
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- National High-Throughput DNA Sequencing Center, Copenhagen, Denmark
| | - Sébastien Lepetz
- Centre National de la Recherche Scientifique, Muséum national d’histoire naturelle, Sorbonne Universités, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 55 rue Buffon, 75005 Paris, France
| | | | - Catherine Thèves
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Saleh Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed H. Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khaled Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, 1580 Avenches, Switzerland
| | - Zainolla Samashev
- Branch of Institute of Archaeology Margulan, Republic Avenue 24-405, 010000 Astana, Republic of Kazakhstan
| | - Henri-Paul Francfort
- CNRS, UMR 7041 Archéologie et Sciences de l’Antiquité, Archéologie de l'Asie Centrale, Maison René Ginouvès, 21 allée de l’Université, 92023 Nanterre, France
| | - Norbert Benecke
- German Archaeological Institute, Department of Natural Sciences, Berlin, 14195 Berlin, Germany
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin 10315, Germany
| | - Christine Keyser
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
- Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - Bertrand Ludes
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
- Institut Médico-Légal, Université Paris Descartes, Paris, France
| | - Eric Crubézy
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
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Dürig N, Jude R, Holl H, Brooks SA, Lafayette C, Jagannathan V, Leeb T. Whole genome sequencing reveals a novel deletion variant in the KIT
gene in horses with white spotted coat colour phenotypes. Anim Genet 2017; 48:483-485. [DOI: 10.1111/age.12556] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2017] [Indexed: 01/24/2023]
Affiliation(s)
- N. Dürig
- Vetsuisse Faculty; Institute of Genetics; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
| | - R. Jude
- Vetsuisse Faculty; Institute of Genetics; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
- RJC; 53919 Weilerswist Germany
| | - H. Holl
- Department of Animal Sciences; University of Florida; Gainesville FL 32611-0910 USA
- Etalon Inc.; Menlo Park CA 94025 USA
| | - S. A. Brooks
- Department of Animal Sciences; University of Florida; Gainesville FL 32611-0910 USA
| | | | - V. Jagannathan
- Vetsuisse Faculty; Institute of Genetics; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
| | - T. Leeb
- Vetsuisse Faculty; Institute of Genetics; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
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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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Martin L, Damaso N, Mills D. Detection of single nucleotide polymorphisms (SNP) in equine coat color genes using SNaPshot
TM
multiplex kit or pluronic F‐108 tri‐block copolymer and capillary electrophoresis. Electrophoresis 2016; 37:2862-2866. [DOI: 10.1002/elps.201600245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/29/2016] [Accepted: 08/09/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Lauren Martin
- Department of Chemistry and Biochemistry Florida International University Miami FL USA
- International Forensic Research Institute Florida International University Miami FL USA
- Department of Biological Sciences Florida International University Miami FL USA
| | - Natalie Damaso
- Department of Chemistry and Biochemistry Florida International University Miami FL USA
- International Forensic Research Institute Florida International University Miami FL USA
- Department of Biological Sciences Florida International University Miami FL USA
| | - DeEtta Mills
- International Forensic Research Institute Florida International University Miami FL USA
- Department of Biological Sciences Florida International University Miami FL USA
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Dürig N, Jude R, Jagannathan V, Leeb T. A novelMITFvariant in a white American Standardbred foal. Anim Genet 2016; 48:123-124. [PMID: 27592871 DOI: 10.1111/age.12484] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Nicole Dürig
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; 3001 Bern Switzerland
| | - Rony Jude
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; 3001 Bern Switzerland
- RJC; 53919 Weilerswist Germany
| | - Vidhya Jagannathan
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; 3001 Bern Switzerland
| | - Tosso Leeb
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; 3001 Bern Switzerland
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40
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Distribution of coat-color-associated alleles in the domestic horse population and Przewalski's horse. J Appl Genet 2016; 57:519-525. [PMID: 27194311 DOI: 10.1007/s13353-016-0352-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 04/03/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
Abstract
Considering the hidden mode of inheritance of some coat-color-associated alleles, we investigated the presence/absence of coat-color-associated alleles in 1093 domestic horses of 55 breeds and 20 specimens of Przewalski's horse. For coat-color genotyping, allele specific PCR, pyrosequencing and Li-Cor analyses were conducted on 12 coat-color-associated alleles of five genes. Our data provide deep insight into the distribution of coat-color-associated alleles within breeds. We found that the alleles for the basic colorations (bay, black, and chestnut) are widely distributed and occur in nearly all breeds. Alleles leading to dilutions or patterns are rare in domestic breeds and were not found in Przewalski's horse. Higher frequencies of these alleles are only found in breeds that are selected for their expressed phenotypes (e.g., Kinsky horse, Lewitzer, Tinker). Nevertheless, our study produced strong evidence that molecular testing of the coat color is necessary for well-defined phenotyping to avoid unexpected colorations of offspring that can result in legal action.
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41
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Holl HM, Brooks SA, Archer S, Brown K, Malvick J, Penedo MCT, Bellone RR. Variant in theRFWD3gene associated withPATN1, a modifier of leopard complex spotting. Anim Genet 2015; 47:91-101. [DOI: 10.1111/age.12375] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2015] [Indexed: 01/11/2023]
Affiliation(s)
- H. M. Holl
- Department of Animal Science; Cornell University; Ithaca NY 14853 USA
| | - S. A. Brooks
- Department of Animal Science; Cornell University; Ithaca NY 14853 USA
| | | | - K. Brown
- Department of Biology; University of Tampa; Tampa FL 33606 USA
| | - J. Malvick
- Veterinary Genetics Laboratory; School of Veterinary Medicine; University of California-Davis; Davis CA 95616 USA
| | - M. C. T. Penedo
- Veterinary Genetics Laboratory; School of Veterinary Medicine; University of California-Davis; Davis CA 95616 USA
| | - R. R. Bellone
- Department of Population Health and Reproduction; Veterinary Genetics Laboratory; School of Veterinary Medicine; University of California-Davis; Davis CA 95616 USA
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42
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Haase B, Jagannathan V, Rieder S, Leeb T. A novelKITvariant in an Icelandic horse with white-spotted coat colour. Anim Genet 2015; 46:466. [DOI: 10.1111/age.12313] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Bianca Haase
- Faculty of Veterinary Science; University of Sydney; Sydney 2006 NSW Australia
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; 3001 Bern Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; 3001 Bern Switzerland
| | - Stefan Rieder
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; 3001 Bern Switzerland
- Agroscope; Swiss National Stud Farm; 1580 Avenches Switzerland
| | - Tosso Leeb
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
- Swiss Competence Center of Animal Breeding and Genetics; University of Bern; Bern University of Applied Sciences HAFL & Agroscope; 3001 Bern Switzerland
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Abstract
Practical relevance: The health of the cat mirrors a complex interaction between its environment (nurture) and its genetics (nature). To date, over 70 genetic mutations (variants) have been defined in the cat; many involve diseases, structural anomalies, coat color and texture, including numerous that are clinically relevant. This trend will continue as more of the feline genome is deciphered. Genetic testing, and eventually whole-genome sequencing, should become routine diagnostic tools in feline healthcare within the foreseeable future. Global importance: Cat breeds have dispersed around the world. Thus, feline medicine clinicians should be aware of breeds common to their region and common mutations found within those regional populations. Random-bred populations of domestic cats can also have defined genetic characteristics and mutations, which are equally worthy of understanding by feline medicine clinicians. Outline: This article reviews the chronology and evolution of genetic and genomic tools pertinent to feline medicine. Possible strategies for mapping genetic traits and defects, and how these impact on feline health, are also discussed. The focus is on three historical periods: (1) research conducted before the availability of the cat genome; (2) research performed immediately after the availability of sequences of the cat genome; and (3) current research that goes beyond one cat genome and utilizes the genome sequences of many cats. Evidence base: The data presented are extracted from peer-reviewed publications pertaining to mutation identification, and relevant articles concerning heritable traits and/or diseases. The authors draw upon their personal experience and expertise in feline genetics.
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Abstract
Horses are valued for the beauty and variety of colouration and coat patterning. To date, eleven different genes have been characterized that contribute to the variation observed in the horse. Unfortunately, mutations involving pigmentation often lead to deleterious effects in other systems, some of which have been described in the horse. This review focuses on six such pleiotropic effects or associations with pigmentation genes. These include neurological defects (lethal white foal syndrome and lavender foal syndrome), hearing defects, eye disorders (congenital stationary night blindness and multiple congenital ocular anomalies), as well as horse-specific melanoma. The pigmentation phenotype, disorder phenotype, mode of inheritance, genetic or genomic methods utilized to identify the genes involved and, if known, the causative mutations, molecular interactions and other susceptibility loci are discussed. As our understanding of pigmentation in the horse increases, through the use of novel genomic tools, we are likely to unravel yet unknown pleiotropic effects and determine additional interactions between previously discovered loci.
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Affiliation(s)
- R R Bellone
- Department of Biology, University of Tampa, 401 W. Kennedy Blvd., Tampa, FL 33606, USA.
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45
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Haase B, Rieder S, Leeb T. Two variants in the KIT gene as candidate causative mutations for a dominant white and a white spotting phenotype in the donkey. Anim Genet 2015; 46:321-4. [PMID: 25818843 DOI: 10.1111/age.12282] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2014] [Indexed: 11/28/2022]
Abstract
White spotting phenotypes have been intensively studied in horses, and although similar phenotypes occur in the donkey, little is known about the molecular genetics underlying these patterns in donkeys. White spotting in donkeys can range from only a few white areas to almost complete depigmentation and is characterised by a loss of pigmentation usually progressing from a white spot in the hip area. Completely white-born donkeys are rare, and the phenotype is characterised by the complete absence of pigment resulting in pink skin and a white coat. A dominant mode of inheritance has been demonstrated for spotting in donkeys. Although the mode of inheritance for the completely white phenotype in donkeys is not clear, the phenotype shows similarities to dominant white in horses. As variants in the KIT gene are known to cause a range of white phenotypes in the horse, we investigated the KIT gene as a potential candidate gene for two phenotypes in the donkey, white spotting and white. A mutation analysis of all 21 KIT exons identified a missense variant in exon 4 (c.662A>C; p.Tyr221Ser) present only in a white-born donkey. A second variant affecting a splice donor site (c.1978+2T>A) was found exclusively in donkeys with white spotting. Both variants were absent in 24 solid-coloured controls. To the authors' knowledge, this is the first study investigating genetic mechanisms underlying white phenotypes in donkeys. Our results suggest that two independent KIT alleles are probably responsible for white spotting and white in donkeys.
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Affiliation(s)
- B Haase
- Faculty of Veterinary Science, University of Sydney, Sydney, 2006, NSW, Australia
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Johnson JL, Kozysa A, Kharlamova AV, Gulevich RG, Perelman PL, Fong HWF, Vladimirova AV, Oskina IN, Trut LN, Kukekova AV. Platinum coat color in red fox (Vulpes vulpes) is caused by a mutation in an autosomal copy of KIT. Anim Genet 2015; 46:190-9. [PMID: 25662789 DOI: 10.1111/age.12270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2014] [Indexed: 12/30/2022]
Abstract
The red fox (Vulpes vulpes) demonstrates a variety of coat colors including platinum, a common phenotype maintained in farm-bred fox populations. Foxes heterozygous for the platinum allele have a light silver coat and extensive white spotting, whereas homozygosity is embryonic lethal. Two KIT transcripts were identified in skin cDNA from platinum foxes. The long transcript was identical to the KIT transcript of silver foxes, whereas the short transcript, which lacks exon 17, was specific to platinum. The KIT gene has several copies in the fox genome: an autosomal copy on chromosome 2 and additional copies on the B chromosomes. To identify the platinum-specific KIT sequence, the genomes of one platinum and one silver fox were sequenced. A single nucleotide polymorphism (SNP) was identified at the first nucleotide of KIT intron 17 in the platinum fox. In platinum foxes, the A allele of the SNP disrupts the donor splice site and causes exon 17, which is part of a segment that encodes a conserved tyrosine kinase domain, to be skipped. Complete cosegregation of the A allele with the platinum phenotype was confirmed by linkage mapping (LOD 25.59). All genotyped farm-bred platinum foxes from Russia and the US were heterozygous for the SNP (A/G), whereas foxes with different coat colors were homozygous for the G allele. Identification of the platinum mutation suggests that other fox white-spotting phenotypes, which are allelic to platinum, would also be caused by mutations in the KIT gene.
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Affiliation(s)
- J L Johnson
- Animal Sciences Department, College of ACES, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Jun J, Cho YS, Hu H, Kim HM, Jho S, Gadhvi P, Park KM, Lim J, Paek WK, Han K, Manica A, Edwards JS, Bhak J. Whole genome sequence and analysis of the Marwari horse breed and its genetic origin. BMC Genomics 2014; 15 Suppl 9:S4. [PMID: 25521865 PMCID: PMC4290615 DOI: 10.1186/1471-2164-15-s9-s4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characteristics, including inwardly turned ear tips. It is thought to have originated from the crossbreeding of local Indian ponies with Arabian horses beginning in the 12th century. Results We generated 101 Gb (~30 × coverage) of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. The sequences were mapped to the horse reference genome at a mapping rate of ~98% and with ~95% of the genome having at least 10 × coverage. A total of 5.9 million single nucleotide variations, 0.6 million small insertions or deletions, and 2,569 copy number variation blocks were identified. We confirmed a strong Arabian and Mongolian component in the Marwari genome. Novel variants from the Marwari sequences were annotated, and were found to be enriched in olfactory functions. Additionally, we suggest a potential functional genetic variant in the TSHZ1 gene (p.Ala344>Val) associated with the inward-turning ear tip shape of the Marwari horses. Conclusions Here, we present an analysis of the Marwari horse genome. This is the first genomic data for an Asian breed, and is an invaluable resource for future studies of genetic variation associated with phenotypes and diseases in horses.
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Hauswirth R, Jude R, Haase B, Bellone RR, Archer S, Holl H, Brooks SA, Tozaki T, Penedo MCT, Rieder S, Leeb T. Novel variants in theKITandPAX3genes in horses with white-spotted coat colour phenotypes. Anim Genet 2013; 44:763-5. [DOI: 10.1111/age.12057] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Regula Hauswirth
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
| | - Rony Jude
- Certagen GmbH; Marie-Curie-Str. 1 53359 Rheinbach Germany
| | - Bianca Haase
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
- Faculty of Veterinary Science; University of Sydney; Sydney 2006 NSW Australia
| | | | | | - Heather Holl
- Department of Animal Science; Cornell University, Ithaca; NY 14853 USA
| | | | - Teruaki Tozaki
- Department of Molecular Genetics; Laboratory of Racing Chemistry; Utsunomiya Tochigi 320-0851 Japan
| | - Maria Cecilia T. Penedo
- Veterinary Genetics Laboratory; School of Veterinary Medicine; University of California-Davis; Davis CA 95616 USA
| | - Stefan Rieder
- Agroscope ALP-Haras; Swiss National Stud Farm; 1580 Avenches Switzerland
| | - Tosso Leeb
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
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49
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Hoque MR, Lee SH, Lim DJ, Cho IC, Choi NR, Seo DW, Lee JH. Investigation of KIT Gene Polymorphisms in Korean Cattle. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2012. [DOI: 10.5187/jast.2012.54.6.411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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50
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Jackling FC, Johnson WE, Appleton BR. The genetic inheritance of the blue-eyed white phenotype in alpacas (Vicugna pacos). J Hered 2012; 105:847-57. [PMID: 23144493 DOI: 10.1093/jhered/ess093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
White-spotting patterns in mammals can be caused by mutations in the gene KIT, whose protein is necessary for the normal migration and survival of melanocytes from the neural crest. The alpaca (Vicugna pacos) blue-eyed white (BEW) phenotype is characterized by 2 blue eyes and a solid white coat over the whole body. Breeders hypothesize that the BEW phenotype in alpacas is caused by the combination of the gene causing gray fleece and a white-spotting gene. We performed an association study using KIT flanking and intragenic markers with 40 unrelated alpacas, of which 17 were BEW. Two microsatellite alleles at KIT-related markers were significantly associated (P < 0.0001) with the BEW phenotype (bew1 and bew2). In a larger cohort of 171 related individuals, we identify an abundance of an allele (bew1) in gray animals and the occurrence of bew2 homozygotes that are solid white with pigmented eyes. Association tests accounting for population structure and familial relatedness are consistent with a proposed model where these alleles are in linkage disequilibrium with a mutation or mutations that contribute to the BEW phenotype and to individual differences in fleece color.
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Affiliation(s)
- Felicity C Jackling
- From the Department of Genetics, The University of Melbourne, Melbourne 3010, Australia Laboratory of Genomic Diversity, NCI-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Warren E Johnson
- From the Department of Genetics, The University of Melbourne, Melbourne 3010, Australia Laboratory of Genomic Diversity, NCI-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Belinda R Appleton
- From the Department of Genetics, The University of Melbourne, Melbourne 3010, Australia Laboratory of Genomic Diversity, NCI-Frederick, National Institutes of Health, Frederick, MD 21702
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