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Maciel SVSA, Oliveira IPP, Senes BB, Silva JAIDV, Feitosa FLB, Alves JS, Costa RB, de Camargo GMF. Genomic regions associated with coat color in Gir cattle. Genome 2024; 67:233-242. [PMID: 38579337 DOI: 10.1139/gen-2023-0115] [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] [Indexed: 04/07/2024]
Abstract
Indicine cattle breeds are adapted to the tropical climate, and their coat plays an important role in this process. Coat color influences thermoregulation and the adhesion of ectoparasites and may be associated with productive and reproductive traits. Furthermore, coat color is used for breed qualification, with breeders preferring certain colors. The Gir cattle is characterized by a wide variety of coat colors. Therefore, we performed genome-wide association studies to identify candidate genes for coat color in Gir cattle. Different phenotype scenarios were considered in the analyses and regions were identified on eight chromosomes. Some regions and many candidate genes are influencing coat color in the Gir cattle, which was found to be a polygenic trait. The candidate genes identified have been associated with white spotting patterns and base coat color in cattle and other species. In addition, a possible epistatic effect on coat color determination in the Gir cattle was suggested. This is the first published study that identified genomic regions and listed candidate genes associated with coat color in Gir cattle. The findings provided a better understanding of the genetic architecture of the trait in the breed and will allow to guide future fine-mapping studies for the development of genetic markers for selection.
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Liu X, Peng Y, Zhang X, Wang X, Chen W, Kou X, Liang H, Ren W, Khan MZ, Wang C. Coloration in Equine: Overview of Candidate Genes Associated with Coat Color Phenotypes. Animals (Basel) 2024; 14:1802. [PMID: 38929421 PMCID: PMC11200706 DOI: 10.3390/ani14121802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Variation in coat color among equids has attracted significant interest in genetics and breeding research. The range of colors is primarily determined by the type, concentration, and distribution of melanin pigments, with the balance between eumelanin and pheomelanin influenced by numerous genetic factors. Advances in genomic and sequencing technologies have enabled the identification of several candidate genes that influence coat color, thereby clarifying the genetic basis of these diverse phenotypes. In this review, we concisely categorize coat coloration in horses and donkeys, focusing on the biosynthesis and types of melanin involved in pigmentation. Moreover, we highlight the regulatory roles of some key candidate genes, such as MC1R, TYR, MITF, ASIP, and KIT, in coat color variation. Moreover, the review explores how coat color relates to selective breeding and specific equine diseases, offering valuable insights for developing breeding strategies that enhance both the esthetic and health aspects of equine species.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Muhammad Zahoor Khan
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 522000, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 522000, China
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The Genetic Basis of Piebald Coat Colour in Hucul Horses in the Context of White Markings and Crypto-Tobiano as a Breeding Problem in Poland. ANNALS OF ANIMAL SCIENCE 2019. [DOI: 10.2478/aoas-2019-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
The aim of the study was to analyse the genetic basis of piebald coat colour in Hucul horses and to verify their coat colour in breeding records. Tests were performed with DNA purified from the whole blood samples of 242 Hucul horses with different coat colour patterns. DNA was analysed to identify an inversion in ECA3 (PCR). The results confirmed that the inversion on ECA3 is a direct factor determining piebald (tobiano) colour in the analysed Hucul horses. No inversion was observed in any of the solid coloured horses, but it was present in all the piebald ones. It was also identified in 18% (11 of 61) of the horses from the group of horses qualified in the passport as solid coloured with white markings. In fact, these horses had the tobiano gene that is phenotypically identifiable as crypto-tobiano, which may give the false impression of having white markings and lead to error when describing a horse. This is an important issue, in particular with regard to the breed standard, which eliminates Hucul horses with white markings from breeding.
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Validation of high-resolution melting analysis as a diagnostic tool for endothelin receptor B mutation in American Paint horses and allele frequency estimation. Mol Cell Probes 2018; 41:52-56. [PMID: 30096357 DOI: 10.1016/j.mcp.2018.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/17/2018] [Accepted: 08/07/2018] [Indexed: 11/21/2022]
Abstract
Overo lethal white foal syndrome (OLWFS) is a genetic disorder caused by a dinucleotide mutation in the endothelin receptor type B (EDNRB) gene leading to the death of affected foals shortly after birth. The use of rapid and reliable genetic testing is imperative for the early diagnosis of the mutation avoiding, therefore, either additional suffering or the production of affected animals. In the present study, we developed and validated a high-resolution melting (HRM) genotyping assay to detect the OLWFS causative mutation, and we also determined the frequency of heterozygotes among American Paint horses in Brazil. The HRM genotyping assay resulted in a high sensitivity, specificity, and positive and negative predictive values. The overall estimated frequency of heterozygotes was 21.6%; however, this frequency increased to 89.5% when considering only overo horses. The HRM assay optimized here was a reliable and suitable method for the detection of the dinucleotide mutation observed in the EDNRB gene resulting in a fast, accurate, and precise diagnostic tool. The causative gene mutation of OLWFS is present in heterozygosity in the American Paint Horse population in Brazil and is highly frequent among overo horses.
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Kim NY, Bhuiyan MSA, Chae HS, Baek KS, Son JK, Shin SM, Woo JH, Park SH, Lee SH. Genome-wide association study for tobiano spotting coat color in Korean Jeju × Thoroughbred horse population. Anim Genet 2017; 48:728-729. [PMID: 28850680 DOI: 10.1111/age.12596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Nam Young Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | | | - Hyun Seok Chae
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | - Kwang Soo Baek
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | - Jun Kyu Son
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | - Sang Min Shin
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | - Jae Hoon Woo
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | - Seol Hwa Park
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | - Seung Hwan Lee
- Division of Animal & Dairy Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Korea
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Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L. Ancient genomic changes associated with domestication of the horse. Science 2017; 356:442-445. [DOI: 10.1126/science.aam5298] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Ancient genomics of horse domesticationThe domestication of the horse was a seminal event in human cultural evolution. Libradoet al.obtained genome sequences from 14 horses from the Bronze and Iron Ages, about 2000 to 4000 years ago, soon after domestication. They identified variants determining coat color and genes selected during the domestication process. They could also see evidence of admixture with archaic horses and the demography of the domestication process, which included the accumulation of deleterious variants. The horse appears to have undergone a different type of domestication process than animals that were domesticated simply for food.Science, this issue p.442
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Affiliation(s)
- Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Charleen Gaunitz
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Mélanie Pruvost
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris Diderot, 75205 Paris cedex 13, France
| | - Anders Albrechtsen
- Bioinformatics Center, Department of Biology, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Antoine Fages
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Naveed Khan
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | | | - Aitor Serres-Armero
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Lukas F. K. Kuderna
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Inna S. Povolotskaya
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- National High-Throughput DNA Sequencing Center, Copenhagen, Denmark
| | - Sébastien Lepetz
- Centre National de la Recherche Scientifique, Muséum national d’histoire naturelle, Sorbonne Universités, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 55 rue Buffon, 75005 Paris, France
| | | | - Catherine Thèves
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Saleh Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed H. Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khaled Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, 1580 Avenches, Switzerland
| | - Zainolla Samashev
- Branch of Institute of Archaeology Margulan, Republic Avenue 24-405, 010000 Astana, Republic of Kazakhstan
| | - Henri-Paul Francfort
- CNRS, UMR 7041 Archéologie et Sciences de l’Antiquité, Archéologie de l'Asie Centrale, Maison René Ginouvès, 21 allée de l’Université, 92023 Nanterre, France
| | - Norbert Benecke
- German Archaeological Institute, Department of Natural Sciences, Berlin, 14195 Berlin, Germany
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin 10315, Germany
| | - Christine Keyser
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
- Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - Bertrand Ludes
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
- Institut Médico-Légal, Université Paris Descartes, Paris, France
| | - Eric Crubézy
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
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Kim NY, Shin KY, Lee CE, Han SH, Lee SS, Park YS, Ko MS, Hong HJ, Yang JH, Jang DJ, Yang YH. Genetic Characterization of Wolla Coat Color in Jeju Horses. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2012. [DOI: 10.5187/jast.2012.54.5.375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Svensson EM, Telldahl Y, Sjöling E, Sundkvist A, Hulth H, Sjøvold T, Götherström A. Coat colour and sex identification in horses from Iron Age Sweden. Ann Anat 2012; 194:82-7. [PMID: 22154005 DOI: 10.1016/j.aanat.2011.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 11/04/2011] [Accepted: 11/04/2011] [Indexed: 10/15/2022]
Abstract
Domestication of animals and plants marked a turning point in human prehistory. To date archaeology, archaeozoology and genetics have shed light on when and where all of our major livestock species were domesticated. Phenotypic changes associated with domestication have occurred in all farm animals. Coat colour is one of the traits that have been subjected to the strongest human selection throughout history. Here we use genotyping of coat colour SNPs in horses to investigate whether there were any regional differences or preferences for specific colours associated with specific cultural traditions in Iron Age Sweden. We do this by identifying the sex and coat colour of horses sacrificed at Skedemosse, Öland (Sweden) during the Iron Age, as well as in horses from two sites in Uppland, Ultuna and Valsgärde (dated to late Iron Age). We show that bay, black and chestnut colours were all common and two horses with tobiano spotting were found. We also show how the combination of sex identification with genotyping of just a few SNPs underlying the basic coat colours can be used to identify the minimum number of individuals at a site on a higher level than morphological methods alone. Although separated by 500 km and from significantly different archaeological contexts the horses at Skedemosse and Ultuna are quite homogenous when it comes to coat colour phenotypes, indicating that there were no clear geographical variation in coat colouration in Sweden during the late Iron Age and early Viking Age.
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Affiliation(s)
- Emma M Svensson
- Department of Evolutionary Biology, EBC, Uppsala University, Sweden.
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McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guérin G, Hasegawa T, Hill EW, Leeb T, Lindgren G, Penedo MCT, Røed KH, Ryder OA, Swinburne JE, Tozaki T, Valberg SJ, Vaudin M, Lindblad-Toh K, Wade CM, Mickelson JR. A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genet 2012; 8:e1002451. [PMID: 22253606 PMCID: PMC3257288 DOI: 10.1371/journal.pgen.1002451] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 11/21/2011] [Indexed: 11/18/2022] Open
Abstract
An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50-100 kb and reached background levels within 1-2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of ∼750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species.
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Affiliation(s)
- Molly E McCue
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
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Coelho E, Oliveira D, Teixeira C. Testes bioquímico (albumina e proteína de ligação da vitamina D) e molecular (gene KIT) para detecção de marcadores genéticos para pelagem tobiana em cavalos Pampa e Paint. ARQ BRAS MED VET ZOO 2010. [DOI: 10.1590/s0102-09352010000300031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Foram utilizados 159 cavalos Pampa, registrados na Associação Brasileira dos Criadores de Cavalo Pampa, e um grupo-controle, de 32 cavalos da raça Paint, ambos os grupos provenientes de plantéis de diferentes regiões brasileiras, com o objetivo de comparar os testes bioquímico e molecular para detecção de marcadores genéticos para pelagem tobiana em cavalos Pampa. Houve diferença significativa (P<0,001) entre os testes bioquímico e molecular, nos cavalos Pampa, mas o mesmo fato não ocorreu com os da raça Paint. Os resultados mostraram que o marcador molecular (KIT) foi mais eficiente na identificação dos prováveis cavalos homozigotos do que os marcadores bioquímicos albumina (Al) e proteína de ligação da vitamina D (Gc), em ambas as raças.
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Hirota KI, Kakoi H, Gawahara H, Hasegawa T, Tozaki T. Construction and validation of parentage testing for thoroughbred horses by 53 single nucleotide polymorphisms. J Vet Med Sci 2010; 72:719-26. [PMID: 20124759 DOI: 10.1292/jvms.09-0486] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We characterized the SNP 53 JPN System for parentage verification during horse registry. The SNP 53 JPN System was constructed using 53 highly polymorphic single nucleotide polymorphisms (SNPs), which were amplified and genotyped with 2 multiplex assays. The SNP 53 JPN System showed good resolution for 95 unrelated thoroughbreds, and the exclusion probability (PE01) for each SNP ranged from 11.5 to 23.0%, resulting in a total PE01 value of 99.996%. These results indicate that the SNP 53 JPN System is useful for parentage testing of thoroughbreds. Of the 53 SNPs, 8 SNPs could be used to exclude a pseudo parent and sib combination found using the 2006 International Society for Animal Genetics (ISAG) horse comparison test, as efficiently as the parentage testing systems using short tandem repeats (STRs). Thus, we concluded that the SNP 53 JPN System could provide sufficient and reliable information for routine parentage testing of thoroughbred.
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Affiliation(s)
- Kei-ichi Hirota
- Department of Molecular Genetics, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, Japan
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Liu L, Harris B, Keehan M, Zhang Y. Genome scan for the degree of white spotting in dairy cattle. Anim Genet 2009; 40:975-7. [DOI: 10.1111/j.1365-2052.2009.01936.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chowdhary BP, Raudsepp T. The horse genome derby: racing from map to whole genome sequence. Chromosome Res 2008; 16:109-27. [PMID: 18274866 DOI: 10.1007/s10577-008-1204-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The map of the horse genome has undergone unprecedented expansion during the past six years. Beginning from a modest collection of approximately 300 mapped markers scattered on the 31 pairs of autosomes and the X chromosome in 2001, today the horse genome is among the best-mapped in domestic animals. Presently, high-resolution linearly ordered gene maps are available for all autosomes as well as the X and the Y chromosome. The approximately 4350 mapped markers distributed over the approximately 2.68 Gbp long equine genome provide on average 1 marker every 620 kb. Among the most remarkable developments in equine genome analysis is the availability of the assembled sequence (EquCab2) of the female horse genome and the generation approximately 1.5 million single nucleotide polymorphisms (SNPs) from diverse breeds. This has triggered the creation of new tools and resources like the 60K SNP-chip and whole genome expression microarrays that hold promise to study the equine genome and transcriptome in ways not previously envisaged. As a result of these developments it is anticipated that, during coming years, the genetics underlying important monogenic traits will be analyzed with improved accuracy and speed. Of larger interest will be the prospects of dissecting the genetic component of various complex/multigenic traits that are of vital significance for equine health and welfare. The number of investigations recently initiated to study a multitude of such traits hold promise for improved diagnostics, prevention and therapeutic approaches for horses.
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Affiliation(s)
- Bhanu P Chowdhary
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843-4458, USA.
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Haase B, Jude R, Brooks SA, Leeb T. An equine chromosome 3 inversion is associated with the tobiano spotting pattern in German horse breeds. Anim Genet 2008; 39:306-9. [DOI: 10.1111/j.1365-2052.2008.01715.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Brooks SA, Lear TL, Adelson DL, Bailey E. A chromosome inversion near the KIT gene and the Tobiano spotting pattern in horses. Cytogenet Genome Res 2008; 119:225-30. [PMID: 18253033 DOI: 10.1159/000112065] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2007] [Indexed: 10/22/2022] Open
Abstract
Tobiano is a white spotting pattern in horses caused by a dominant gene, Tobiano(TO). Here, we report TO associated with a large paracentric chromosome inversion on horse chromosome 3. DNA sequences flanking the inversion were identified and a PCR test was developed to detect the inversion. The inversion was only found in horses with the tobiano pattern, including horses with diverse genetic backgrounds, which indicated a common genetic origin thousands of years ago. The inversion does not interrupt any annotated genes, but begins approximately 100 kb downstream of the KIT gene. This inversion may disrupt regulatory sequences for the KIT gene and cause the white spotting pattern.
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Affiliation(s)
- S A Brooks
- Department of Veterinary Science, University of Kentucky, Lexington, KY, USA.
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Kuehn C, Weikard R. Multiple splice variants within the bovine silver homologue (SILV) gene affecting coat color in cattle indicate a function additional to fibril formation in melanophores. BMC Genomics 2007; 8:335. [PMID: 17892572 PMCID: PMC2099443 DOI: 10.1186/1471-2164-8-335] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 09/24/2007] [Indexed: 11/16/2022] Open
Abstract
Background The silver homologue(SILV) gene plays a major role in melanosome development. SILV is a target for studies concerning melanoma diagnostics and therapy in humans as well as on skin and coat color pigmentation in many species ranging from zebra fish to mammals. However, the precise functional cellular mechanisms, in which SILV is involved, are still not completely understood. While there are many studies addressing SILV function upon a eumelaneic pigment background, there is a substantial lack of information regarding the further relevance of SILV, e.g. for phaeomelanosome development. Results In contrast to previous results in other species reporting SILV expression exclusively in pigmented tissues, our experiments provide evidence that the bovine SILV gene is expressed in a variety of tissues independent of pigmentation. Our data show that the bovine SILV gene generates an unexpectedly large number of different transcripts occurring in skin as well as in non-pigmented tissues, e.g. liver or mammary gland. The alternative splice sites are generated by internal splicing and primarily remove complete exons. Alternative splicing predominantly affects the repeat domain of the protein, which has a functional key role in fibril formation during eumelanosome development. Conclusion The expression of the bovine SILV gene independent of pigmentation suggests SILV functions exceeding melanosome development in cattle. This hypothesis is further supported by transcript variants lacking functional key elements of the SILV protein relevant for eumelanosome development. Thus, the bovine SILV gene can serve as a model for the investigation of the putative additional functions of SILV. Furthermore, the splice variants of the bovine SILV gene represent a comprehensive natural model to refine the knowledge about functional domains in the SILV protein. Our study exemplifies that the extent of alternative splicing is presumably much higher than previously estimated and that alternatively spliced transcripts presumably can generate molecules of deviating function compared to their constitutive counterpart.
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Affiliation(s)
- Christa Kuehn
- Research Institute for the Biology of Farm Animals (FBN), Res. Unit Molecular Biology, Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Rosemarie Weikard
- Research Institute for the Biology of Farm Animals (FBN), Res. Unit Molecular Biology, Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
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Coelho E, Oliveira D, Cothran E, Teixeira C, Nunes R. Teste de marcadores bioquímicos na identificação de prováveis indivíduos homozigotos dominantes para o gene tobiano em cavalos Pampa. ARQ BRAS MED VET ZOO 2007. [DOI: 10.1590/s0102-09352007000400027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Utilizaram-se 195 cavalos Pampa e um grupo-controle de 41 cavalos da raça Paint, provenientes de plantéis de várias regiões brasileiras, com o objetivo de avaliar a eficiência do teste mediante uso de marcadores bioquímicos: albumina (Al) e proteína de ligação da vitamina D (Gc), para identificação dos possíveis indivíduos homozigotos dominantes para o padrão de pelagem tobiano nos cavalos Pampa. Não foram encontrados genótipos AlBB e GcSS, revelando indício de quebra de ligação gênica entre tais locos e o loco tobiano e a ineficácia do teste bioquímico na detecção dos prováveis indivíduos homozigotos dominantes para o padrão de pelagem tobiano nos cavalos Pampa.
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Brooks SA, Bailey E. Exon skipping in the KIT gene causes a Sabino spotting pattern in horses. Mamm Genome 2005; 16:893-902. [PMID: 16284805 DOI: 10.1007/s00335-005-2472-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Accepted: 08/09/2005] [Indexed: 11/25/2022]
Abstract
Sabino (SB) is a white spotting pattern in the horse characterized by white patches on the face, lower legs, or belly, and interspersed white hairs on the midsection. Based on comparable phenotypes in humans and pigs, the KIT gene was investigated as the origin of the Sabino phenotype. In this article we report the genetic basis of one type of Sabino spotting pattern in horses that we call Sabino 1, with the alleles represented by the symbols SB1 and sb1. Transcripts of KIT were characterized by reverse transcriptase polymerase chain reaction (RT-PCR) and sequencing cDNA from horses with the genotypes SB1/SB1, SB1/sb1, and sb1/sb1. Horses with the Sabino 1 trait produced a splice variant of KIT that did not possess exon 17. Genomic DNA sequencing of KIT revealed a single nucleotide polymorphism (SNP) caused by a base substitution for T with A in intron 16, 1037 bases following exon 16. The SNP associated with SB1 was designated KI16+1037A. This substitution eliminated a MnlI restriction site and allowed the use of PCR-RFLP to characterize individuals for this base change. Complete linkage was observed between this SNP and Sabino 1 in the Tennessee Walking Horse families (LOD = 9.02 for Theta = 0). Individual horses from other breeds were also tested. All five horses homozygous for this SNP were white, and all 68 horses with one copy of this SNP either exhibited the Sabino 1 phenotype or were multipatterned. Some multipatterned individuals appeared white due to the additive effect of white spotting patterns. However, 13 horses with other Sabino-type patterns did not have this SNP. Based on these results we propose the following: (1) this SNP, found within intron 16, is responsible for skipping of exon 17 and the SB1 phenotype, (2) the White and Sabino phenotypes are heterogeneous and this mechanism is not the only way to produce the pattern described as "Sabino" or "White," and (3) homozygosity for SB1 results in a complete or nearly completely white phenotype.
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Affiliation(s)
- Samantha A Brooks
- Department of Veterinary Science, 108 Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky 40546-0099, USA.
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Mau C, Poncet PA, Bucher B, Stranzinger G, Rieder S. Genetic mapping of dominant white (W), a homozygous lethal condition in the horse (Equus caballus). J Anim Breed Genet 2004. [DOI: 10.1111/j.1439-0388.2004.00481.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chowdhary BP, Bailey E. Equine genomics: galloping to new frontiers. Cytogenet Genome Res 2004; 102:184-8. [PMID: 14970700 DOI: 10.1159/000075746] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2003] [Accepted: 09/03/2003] [Indexed: 11/19/2022] Open
Abstract
Analysis of the horse genome is proceeding at a rapid pace. Within a short span of 6-7 years, approximately 1,500 markers have been mapped in horse, of which at least half are genes/ESTs. Health, performance and phenotypic characteristic are of major concern/interest to horse breeders and owners. Current efforts to analyze the equine genome are primarily aimed at developing critical resources (including an advanced gene map) that could readily be used in the near future to i) identify genes and mutations responsible for inherited equine diseases/disorders and to formulate approaches for accurate diagnostics, therapeutics and prevention, ii) discover genes associated with various other traits of significance, e.g. fertility, disease resistance, coat color and athletic performance etc., and iii) use functional genomic approaches to identify gene regulatory events involved in the manifestation of various diseases.
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Affiliation(s)
- B P Chowdhary
- Department of Veterinary Anatomy & Public Health, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843-4458, USA.
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