1
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Zhang C, Xu M, Yang M, Liao A, Lv P, Liu X, Chen Y, Liu H, He Z. Efficient generation of cloned cats with altered coat colour by editing of the KIT gene. Theriogenology 2024; 222:54-65. [PMID: 38621344 DOI: 10.1016/j.theriogenology.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024]
Abstract
Coat colour largely determines the market demand for several cat breeds. The KIT proto-oncogene (KIT) gene is a key gene controlling melanoblast differentiation and melanogenesis. KIT mutations usually cause varied changes in coat colour in mammalian species. In this study, we used a pair of single-guide RNAs (sgRNAs) to delete exon 17 of KIT in somatic cells isolated from two different Chinese Li Hua feline foetuses. Edited cells were used as donor nuclei for somatic cell nuclear transfer (SCNT) to generate cloned embryos presenting an average cleavage rate exceeding 85%, and an average blastocyst formation rate exceeding 9.5%. 131 cloned embryos were transplanted into four surrogates, and all surrogates carried their pregnancies to term, and delivered 4.58% (6/131) alive cloned kittens, with 1.53% (2/131) being KIT-edited heterozygotes (KITD17/+). The KITD17/+ cats presented an obvious darkness reduction in the mackerel tabby coat. Immunohistochemical analysis (IHC) of skin tissues indicated impaired proliferation and differentiation of melanoblasts caused by the lack of exon17 in feline KIT. To our knowledge, this is the first report on coat colour modification of cats through gene editing. The findings could facilitate further understanding of the regulatory role of KIT on feline coat colour and provide a basis for the breeding of cats with commercially desired coat colour.
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Affiliation(s)
- Chong Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Meina Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Min Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Alian Liao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Peiru Lv
- Henan Liosio Biotechnology Co., Ltd, PR China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Hongbo Liu
- Henan Liosio Biotechnology Co., Ltd, PR China.
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China.
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2
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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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3
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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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4
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Stroupe S, Martone C, McCann B, Juras R, Kjöllerström HJ, Raudsepp T, Beard D, Davis BW, Derr JN. Chromosome-level reference genome for North American bison (Bison bison) and variant database aids in identifying albino mutation. G3 (BETHESDA, MD.) 2023; 13:jkad156. [PMID: 37481261 PMCID: PMC10542314 DOI: 10.1093/g3journal/jkad156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/24/2023]
Abstract
We developed a highly contiguous chromosome-level reference genome for North American bison to provide a platform to evaluate the conservation, ecological, evolutionary, and population genomics of this species. Generated from a F1 hybrid between a North American bison dam and a domestic cattle bull, completeness and contiguity exceed that of other published bison genome assemblies. To demonstrate the utility for genome-wide variant frequency estimation, we compiled a genomic variant database consisting of 3 true albino bison and 44 wild-type pelage color bison. Through the examination of genomic variants fixed in the albino cohort and absent in the controls, we identified a nonsynonymous single nucleotide polymorphism (SNP) mutation on chromosome 29 in exon 3 of the tyrosinase gene (c.1114C>T). A TaqMan SNP Genotyping Assay was developed to genotype this SNP in a total of 283 animals across 29 herds. This assay confirmed the absence of homozygous variants in all animals except 7 true albino bison included in this study. In addition, the only heterozygous animals identified were 2 wild-type pelage color dams of albino offspring. Therefore, we propose that this new high-quality bison genome assembly and incipient variant database provides a highly robust and informative resource for genomics investigations for this iconic North American species.
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Affiliation(s)
- Sam Stroupe
- Department of Veterinary Pathobiology, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
| | - Carly Martone
- Department of Veterinary Pathobiology, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
| | - Blake McCann
- National Park Service, Theodore Roosevelt National Park, Medora, ND 58645, USA
| | - Rytis Juras
- Department of Veterinary Integrative Biosciences, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
| | - Helena Josefina Kjöllerström
- Department of Veterinary Integrative Biosciences, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
| | - Donald Beard
- Texas Parks and Wildlife, Caprock Canyons State Park & Trailway, Quitaque, TX 79255, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
- Department of Small Animal Clinical Sciences, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
| | - James N Derr
- Department of Veterinary Pathobiology, Texas A&M University School of Veterinary Medicine and Biomedical Science, College Station, TX 77843, USA
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5
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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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6
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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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7
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Zhang F, Wang C, Xu H, Xia X, Luo X, Li K, Han J, Lei C, Chen N, Yue X. Genomic analysis reveals a KIT-related chromosomal translocation associated with the white coat phenotype in yak. J Anim Breed Genet 2023; 140:330-342. [PMID: 36789788 DOI: 10.1111/jbg.12761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 01/25/2023] [Indexed: 02/16/2023]
Abstract
White coat pigmentation is a striking phenotype of many domesticated species and has various genetic controls. The Tianzhu White yak, an indigenous breed with a complete white coat, has fascinated Tibetans for centuries. However, the genetic basis of this trait remains unknown. Here, we conducted population genomics analysis and genome-wide association study based on the whole-genome sequencing data of 38 white and 59 non-white-coated yak. The results revealed the presence of KIT-linked Cs alleles characterized by the translocations between chromosomes 6 and 29 in all-white yak. Furthermore, structural variations showed additional duplications of the Cs alleles in white yak compared with colour-sidedness cattle. Interestingly, the Cs alleles associated with the white coat phenotype in yak were found to have introgressed from taurine cattle. Our findings unveil the shared genetic control of the white coat phenotype and its evolution in closely related bovine species.
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Affiliation(s)
- Fengwei Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chong Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Haiyue Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaihui Li
- Extending Station for Animal Husbandry and Veterinary Technology of Tianzhu Tibetan Autonomous County, Tianzhu, China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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8
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Murakami S, Tsuchiya K, Nakata K, Nishikata M, Kitada K, Suzuki H. A Kit Mutation Associated with Black-Eyed White Phenotype in the Grey Red-Backed Vole, Myodes rufocanus. MAMMAL STUDY 2022. [DOI: 10.3106/ms2022-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Shota Murakami
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kimiyuki Tsuchiya
- Laboratory of Bioresources, Applied Biology Co. Ltd, Minato-ku, Tokyo, Japan
| | - Keisuke Nakata
- Forestry Research Institute, Hokkaido Research Organization, Bibai, Hokkaido, Japan
| | - Mana Nishikata
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kazuhiro Kitada
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
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9
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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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10
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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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11
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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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12
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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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13
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Brancalion L, Haase B, Wade CM. Canine coat pigmentation genetics: a review. Anim Genet 2021; 53:3-34. [PMID: 34751460 DOI: 10.1111/age.13154] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/21/2021] [Accepted: 10/20/2021] [Indexed: 11/27/2022]
Abstract
Our understanding of canine coat colour genetics and the associated health implications is developing rapidly. To date, there are 15 genes with known roles in canine coat colour phenotypes. Many coat phenotypes result from complex and/or epistatic genetic interactions among variants within and between loci, some of which remain unidentified. Some genes involved in canine pigmentation have been linked to aural, visual and neurological impairments. Consequently, coat pigmentation in the domestic dog retains considerable ethical and economic interest. In this paper we discuss coat colour phenotypes in the domestic dog, the genes and variants responsible for these phenotypes and any proven coat colour-associated health effects.
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Affiliation(s)
- L Brancalion
- Faculty of Science, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, 2006, Australia
| | - B Haase
- Faculty of Science, School of Veterinary Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - C M Wade
- Faculty of Science, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, 2006, Australia
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14
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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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15
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A complex genetic architecture in zebrafish relatives Danio quagga and D. kyathit underlies development of stripes and spots. PLoS Genet 2021; 17:e1009364. [PMID: 33901178 PMCID: PMC8102007 DOI: 10.1371/journal.pgen.1009364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/06/2021] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
Vertebrate pigmentation is a fundamentally important, multifaceted phenotype. Zebrafish, Danio rerio, has been a valuable model for understanding genetics and development of pigment pattern formation due to its genetic and experimental tractability, advantages that are shared across several Danio species having a striking array of pigment patterns. Here, we use the sister species D. quagga and D. kyathit, with stripes and spots, respectively, to understand how natural genetic variation impacts phenotypes at cellular and organismal levels. We first show that D. quagga and D. kyathit phenotypes resemble those of wild-type D. rerio and several single locus mutants of D. rerio, respectively, in a morphospace defined by pattern variation along dorsoventral and anteroposterior axes. We then identify differences in patterning at the cellular level between D. quagga and D. kyathit by repeated daily imaging during pattern development and quantitative comparisons of adult phenotypes, revealing that patterns are similar initially but diverge ontogenetically. To assess the genetic architecture of these differences, we employ reduced-representation sequencing of second-generation hybrids. Despite the similarity of D. quagga to D. rerio, and D. kyathit to some D. rerio mutants, our analyses reveal a complex genetic basis for differences between D. quagga and D. kyathit, with several quantitative trait loci contributing to variation in overall pattern and cellular phenotypes, epistatic interactions between loci, and abundant segregating variation within species. Our findings provide a window into the evolutionary genetics of pattern-forming mechanisms in Danio and highlight the complexity of differences that can arise even between sister species. Further studies of natural genetic diversity underlying pattern variation in D. quagga and D. kyathit should provide insights complementary to those from zebrafish mutant phenotypes and more distant species comparisons. Pigment patterns of fishes are diverse and function in a wide range of behaviors. Common pattern themes include stripes and spots, exemplified by the closely related minnows Danio quagga and D. kyathit, respectively. We show that these patterns arise late in development owing to alterations in the development and arrangements of pigment cells. In the closely related model organism zebrafish (D. rerio) single genes can switch the pattern from stripes to spots. Yet, we show that pattern differences between D. quagga and D. kyathit have a more complex genetic basis, depending on multiple genes and interactions between these genes. Our findings illustrate the importance of characterizing naturally occurring genetic variants, in addition to laboratory induced mutations, for a more complete understanding of pigment pattern development and evolution.
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16
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Kawakami T, Jensen MK, Slavney A, Deane PE, Milano A, Raghavan V, Ford B, Chu ET, Sams AJ, Boyko AR. R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting. PLoS One 2021; 16:e0248233. [PMID: 33755696 PMCID: PMC7987146 DOI: 10.1371/journal.pone.0248233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/22/2021] [Indexed: 11/18/2022] Open
Abstract
Structural variations (SVs) represent a large fraction of all genetic diversity, but how this genetic diversity is translated into phenotypic and organismal diversity is unclear. Explosive diversification of dog coat color and patterns after domestication can provide a unique opportunity to explore this question; however, the major obstacle is to efficiently collect a sufficient number of individuals with known phenotypes and genotypes of hundreds of thousands of markers. Using customer-provided information about coat color and patterns of dogs tested on a commercial canine genotyping platform, we identified a genomic region on chromosome 38 that is strongly associated with a mottled coat pattern (roaning) by genome-wide association study. We identified a putative causal variant in this region, an 11-kb tandem duplication (11,131,835–11,143,237) characterized by sequence read coverage and discordant reads of whole-genome sequence data, microarray probe intensity data, and a duplication-specific PCR assay. The tandem duplication is in an intronic region of usherin gene (USH2A), which was perfectly associated with roaning but absent in non-roaned dogs. We detected strong selection signals in this region characterized by reduced nucleotide diversity (π), increased runs of homozygosity, and extended haplotype homozygosity in Wirehaired Pointing Griffons and Australian Cattle Dogs (typically roaned breeds), as well as elevated genetic difference (FST) between Wirehaired Pointing Griffon (roaned) and Labrador Retriever (non-roaned). Surprisingly, all Dalmatians (N = 262) carried the duplication embedded in identical or similar haplotypes with roaned dogs, indicating this region as a shared target of selection during the breed’s formation. We propose that the Dalmatian’s unique spots were a derived coat pattern by establishing a novel epistatic interaction between roaning “R-locus” on chromosome 38 and an uncharacterized modifier locus. These results highlight the utility of consumer-oriented genotype and phenotype data in the discovery of genomic regions contributing to phenotypic diversity in dogs.
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Affiliation(s)
- Takeshi Kawakami
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
- * E-mail: (ARB); (TK)
| | - Meghan K. Jensen
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Andrea Slavney
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Petra E. Deane
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Ausra Milano
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Vandana Raghavan
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Brett Ford
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Erin T. Chu
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Aaron J. Sams
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Adam R. Boyko
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail: (ARB); (TK)
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17
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Liang D, Zhao P, Si J, Fang L, Pairo-Castineira E, Hu X, Xu Q, Hou Y, Gong Y, Liang Z, Tian B, Mao H, Yindee M, Faruque MO, Kongvongxay S, Khamphoumee S, Liu GE, Wu DD, Barker JSF, Han J, Zhang Y. Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis). Mol Biol Evol 2021; 38:1122-1136. [PMID: 33212507 PMCID: PMC7947781 DOI: 10.1093/molbev/msaa279] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3' truncated and containing only 5' UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5' UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.
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Affiliation(s)
- Dong Liang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Pengju Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jingfang Si
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lingzhao Fang
- Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Erola Pairo-Castineira
- Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Xiaoxiang Hu
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Yali Hou
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yu Gong
- Guizhou Domestic Animal Genetic Resources Management Station, Guiyang, China
| | - Zhengwen Liang
- Agriculture and Rural Affairs Bureau of Fenggang County, Zunyi, China
| | - Bing Tian
- Animal Disease Prevention and Control Station of Zunyi City, Zunyi, China
| | - Huaming Mao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Marnoch Yindee
- Akkhararatchakumari Veterinary College (AVC), Walailak University, Nakorn Si Thammarat, Thailand
| | - Md Omar Faruque
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Siton Kongvongxay
- Livestock Research Center, National Agriculture and Forestry Research Institute, Ministry of Agriculture and Forestry, Vientiane, Lao PDR
| | - Souksamlane Khamphoumee
- Livestock Research Center, National Agriculture and Forestry Research Institute, Ministry of Agriculture and Forestry, Vientiane, Lao PDR
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD
| | - Dong-Dong Wu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - James Stuart F Barker
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yi Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China
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18
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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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19
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Influence of coat color on genetic parameter estimates in horses. J Appl Genet 2021; 62:297-306. [PMID: 33606160 DOI: 10.1007/s13353-021-00616-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/05/2021] [Accepted: 02/05/2021] [Indexed: 11/27/2022]
Abstract
The aim of this study was to verify the effect of the inclusion of coat color on the genetic parameter estimation for linear measurements in Campolina horses. Two models (1 and 2) were applied. For model 1, coat color effect was not included as variable of the contemporary group formation; in model 2, it was included. Model 2 presented the best fitting with a Deviance Information Criterion (DIC) of -979,459.020 compared with -1,818,458.572 DIC from model 1. The average of heritability estimates ranged from low to high magnitude (0.15 to 0.53) for model 1 and from moderate to high magnitude for model 2 (0.21 to 0.47). The estimated values varied according to the analyses (models 1 and 2). The highest heritability was found for withers height (0.52), croup height (0.53), and back height (0.51). The genetic correlations ranged from values of moderate to high magnitude for models 1 (0.23 to 0.98) and 2 (0.29 to 0.99), respectively. The finding that genetic variance differed among models 1 and 2 may indicate that genotypes react differently to different coat colors, a fact implying the existence of interaction between these traits and the effect under study. The coat color influence might be explained as a pleiotropic effect of the genes that cause this phenotypic variation and also influence morphometric measures. The inclusion of the coat color effect better estimated the additive genetic variance of morphometric traits in horses. As a consequence, the genetic parameters were also more accurately estimated when it is included in the evaluation model.
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20
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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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21
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Martin K, Patterson Rosa L, Vierra M, Foster G, Brooks SA, Lafayette C. De novo mutation of KIT causes extensive coat white patterning in a family of Berber horses. Anim Genet 2020; 52:135-137. [PMID: 33111383 DOI: 10.1111/age.13017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2020] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | - Samantha A Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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22
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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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23
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Tanaka J, Grahn R, Bellone RR. Evidence supports white spotting in donkeys as a homozygous lethal condition. Anim Genet 2020; 51:840-842. [PMID: 32657451 DOI: 10.1111/age.12983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2020] [Indexed: 12/01/2022]
Affiliation(s)
- Jocelyn Tanaka
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Robert Grahn
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.,Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
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24
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Indication of Premelanosome Protein (PMEL) Expression Outside of Pigmented Bovine Skin Suggests Functions Beyond Eumelanogenesis. Genes (Basel) 2020; 11:genes11070788. [PMID: 32668786 PMCID: PMC7397160 DOI: 10.3390/genes11070788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 01/23/2023] Open
Abstract
The premelanosome protein (PMEL) is important for fibril formation within melanosomes during vertebrate melanogenesis. Fibrils form a matrix for pigment deposition within pigmented tissues such as skin and hair. PMEL mutations are known to modulate eumelanic pigmentation in vertebrates. However, in bovines, PMEL mutations were also found to alter pheomelanic pigmentation resulting in coat color dilution. Furthermore, epistatic effects of a mutated PMEL allele were detected in the phenotypic expression of the bovine hair defect "rat-tail syndrome" (RTS) characterized by charcoal coat color and hair deformation. Reports about PMEL gene expression in non-pigmented tissues raised the hypothesis that there may be unknown functions of the PMEL protein beyond eumelanin deposition to PMEL fibrils. In our study, we analysed the PMEL protein expression in pigmented skin and non-pigmented bovine tissues (non-pigmented skin, thyroid gland, rumen, liver, kidney, and adrenal gland cortex). We found that a processed form of the bovine PMEL protein is expressed in pigmented as well as in non-pigmented tissues, which is in line with gene expression data from targeted RT-PCR and whole transcriptome RNAseq analysis. The PMEL protein is located in membranes and within the cytosol of epithelial cells. Based on our data from bovine tissues, we concluded that at least in cattle PMEL potentially has additional, yet unexplored functions, which might contribute to effects of PMEL mutations on pheomelanin coat color dilution and charcoal coat color in RTS animals. However, indication of PMEL protein in unpigmented cells and tissues will require further confirmation in the future, because there have been no confirmed reports before, which had detected bovine PMEL protein with specific antibodies either in pigmented or unpigmented tissue.
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25
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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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26
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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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27
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Naval-Sánchez M, Porto-Neto LR, Cardoso DF, Hayes BJ, Daetwyler HD, Kijas J, Reverter A. Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB. Genet Sel Evol 2020; 52:27. [PMID: 32460767 PMCID: PMC7251699 DOI: 10.1186/s12711-020-00546-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 05/11/2020] [Indexed: 01/14/2023] Open
Abstract
Background Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome. Results We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB, IRAK3, ENSBTAG00000026993, GRIP1 and part of HMGA2. Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B (HELB) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N’Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2-CNV, which is located in the same region. Conclusions Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultra-violet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.
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Affiliation(s)
- Marina Naval-Sánchez
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia. .,Institute of Molecular Biosciences, The University of Queensland, 306 Carmody Road, St. Lucia, Brisbane, QLD, 4067, Australia.
| | - Laercio R Porto-Neto
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Diercles F Cardoso
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia.,Department of Animal Science, School of Agricultural and Veterinarian Sciences, Sao Paulo State University (UNESP), Jaboticabal, SP, Brazil.,Centre for Genetic Improvement of Livestock, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4067, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - James Kijas
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Antonio Reverter
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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29
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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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30
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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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31
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Henkel J, Saif R, Jagannathan V, Schmocker C, Zeindler F, Bangerter E, Herren U, Posantzis D, Bulut Z, Ammann P, Drögemüller C, Flury C, Leeb T. Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes. PLoS Genet 2019; 15:e1008536. [PMID: 31841508 PMCID: PMC6936872 DOI: 10.1371/journal.pgen.1008536] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/30/2019] [Accepted: 11/23/2019] [Indexed: 12/16/2022] Open
Abstract
Domestication and human selection have formed diverse goat breeds with characteristic phenotypes. This process correlated with the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity, so called selection signatures or selective sweeps. Using whole genome sequencing of DNA pools (pool-seq) from 20 genetically diverse modern goat breeds and bezoars, we identified 2,239 putative selection signatures. In two Pakistani goat breeds, Pak Angora and Barbari, we found selection signatures in a region harboring KIT, a gene involved in melanoblast development, migration, and survival. The search for candidate causative variants responsible for these selective sweeps revealed two different copy number variants (CNVs) downstream of KIT that were exclusively present in white Pak Angora and white-spotted Barbari goats. Several Swiss goat breeds selected for specific coat colors showed selection signatures at the ASIP locus encoding the agouti signaling protein. Analysis of these selective sweeps revealed four different CNVs associated with the white or tan (AWt), Swiss markings (Asm), badgerface (Ab), and the newly proposed peacock (Apc) allele. RNA-seq analyses on skin samples from goats with the different CNV alleles suggest that the identified structural variants lead to an altered expression of ASIP between eumelanistic and pheomelanistic body areas. Our study yields novel insights into the genetic control of pigmentation by identifying six functionally relevant CNVs. It illustrates how structural changes of the genome have contributed to phenotypic evolution in domestic goats. Domestic animals have been selected for hundreds or sometimes even thousands of years for traits that were appreciated by their human owners. This process correlated with the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity, so called selection signatures or selective sweeps. We conducted a comprehensive screen for selection signatures in 20 phenotypically and genetically diverse modern goat breeds and identified a total of 2,239 putative selection signatures in our dataset. Follow-up experiments on selection signatures harboring known candidate genes for coat color revealed six different copy number variants (CNVs). Two of these CNVs were located in the 3’-flanking region of KIT and associated with a completely white coat color phenotype in Pak Angora goats and a white-spotted coat color phenotype in Barbari goats, respectively. The other four CNVs were located at the ASIP locus. They were associated with four different types of coat color patterning in seven Swiss goat breeds. Their functional effect is mediated by region-specific quantitative changes in ASIP mRNA expression. Our study illustrates how structural changes of the genome have contributed to phenotypic evolution in domestic goats.
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Affiliation(s)
- Jan Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Rashid Saif
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute of Biotechnology, Gulab Devi Educational Complex, Lahore, Pakistan
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Corinne Schmocker
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Flurina Zeindler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | - Ursula Herren
- Swiss Goat Breeding Association, Zollikofen, Switzerland
| | | | - Zafer Bulut
- Department of Biochemistry, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
- * E-mail:
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32
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Rochus CM, Westberg Sunesson K, Jonas E, Mikko S, Johansson AM. Mutations in ASIP and MC1R: dominant black and recessive black alleles segregate in native Swedish sheep populations. Anim Genet 2019; 50:712-717. [PMID: 31475378 DOI: 10.1111/age.12837] [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] [Accepted: 07/08/2019] [Indexed: 01/03/2023]
Abstract
By studying genes associated with coat colour, we can understand the role of these genes in pigmentation but also gain insight into selection history. North European short-tailed sheep, including Swedish breeds, have variation in their coat colour, making them good models to expand current knowledge of mutations associated with coat colour in sheep. We studied ASIP and MC1R, two genes with known roles in pigmentation, and their association with black coat colour. We did this by sequencing the coding regions of ASIP in 149 animals and MC1R in 129 animals from seven native Swedish sheep breeds in individuals with black, white or grey fleece. Previously known mutations in ASIP [recessive black allele: g.100_105del (D5 ) and/or g.5172T>A] were associated with black coat colour in Klövsjö and Roslag sheep breeds and mutations in both ASIP and MC1R (dominant black allele: c.218T>A and/or c.361G>A) were associated with black coat colour in Swedish Finewool. In Gotland, Gute, Värmland and Helsinge sheep breeds, coat colour inheritance was more complex: only 11 of 16 individuals with black fleece had genotypes that could explain their black colour. These breeds have grey individuals in their populations, and grey is believed to be a result of mutations and allelic copy number variation within the ASIP duplication, which could be a possible explanation for the lack of a clear inheritance pattern in these breeds. Finally, we found a novel missense mutation in MC1R (c.452G>A) in Gotland, Gute and Värmland sheep and evidence of a duplication of MC1R in Gotland sheep.
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Affiliation(s)
- C M Rochus
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden.,UFR Génétique, Élevage et Reproduction, Sciences de la Vie et Santé, AgroParisTech, Université Paris Saclay, 16 rue Claude Bernard, F-75231, Paris Cedex 05, France.,Génétique Physiologie Systèmes d'Elevage, Animal Genetics Division, INRA, 24 chemin de Borde-Rouge-Auzeville Tolosane, F-31326 Castanet-Tolosan, France
| | - K Westberg Sunesson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - E Jonas
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - S Mikko
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - A M Johansson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
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33
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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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34
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Shang S, Yu Y, Zhao Y, Dang W, Zhang J, Qin X, Irwin DM, Wang Q, Liu F, Wang Z, Zhang S, Wang Z. Synergy between MC1R and ASIP for coat color in horses (Equus caballus)1. J Anim Sci 2019; 97:1578-1585. [PMID: 30785190 DOI: 10.1093/jas/skz071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/13/2019] [Indexed: 11/13/2022] Open
Abstract
Through domestication and human selection, horses have acquired various coat colors, including seven phenotypes: black, brown, dark bay, bay, chestnut, white, and gray. Here we determined the genotypes for melanocortin-1 receptor (MC1R) and agouti signaling protein (ASIP) in 709 horses from 15 breeds. We found that the EEEE genotype frequency at MC1R decreased from dark to light colors (black = 64.5%, brown = 67.5%, dark bay = 47.0%, bay = 16.5%, and chestnut = 0.0%), whereas the AAAA genotype frequency at ASIP increased as coat color lightened (black = 0.0%, brown = 22.9%, dark bay = 69.2%, and bay = 83.0%). When combined genotypes at MC1R and ASIP were examined, different advantage genotype combinations were found for each color: black EEEE-AaAa (64.5%), brown EEEE-AAAa (47.0%), dark bay EEEE-AAAA, and EEEe-AAAA (36.2% and 33.0%, totally 69.2%), bay EEEe-AAAA (69.6%), and chestnut EeEe-AAAA (62.6%). The χ2 test showed that the phenotypes of horse coat colors were significantly related with the genotypes of MC1R and ASIP (p < 0.001). Furthermore, in contrast to a previous study where AaAa was only found in black, chestnut, and gray horses, we also found this allele in brown, dark bay, bay, and white horses. These results indicated that MC1R and ASIP may synergistically affect the levels of melanin in equine coat colors and that additional genes are likely involved in regulating coat colors, especially for white and gray colors. Our research provides new data for further studies on the synergetic actions of MC1R and ASIP in coat color of horses.
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Affiliation(s)
- Songyang Shang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yan Yu
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuxin Zhao
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Wanyi Dang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Junpeng Zhang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xia Qin
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Qin Wang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Fei Liu
- Shenyang Institute of Animal Husbandry and Veterinary Science, Shenyang, China
| | - Zhenshan Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Shuyi Zhang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhe Wang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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35
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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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36
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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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37
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Li J, Chen W, Wu S, Ma T, Jiang H, Zhang Q. Differential expression of MC1R gene in Liaoning Cashmere goats with different coat colors. Anim Biotechnol 2019; 30:273-278. [DOI: 10.1080/10495398.2018.1485681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- JianPing Li
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Wei Chen
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - SuFang Wu
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Tao Ma
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - HuaiZhi Jiang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - QiaoLing Zhang
- College of Veterinary Medicine, Jilin University, Changchun, China
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38
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Abstract
KIT is a receptor tyrosine kinase that after binding to its ligand stem cell factor activates signaling cascades linked to biological processes such as proliferation, differentiation, migration and cell survival. Based on studies performed on SCF and/or KIT mutant animals that presented anemia, sterility, and/or pigmentation disorders, KIT signaling was mainly considered to be involved in the regulation of hematopoiesis, gametogenesis, and melanogenesis. More recently, novel animal models and ameliorated cellular and molecular techniques have led to the discovery of a widen repertoire of tissue compartments and functions that are being modulated by KIT. This is the case for the lung, heart, nervous system, gastrointestinal tract, pancreas, kidney, liver, and bone. For this reason, the tyrosine kinase inhibitors that were originally developed for the treatment of hemato-oncological diseases are being currently investigated for the treatment of non-oncological disorders such as asthma, rheumatoid arthritis, and alzheimer's disease, among others. The beneficial effects of some of these tyrosine kinase inhibitors have been proven to depend on KIT inhibition. This review will focus on KIT expression and regulation in healthy and pathologic conditions other than cancer. Moreover, advances in the development of anti-KIT therapies, including tyrosine kinase inhibitors, and their application will be discussed.
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Population study of the Pura Raza Español Horse regarding its coat colour. ANNALS OF ANIMAL SCIENCE 2018. [DOI: 10.2478/aoas-2018-0016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
Coat colour has always been a valuable trait for horse breeders. However, preferences for this feature have changed over the years. In this research, the Pura Raza Español horse (PRE) population was divided into four subpopulations (Grey, Bay, Black and Others), according to the most frequent coat colours and those of their ancestors. The purpose was to analyse genetic variability, reproductive parameters and distances among subpopulations during three key periods in the history of the breed: before 1960, from 1960 to 2000 and after 2000. The subpopulations composed of animals with ancestors with the same coat colour showed higher values of recent inbreeding (ranging from 7.13% to 10.44%) and a greater Nei’s minimum distance between them, as a result of more inbred matings than those carried out in families with members with different coat colours. Non-pure subpopulations also showed more similar recent inbreeding values (between 6.63% and 6.74%). Strikingly, the productive life of Pure bay, Pure black and other subpopulations with minority coat colours was considerably longer (10.79, 10.08 and 9.11 years, respectively) compared to the values of grey PRE horses (6.01 and 7.98 years), which is the subpopulation with the highest census. These results, together with shorter generation intervals of black stallion-offspring (5.51 years via father-son and 6.39 years via father-daughter) and the fact that this coat colour was not present in the breed until two decades ago, highlight the recent trend towards the breeding of black animals.
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Hoban R, Castle K, Hamilton N, Haase B. Novel KIT variants for dominant white in the Australian horse population. Anim Genet 2018; 49:99-100. [PMID: 29333746 DOI: 10.1111/age.12627] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Rhiarn Hoban
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Kao Castle
- Practical Horse Genetics, Redfern, NSW, 2016, Australia
| | - Natasha Hamilton
- School of Life and Environmental Science, Faculty of Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Bianca Haase
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camperdown, NSW, 2006, Australia
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Li B, He X, Zhao Y, Bai D, Shiraigo W, Zhao Q, Manglai D. Regulatory pathway analysis of coat color genes in Mongolian horses. Hereditas 2017; 155:13. [PMID: 28974924 PMCID: PMC5622463 DOI: 10.1186/s41065-017-0048-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 09/18/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Studies on the molecular genetics of horse skin pigmentation have typically focused on very few genes and proteins. In this study, we used Illumina sequencing to determine the global gene expression profiles in horses with white-colored coats and those with black-colored coats, with the goal of identifying novel genes that could regulate horse coat color. RESULTS Genes encoding ribosomal-associated proteins were highly expressed in horse skin. We found a total of 231 unigenes that were differentially expressed between horses with white coats and horses with black coats; 119 were down-regulated, and 112 were up-regulated. Many of the up-regulated genes in black horses, such as genes related to tyrosine metabolism, may directly regulate dark coat color. Keratin genes, MIA family genes, fatty acid-related genes, and melanoma-associated genes were also differentially regulated, which suggests that they may play important roles in coat color formation. CONCLUSIONS These findings show that the transcription profiles from white and black horse skin provide useful information to understand the genetics underlying the control of skin melanin synthesis in horses, which may enhance our knowledge of human skin diseases, such as melanoma and albinism.
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Affiliation(s)
- Bei Li
- College of Animal Science, Inner Mongolia Agricultural University, Huhhot, 010018 People’s Republic of China
| | - Xiaolong He
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot, 010031 People’s Republic of China
| | - Yiping Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Huhhot, 010018 People’s Republic of China
| | - Dongyi Bai
- College of Animal Science, Inner Mongolia Agricultural University, Huhhot, 010018 People’s Republic of China
| | - Wunierfu Shiraigo
- College of Animal Science, Inner Mongolia Agricultural University, Huhhot, 010018 People’s Republic of China
| | - Qinan Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Huhhot, 010018 People’s Republic of China
| | - Dugarjaviin Manglai
- College of Animal Science, Inner Mongolia Agricultural University, Huhhot, 010018 People’s Republic of China
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42
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Capomaccio S, Milanesi M, Nocelli C, Giontella A, Verini-Supplizi A, Branca M, Silvestrelli M, Cappelli K. Splicing site disruption in the KIT
gene as strong candidate for white dominant phenotype in an Italian Trotter. Anim Genet 2017; 48:727-728. [DOI: 10.1111/age.12590] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Stefano Capomaccio
- Centro di Studio del Cavallo Sportivo; University of Perugia; 06126 Perugia Italy
| | - Marco Milanesi
- Istituto di Zootecnica; Università Cattolica del Sacro Cuore; 29122 Piacenza Italy
| | - Cristina Nocelli
- Scuola del Farmaco e dei Prodotti per la Salute; University of Camerino; 62032 Camerino Italy
| | - Andrea Giontella
- Centro di Studio del Cavallo Sportivo; University of Perugia; 06126 Perugia Italy
| | | | - Michele Branca
- Centro di Studio del Cavallo Sportivo; University of Perugia; 06126 Perugia Italy
| | | | - Katia Cappelli
- Centro di Studio del Cavallo Sportivo; University of Perugia; 06126 Perugia Italy
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43
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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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44
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Holl HM, Brooks SA, Carpenter ML, Bustamante CD, Lafayette C. A novel splice mutation within equine KIT
and the W15
allele in the homozygous state lead to all white coat color phenotypes. Anim Genet 2017; 48:497-498. [DOI: 10.1111/age.12554] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2017] [Indexed: 11/28/2022]
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45
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Negro S, Imsland F, Valera M, Molina A, Solé M, Andersson L. Association analysis of KIT
, MITF
, and PAX3
variants with white markings in Spanish horses. Anim Genet 2017; 48:349-352. [DOI: 10.1111/age.12528] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2016] [Indexed: 11/29/2022]
Affiliation(s)
- S. Negro
- Department Agro-Forestal Sciences; Seville University; 41013 Sevilla Spain
| | - F. Imsland
- Science for Life Laboratory; Department of Medical Biochemistry and Microbiology; Uppsala University; 75123 Uppsala Sweden
| | - M. Valera
- Department Agro-Forestal Sciences; Seville University; 41013 Sevilla Spain
| | - A. Molina
- Department of Genetics; Cordoba University; 14071 Cordoba Spain
| | - M. Solé
- Department Agro-Forestal Sciences; Seville University; 41013 Sevilla Spain
| | - L. Andersson
- Science for Life Laboratory; Department of Medical Biochemistry and Microbiology; Uppsala University; 75123 Uppsala Sweden
- Department of Animal Breeding and Genetics; Swedish University of Agricultural Sciences; 75007 Uppsala Sweden
- Department of Veterinary Integrative Biosciences; Texas A&M University; College Station TX 77843 USA
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46
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Dorado J, Anaya G, Bugno-Poniewierska M, Molina A, Mendez-Sanchez A, Ortiz I, Moreno-Millán M, Hidalgo M, Peral García P, Demyda-Peyrás S. First case of sterility associated with sex chromosomal abnormalities in a jenny. Reprod Domest Anim 2016; 52:227-234. [DOI: 10.1111/rda.12884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 09/27/2016] [Indexed: 12/01/2022]
Affiliation(s)
- J Dorado
- Veterinary Reproduction Group AGR-275; Department of Animal Medicine and Surgery; Veterinary Teaching Hospital; University of Cordoba; Cordoba Spain
| | - G Anaya
- Laboratory of Animal Genomics; MERAGEM AGR-158 Research Group; Department of Genetics; University of Córdoba; Cordoba Spain
| | - M Bugno-Poniewierska
- Department of Animal Genomics and Molecular Biology; National Research Institute of Animal Production; Balice Poland
| | - A Molina
- Laboratory of Animal Genomics; MERAGEM AGR-158 Research Group; Department of Genetics; University of Córdoba; Cordoba Spain
| | - A Mendez-Sanchez
- Department of Anatomy and Comparative Pathology; University of Cordoba; Cordoba Spain
| | - I Ortiz
- Veterinary Reproduction Group AGR-275; Department of Animal Medicine and Surgery; Veterinary Teaching Hospital; University of Cordoba; Cordoba Spain
| | - M Moreno-Millán
- Laboratory of Applied and Molecular Animal Cytogenetics; MERAGEM AGR-158 Research Group; Department of Genetics; University of Cordoba; Cordoba Spain
| | - M Hidalgo
- Veterinary Reproduction Group AGR-275; Department of Animal Medicine and Surgery; Veterinary Teaching Hospital; University of Cordoba; Cordoba Spain
| | - P Peral García
- Facultad de Ciencias Veterinarias; IGEVET - Instituto de Genética Veterinaria UNLP - CONICET LA PLATA; Universidad Nacional de La Plata; La Plata Argentina
| | - S Demyda-Peyrás
- Facultad de Ciencias Veterinarias; IGEVET - Instituto de Genética Veterinaria UNLP - CONICET LA PLATA; Universidad Nacional de La Plata; La Plata Argentina
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47
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Polymorphisms in MC1R and ASIP genes and their association with coat color phenotypes in llamas (Lama glama). Small Rumin Res 2016. [DOI: 10.1016/j.smallrumres.2016.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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48
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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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49
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Leeb T, Müller EJ, Roosje P, Welle M. Genetic testing in veterinary dermatology. Vet Dermatol 2016; 28:4-e1. [PMID: 27425028 DOI: 10.1111/vde.12309] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND Molecular genetics has made significant advances in the analysis of hereditary dermatoses during the last several years. OBJECTIVES To provide an update on currently available genetic tests for skin diseases of dogs, cats and horses, and to aid the veterinary clinician in the appropriate selection and applications of genetic tests. METHODS The scientific literature on the topic was critically reviewed. The list of known causative variants for genodermatoses and hair morphology traits was compiled by searching the Online Mendelian Inheritance in Animals (OMIA) database. RESULTS Genetic testing has become an important diagnostic method in veterinary medicine. Genetic tests can help to establish the correct diagnosis in some diseases with relatively nonspecific signs. Genetic tests are also essential for sustainable breeding programmes and to help minimize the frequency of animals with hereditary diseases. Advances in genetic methodology and bioinformatics already allow genome-wide screening for potential disease causing mutations for research purposes. It is anticipated that this will become a routine process in clinical practice in the future. CONCLUSION AND CLINICAL IMPORTANCE As specific DNA tests and broad genome-wide analyses come into more common use, it is critical that clinicians understand the proper application and interpretation of these test results.
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Affiliation(s)
- Tosso Leeb
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland.,DermFocus, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - Eliane J Müller
- DermFocus, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland.,Vetsuisse Faculty, Institute of Animal Pathology, University of Bern, Länggassstrasse 122, Bern, 3001, Switzerland.,Department of Dermatology, Inselspital, University of Bern, Freiburgstrasse, Bern, 3010, Switzerland
| | - Petra Roosje
- DermFocus, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland.,Vetsuisse Faculty, Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, University of Bern, Länggassstrasse 128, Bern, 3001, Switzerland
| | - Monika Welle
- DermFocus, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland.,Vetsuisse Faculty, Institute of Animal Pathology, University of Bern, Länggassstrasse 122, Bern, 3001, Switzerland
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50
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Menzi F, Keller I, Reber I, Beck J, Brenig B, Schütz E, Leeb T, Drögemüller C. Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation. Sci Rep 2016; 6:28438. [PMID: 27329507 PMCID: PMC4916431 DOI: 10.1038/srep28438] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/06/2016] [Indexed: 02/08/2023] Open
Abstract
The South African Boer goat displays a characteristic white spotting phenotype, in which the pigment is limited to the head. Exploiting the existing phenotype variation within the breed, we mapped the locus causing this white spotting phenotype to chromosome 17 by genome wide association. Subsequent whole genome sequencing identified a 1 Mb copy number variant (CNV) harboring 5 genes including EDNRA. The analysis of 358 Boer goats revealed 3 alleles with one, two, and three copies of this CNV. The copy number is correlated with the degree of white spotting in goats. We propose a hypothesis that ectopic overexpression of a mutant EDNRA scavenges EDN3 required for EDNRB signaling and normal melanocyte development and thus likely lead to an absence of melanocytes in the non-pigmented body areas of Boer goats. Our findings demonstrate the value of domestic animals as reservoir of unique mutants and for identifying a precisely defined functional CNV.
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Affiliation(s)
- Fiona Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Irene Keller
- Department of Clinical Research and Swiss Institute of Bioinformatics, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Irene Reber
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Julia Beck
- Chronix Biomedical, Goetheallee 8, 37073 Göttingen, Germany
| | - Bertram Brenig
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
| | - Ekkehard Schütz
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
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