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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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Zhang W, Jin M, Lu Z, Li T, Wang H, Yuan Z, Wei C. Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep. Animals (Basel) 2023; 13:3265. [PMID: 37893989 PMCID: PMC10603731 DOI: 10.3390/ani13203265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/10/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Wool color is controlled by a variety of genes. Although the gene regulation of some wool colors has been studied in relative depth, there may still be unknown genetic variants and control genes for some colors or different breeds of wool that need to be identified and recognized by whole genome resequencing. Therefore, we used whole genome resequencing data to compare and analyze sheep populations of different breeds by population differentiation index and nucleotide diversity ratios (Fst and θπ ratio) as well as extended haplotype purity between populations (XP-EHH) to reveal selection signals related to wool coloration in sheep. Screening in the non-white wool color group (G1 vs. G2) yielded 365 candidate genes, among which PDE4B, GMDS, GATA1, RCOR1, MAPK4, SLC36A1, and PPP3CA were associated with the formation of non-white wool; an enrichment analysis of the candidate genes yielded 21 significant GO terms and 49 significant KEGG pathways (p < 0.05), among which 17 GO terms and 21 KEGG pathways were associated with the formation of non-white wool. Screening in the white wool color group (G2 vs. G1) yielded 214 candidate genes, including ABCD4, VSX2, ITCH, NNT, POLA1, IGF1R, HOXA10, and DAO, which were associated with the formation of white wool; an enrichment analysis of the candidate genes revealed 9 significant GO-enriched pathways and 19 significant KEGG pathways (p < 0.05), including 5 GO terms and 12 KEGG pathways associated with the formation of white wool. In addition to furthering our understanding of wool color genetics, this research is important for breeding purposes.
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Affiliation(s)
- Wentao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Meilin Jin
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Taotao Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Huihua Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China;
| | - Caihong Wei
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
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3
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Ciosek J, Kimes A, Vinardell T, Miller DC, Antczak DF, Brooks S. Juvenile idiopathic epilepsy in Arabian horses is not a single-gene disorder. J Hered 2023; 114:488-491. [PMID: 37145017 DOI: 10.1093/jhered/esad029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/04/2023] [Indexed: 05/06/2023] Open
Abstract
Valued for their temperament, beauty, athletic ability, and exhibition in the show ring, Arabian horses are an important component of the horse industry. Juvenile idiopathic epilepsy (JIE), a seizure disorder, is most often reported in Arabian foals from birth to 6 months of age. Affected foals exhibit tonic-clonic seizures lasting as long as 5 min and risking secondary complications like temporary blindness and disorientation. Some foals outgrow this condition, while others die or suffer lifelong complications if not treated. Previous work suggested a strong genetic component to JIE and proposed JIE to be a single-gene trait. In this work, we conducted a genome wide association study (GWAS) in 60 cases of JIE and 120 genetically matched controls, identifying loci suggesting JIE is not caused by a single locus. Coat color (chestnut, gray) phenotypes were used as positive control traits to assess the efficacy of GWAS in this population. Future work will attempt to future define candidate regions and explore a polygenic mode of inheritance.
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Affiliation(s)
- Julia Ciosek
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Abigail Kimes
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Tatiana Vinardell
- Equine Veterinary Medical Center, Hamad Bin Khalifa University, Doha, Qatar
| | - Donald C Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Samantha Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
- UF Genetics Institute, University of Florida, Gainesville, FL, USA
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Elkin J, Martin A, Courtier-Orgogozo V, Santos ME. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol Rev Camb Philos Soc 2023; 98:1250-1277. [PMID: 37017088 DOI: 10.1111/brv.12952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
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Affiliation(s)
- Joel Elkin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington, DC, 20052, USA
| | | | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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5
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Breed Distribution and Allele Frequencies of Base Coat Color, Dilution, and White Patterning Variants across 28 Horse Breeds. Genes (Basel) 2022; 13:genes13091641. [PMID: 36140807 PMCID: PMC9498372 DOI: 10.3390/genes13091641] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Since domestication, horses have been selectively bred for various coat colors and white spotting patterns. To investigate breed distribution, allele frequencies, and potential lethal variants for recommendations on genetic testing, 29 variants within 14 genes were investigated in 11,281 horses from 28 breeds. The recessive chestnut ea allele in melanocortin 1 receptor (MC1R) (p.D84N) was identified in four breeds: Knabstrupper, Paint Horse, Percheron, and Quarter Horse. After filtering for relatedness, ea allele frequency in Knabstruppers was estimated at 0.035, thus illustrating the importance of testing for mate selection for base coat color. The Rocky Mountain Horse breed had the highest allele frequency for two of the dilution variants under investigation (Za.f. = 0.32 and Cha.f. = 0.026); marker-assisted selection in this breed could aid in the production of horses with desirable dilute coats with less severe ocular anomalies caused by the silver (Z) allele. With regard to white patterning, nine horses homozygous for the paired box 3 (PAX3) splashed white 2 (SW2) allele (p.C70Y) and six horses homozygous for the KIT proto-oncogene, receptor tyrosine kinase (KIT) sabino 1 (SB1) allele (ECA3g.79544206A>T) were identified, thus determining they are rare and confirming that homozygosity for SW2 is not embryonic lethal. The KIT dominant white 20 (W20) allele (p.R682H) was identified in all but three breeds: Arabian (n = 151), Icelandic Horse (n = 66), and Norwegian Fjord Horse (n = 90). The role of W20 in pigmentation across breeds is not well understood; given the different selection regimes of the breeds investigated, these data provide justification for further evaluating the functional role of this allele in pigmentation. Here, we present the largest dataset reported for coat color variants in horses to date, and these data highlight the importance of breed-specific studies to inform on the proper use of marker-assisted selection and to develop hypotheses related to pigmentation for further testing in horses.
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6
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Todd ET, Tonasso-Calvière L, Chauvey L, Schiavinato S, Fages A, Seguin-Orlando A, Clavel P, Khan N, Pérez Pardal L, Patterson Rosa L, Librado P, Ringbauer H, Verdugo M, Southon J, Aury JM, Perdereau A, Vila E, Marzullo M, Prato O, Tecchiati U, Bagnasco Gianni G, Tagliacozzo A, Tinè V, Alhaique F, Cardoso JL, Valente MJ, Telles Antunes M, Frantz L, Shapiro B, Bradley DG, Boulbes N, Gardeisen A, Horwitz LK, Öztan A, Arbuckle BS, Onar V, Clavel B, Lepetz S, Vahdati AA, Davoudi H, Mohaseb A, Mashkour M, Bouchez O, Donnadieu C, Wincker P, Brooks SA, Beja-Pereira A, Wu DD, Orlando L. The genomic history and global expansion of domestic donkeys. Science 2022; 377:1172-1180. [PMID: 36074859 DOI: 10.1126/science.abo3503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.
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Affiliation(s)
- Evelyn T Todd
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Laure Tonasso-Calvière
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Loreleï Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Antoine Fages
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Pierre Clavel
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France.,Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Lucía Pérez Pardal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
| | | | - Pablo Librado
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Marta Verdugo
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - John Southon
- Earth System Science Department, University of California, Irvine, CA 92697, USA
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Aude Perdereau
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Emmanuelle Vila
- Laboratoire Archéorient, Université Lyon 2, Lyon 69007, France
| | - Matilde Marzullo
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Ornella Prato
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Umberto Tecchiati
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Giovanna Bagnasco Gianni
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | | | - Vincenzo Tinè
- Soprintendenza archeologia belle arti e paesaggio per le province di Verona, Rovigo e Vicenza, Verona 37121, Italy
| | | | - João Luís Cardoso
- ICArEHB, Campus de Gambelas, University of Algarve, Faro 8005-139, Portugal.,Universidade Aberta, Lisbon 1269-001, Portugal
| | - Maria João Valente
- Faculdade de Ciências Humanas e Sociais, Centro de Estudos de Arqueologia, Artes e Ciências do Património, Universidade do Algarve, Faro 8000-117, Portugal
| | - Miguel Telles Antunes
- Centre for Research on Science and Geological Engineering, Universidade NOVA de Lisboa, Lisbon 1099-085, Portugal
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich 80539, Germany.,School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4DQ, United Kingdom
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Nicolas Boulbes
- Institut de Paléontologie Humaine, Fondation Albert Ier, Paris / UMR 7194 HNHP, MNHN-CNRS-UPVD / EPCC Centre Européen de Recherche Préhistorique, Tautavel 66720, France
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditéranéennes, Université Paul Valéry - Site Saint-Charles 2, Montpellier 34090, France
| | - Liora Kolska Horwitz
- National Natural History Collections, Edmond J. Safra Campus, Givat Ram, The Hebrew University, Jerusalem 9190401, Israel
| | - Aliye Öztan
- Archaeology Department, Ankara University, Ankara 06100, Turkey
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul 34320, Turkey
| | - Benoît Clavel
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Sébastien Lepetz
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Ali Akbar Vahdati
- Provincial Office of the Iranian Center for Cultural Heritage, Handicrafts and Tourism Organisation, North Khorassan, Bojnord 9416745775, Iran
| | - Hossein Davoudi
- Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Azadeh Mohaseb
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France.,Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France.,Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran.,Department of Osteology, National Museum of Iran, Tehran 1136918111, Iran
| | - Olivier Bouchez
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castaneet-Tolosan Cedex 31326, France
| | - Cécile Donnadieu
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castaneet-Tolosan Cedex 31326, France
| | - Patrick Wincker
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Samantha A Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Albano Beja-Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,DGAOT, Faculty of Sciences, Universidade do Porto, Porto 4169-007, Portugal.,Sustainable Agrifood Production Research Centre (GreenUPorto), Universidade do Porto, Vairão 4485-646, Portugal
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.,Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
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7
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Schary N, Novak B, Kämper L, Yousf A, Lübbert H. Identification and pharmacological modification of resistance mechanisms to protoporphyrin-mediated photodynamic therapy in human cutaneous squamous cell carcinoma cell lines. Photodiagnosis Photodyn Ther 2022; 39:103004. [PMID: 35811052 DOI: 10.1016/j.pdpdt.2022.103004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/21/2022] [Accepted: 07/06/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Photodynamic therapy (PDT) is clinically approved to treat neoplastic skin diseases such as precursors of cutaneous squamous cell carcinoma (cSCC). In PDT, 5-aminolevulinic acid (5-ALA) drives the selective formation of the endogenous photosensitizer protoporphyrin IX (PpIX). Although 5-ALA PDT is clinically highly effective, resistance might occur due to decreased accumulation of PpIX in certain tumors. Such resistance may be caused by any fundamental step of PpIX accumulation: 5-ALA uptake, PpIX synthesis and PpIX efflux. METHODS We investigated PpIX accumulation and photodynamically induced cell death in PDT refractory SCC-13, PDT susceptible A431, and normal human epidermal keratinocytes (NHEK). Expression of genes associated with cellular PpIX kinetics was investigated on mRNA and protein level. PpIX accumulation and cell death upon illumination were pharmacologically manipulated using drugs targeting 5-ALA uptake, PpIX synthesis or efflux. RESULTS The experiments indicate that taurine transporter (SLC6A6) is the major pathway for 5-ALA uptake in cSCC cells, while being less important in NHEK. Downregulation of PpIX synthesis enzymes in SCC-13 was counteracted by methotrexate (MTX) treatment, which restored PpIX formation and cell death. PpIX efflux inhibitors targeting ABC transporters led to significantly increased PpIX accumulation in SCC-13, thereby fully overcoming resistance. CONCLUSIONS The results indicate a conserved threshold for PpIX accumulation with respect to PDT-resistance. Cells showed increased viability after PDT at PpIX concentrations below 1.5 nM. Selective uptake of 5-ALA via taurine transporter SLC6A6 in cutaneous tumor cells is novel but unrelated to resistance. MTX can partially abrogate resistance by PpIX synthesis enzyme induction, while efflux mechanisms via ABC transporters seem the main driving force and promising drug targets.
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Affiliation(s)
- Nicole Schary
- Department of Animal Physiology, Ruhr-University Bochum, Germany
| | - Ben Novak
- Department of Animal Physiology, Ruhr-University Bochum, Germany; Biofrontera Bioscience GmbH, Leverkusen, Germany.
| | - Laura Kämper
- Department of Animal Physiology, Ruhr-University Bochum, Germany
| | - Aisha Yousf
- Department of Animal Physiology, Ruhr-University Bochum, Germany
| | - Hermann Lübbert
- Department of Animal Physiology, Ruhr-University Bochum, Germany
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8
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Salek Ardestani S, Zandi MB, Vahedi SM, Mahboudi H, Mahboudi F, Meskoob A. Detection of common copy number of variation underlying selection pressure in Middle Eastern horse breeds using whole-genome sequence data. J Hered 2022; 113:421-430. [PMID: 35605262 DOI: 10.1093/jhered/esac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 05/21/2022] [Indexed: 11/14/2022] Open
Abstract
Dareshouri, Arabian, and Akhal-Teke are three Middle Eastern horse breeds that have been selected for endurance and adaptation to harsh climates. Deciphering the genetic characteristics of these horses by tracing selection footprints and copy number of variations will be helpful in improving our understanding of equine breeds' development and adaptation. For this purpose, we sequenced the whole-genome of four Dareshouri horses using Illumina Hiseq panels and compared them with publicly available whole-genome sequences of Arabian (n=3) and Akhal-Teke (n=3) horses . Three tests of FLK, hapFLK, and pooled heterozygosity were applied using a sliding window (window size=100kb, step size=50kb) approach to detect putative selection signals. Copy number variation analysis was applied to investigate copy number of variants (CNVs), and the results were used to suggest selection signatures involving CNVs. Whole-genome sequencing demonstrated 8,837,950 single nucleotide polymorphisms (SNPs) in autosomal chromosomes. We suggested 58 genes and three quantitative trait loci (QTLs), including some related to horse gait, insect bite hypersensitivity, and withers height, based on selective signals detected by adjusted p-value of Mahalanobis distance based on the rank-based P-values (Md-rank-P) method. We proposed 12 genomic regions under selection pressure involving CNVs which were previously reported to be associated with metabolism energy (SLC5A8), champagne dilution in horses (SLC36A1), and synthesis of polyunsaturated fatty acids (FAT2). Only 10 Middle Eastern horses were tested in this study; therefore, the conclusions are speculative. Our findings are useful to better understanding the evolution and adaptation of Middle Eastern horse breeds.
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Affiliation(s)
- Siavash Salek Ardestani
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Canada
| | - Hossein Mahboudi
- Department of Biotechnology, School of Pharmacy, Alborz University of Medical Sciences, Karaj, Iran
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9
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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: 3] [Impact Index Per Article: 1.0] [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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Tomihara K, Satta K, Matsuzaki S, Yoshitake K, Yamamoto K, Uchiyama H, Yajima S, Futahashi R, Katsuma S, Osanai-Futahashi M, Kiuchi T. Mutations in a β-group of solute carrier gene are responsible for egg and eye coloration of the brown egg 4 (b-4) mutant in the silkworm, Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 137:103624. [PMID: 34333110 DOI: 10.1016/j.ibmb.2021.103624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
The brown egg 4 (b-4) is a recessive mutant in the silkworm (Bombyx mori), whose egg and adult compound eyes exhibit a reddish-brown color instead of normal purple and black, respectively. By double digest restriction-site associated DNA sequencing (ddRAD-seq) analysis, we narrowed down a region linked to the b-4 phenotype to approximately 1.1 Mb that contains 69 predicted gene models. RNA-seq analysis in a b-4 strain indicated that one of the candidate genes had a different transcription start site, which generates a short open reading frame. We also found that exon skipping was induced in the same gene due to an insertion of a transposable element in other two b-4 mutant strains. This gene encoded a putative amino acid transporter that belongs to the β-group of solute carrier (SLC) family and is orthologous to Drosophila eye color mutant gene, mahogany (mah). Accordingly, we named this gene Bmmah. We performed CRISPR/Cas9-mediated gene knockout targeting Bmmah. Several adult moths in generation 0 (G0) had totally or partially reddish-brown compound eyes. We also established three Bmmah knockout strains, all of which exhibit reddish-brown eggs and adult compound eyes. Furthermore, eggs from complementation crosses between the b-4 mutants and the Bmmah knockout mutants also exhibited reddish-brown color, which was similar to the b-4 mutant eggs, indicating that Bmmah is responsible for the b-4 phenotypes.
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Affiliation(s)
- Kenta Tomihara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Katsuya Satta
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shohei Matsuzaki
- Graduate School of Science and Engineering, Ibaraki University, Bunkyo 2-1-1, Mito, Ibaraki 310-8512, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kimiko Yamamoto
- Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Science, National Agriculture and Food Research Organization, Owashi 1-2, Tsukuba, Ibaraki 305-8634, Japan
| | - Hironobu Uchiyama
- NODAI Genome Research Center, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shunsuke Yajima
- NODAI Genome Research Center, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya-ku, Tokyo 156-8502, Japan; Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya-ku, Tokyo 156-8502, Japan
| | - Ryo Futahashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Susumu Katsuma
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Mizuko Osanai-Futahashi
- Graduate School of Science and Engineering, Ibaraki University, Bunkyo 2-1-1, Mito, Ibaraki 310-8512, Japan.
| | - Takashi Kiuchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
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11
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van Deventer R, Rhode C, Marx M, Roodt-Wilding R. Elucidation of coat colour genetics in blue wildebeest. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00126-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Patterson Rosa L, Walker N, Mallicote M, MacKay RJ, Brooks SA. Genomic Association of Chronic Idiopathic Anhidrosis to a Potassium Channel Subunit in a Large Animal Model. J Invest Dermatol 2021; 141:2639-2645.e3. [PMID: 34081968 DOI: 10.1016/j.jid.2021.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 02/01/2023]
Abstract
Similar to humans, the horse relies predominantly on the evaporation of sweat from the skin surface to dissipate excess body heat. Loss of the sweat response or anhidrosis can result in life-threatening hyperthermia. Anhidrosis occurs more frequently in some breeds as well as occurs at an increased frequency among individuals with a family history, suggesting a heritable component to the pathology. Given the natural occurrence and indications of genetic components in the etiology, we utilized genomics to better understand the molecular mechanisms involved in sweat response. We performed a case-control (n = 200) GWAS targeting cases of chronic idiopathic anhidrosis in a controlled genetic background to discover the contributing regions and interrogated gene function for roles in the sweating mechanism. A region containing the KCNE4 gene, which encodes the β-subunit of a potassium channel protein with a possible function in sweat gland outflow, was associated (P = 1.13 × 10-07) with chronic idiopathic anhidrosis through GWAS. A candidate mutation (NC_009149.3:g.11813731A > G, rs68643109) disrupting the KCNE4 protein structure could explain the disease but requires further investigation in larger populations. We show the potential role of ion channels and cellular damage in sweat response, correlating anhidrosis as a possible effect of congenital channelopathy.
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Affiliation(s)
- Laura Patterson Rosa
- Department of Animal Sciences, College of Agriculture and Life Sciences, University of Florida, Gainesville, Florida, USA; UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Neely Walker
- School of Animal Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Martha Mallicote
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Robert J MacKay
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Samantha A Brooks
- Department of Animal Sciences, College of Agriculture and Life Sciences, University of Florida, Gainesville, Florida, USA; UF Genetics Institute, University of Florida, Gainesville, Florida, USA.
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Nielsen MMK, Aryal E, Safari E, Mojsoska B, Jenssen H, Prabhala BK. Current State of SLC and ABC Transporters in the Skin and Their Relation to Sweat Metabolites and Skin Diseases. Proteomes 2021; 9:proteomes9020023. [PMID: 34065737 PMCID: PMC8163169 DOI: 10.3390/proteomes9020023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 01/02/2023] Open
Abstract
With a relatively large surface area (2 m2) and 15% of total body mass, the skin forms the largest organ of the human body. The main functions of the skin include regulation of body temperature by insulation or sweating, regulation of the nervous system, regulation of water content, and protection against external injury. To perform these critical functions, the skin encodes genes for transporters responsible for the cellular trafficking of essential nutrients and metabolites to maintain cellular hemostasis. However, the knowledge on the expression, regulation, and function of these transporters is very limited and needs more work to elucidate how these transporters play a role both in disease progression and in healing. Furthermore, SLC and ABC transporters are understudied, and even less studied in skin. There are sparse reports on relation between transporters in skin and sweat metabolites. This mini review focuses on the current state of SLC and ABC transporters in the skin and their relation to sweat metabolites and skin diseases.
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Affiliation(s)
- Marcus M. K. Nielsen
- Institute of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (M.M.K.N.); (E.A.)
| | - Eva Aryal
- Institute of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (M.M.K.N.); (E.A.)
| | - Elnaz Safari
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran;
| | - Biljana Mojsoska
- Institute of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark; (B.M.); (H.J.)
| | - Håvard Jenssen
- Institute of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark; (B.M.); (H.J.)
| | - Bala Krishna Prabhala
- Institute of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (M.M.K.N.); (E.A.)
- Correspondence:
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14
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Chen Y, Hu S, Liu M, Zhao B, Yang N, Li J, Chen Q, Zhou J, Bao G, Wu X. Analysis of Genome DNA Methylation at Inherited Coat Color Dilutions of Rex Rabbits. Front Genet 2021; 11:603528. [PMID: 33552123 PMCID: PMC7859435 DOI: 10.3389/fgene.2020.603528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/15/2020] [Indexed: 12/02/2022] Open
Abstract
Background: The dilution of color in rabbits is associated with many different genetic mechanisms that form different color groups. A number of previous studies have revealed potential regulatory mechanisms by which epigenetics regulate pigmentation. However, the genome-wide DNA methylation involved in animal coat color dilution remains unknown. Results: We compared genome-wide DNA methylation profiles in Rex rabbit hair follicles in a Chinchilla group (Ch) and a diluted Chinchilla group (DCh) through whole-genome bisulfite sequencing (WGBS). Approximately 3.5% of the cytosine sites were methylated in both groups, of which the CG methylation type was in greatest abundance. In total, we identified 126,405 differentially methylated regions (DMRs) between the two groups, corresponding to 11,459 DMR-associated genes (DMGs). Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that these DMGs were principally involved in developmental pigmentation and Wnt signaling pathways. In addition, two DMRs were randomly selected to verify that the WGBS data were reliable using bisulfite sequencing PCR, and seven DMGs were analyzed to establish the relationship between the level of DNA methylation and mRNA expression using qRT-PCR. Due to the limitation of small sample size, replication of the results with a larger sample size would be important in future studies. Conclusion: These findings provide evidence that there is an association between inherited color dilution and DNA methylation alterations in hair follicles, greatly contributing to our understanding of the epigenetic regulation of rabbit pigmentation.
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Affiliation(s)
- Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Shuaishuai Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ming Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Naisu Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qiuran Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Juan Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guolian Bao
- Animal Husbandry and Veterinary Research Institute Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, China
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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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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: 8] [Impact Index Per Article: 2.0] [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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17
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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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18
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Frameshift Variant in MFSD12 Explains the Mushroom Coat Color Dilution in Shetland Ponies. Genes (Basel) 2019; 10:genes10100826. [PMID: 31635058 PMCID: PMC6827053 DOI: 10.3390/genes10100826] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 01/09/2023] Open
Abstract
Mushroom is a unique coat color phenotype in Shetland Ponies characterized by the dilution of the chestnut coat color to a sepia tone and is hypothesized to be a recessive trait. A genome wide association study (GWAS), utilizing the Affymetrix 670K array (MNEc670k) and a single locus mixed linear model analysis (EMMAX), identified a locus on ECA7 for further investigation (Pcorrected = 2.08 × 10−10). This locus contained a 3 Mb run of homozygosity in the 12 mushroom ponies tested. Analysis of high throughput Illumina sequencing data from one mushroom Shetland pony compared to 87 genomes from horses of various breeds, uncovered a frameshift variant, p.Asp201fs, in the MFSD12 gene encoding the major facilitator superfamily domain containing 12 protein. This variant was perfectly concordant with phenotype in 96 Shetland Ponies (P = 1.15 × 10−22), was identified in the closely related Miniature Horse for which the mushroom phenotype is suspected to occur (fmu = 0.02), and was absent in 252 individuals from seven additional breeds not reported to have the mushroom phenotype. MFSD12 is highly expressed in melanocytes and variants in this gene in humans, mice, and dogs impact pigmentation. Given the role of MFSD12 in melanogenesis, we propose that p.Asp201fs is causal for the dilution observed in mushroom ponies.
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Holl HM, Pflug KM, Yates KM, Hoefs‐Martin K, Shepard C, Cook DG, Lafayette C, Brooks SA. A candidate gene approach identifies variants in
SLC
45A2
that explain dilute phenotypes, pearl and sunshine, in compound heterozygote horses. Anim Genet 2019; 50:271-274. [DOI: 10.1111/age.12790] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2019] [Indexed: 02/06/2023]
Affiliation(s)
- H. M. Holl
- Etalon Inc Menlo Park CA 94025 USA
- Department of Animal Sciences University of Florida Gainesville FL 32607 USA
| | - K. M. Pflug
- Department of Animal Sciences University of Florida Gainesville FL 32607 USA
| | - K. M. Yates
- Department of Animal Sciences University of Florida Gainesville FL 32607 USA
| | | | | | - D. G. Cook
- Etalon Inc Menlo Park CA 94025 USA
- Biology Department Morehead State University Morehead KY 40351 USA
| | | | - S. A. Brooks
- Etalon Inc Menlo Park CA 94025 USA
- Department of Animal Sciences University of Florida Gainesville FL 32607 USA
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20
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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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Gaunitz C, Fages A, Hanghøj K, Albrechtsen A, Khan N, Schubert M, Seguin-Orlando A, Owens IJ, Felkel S, Bignon-Lau O, de Barros Damgaard P, Mittnik A, Mohaseb AF, Davoudi H, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Crubézy E, Benecke N, Olsen S, Brown D, Anthony D, Massy K, Pitulko V, Kasparov A, Brem G, Hofreiter M, Mukhtarova G, Baimukhanov N, Lõugas L, Onar V, Stockhammer PW, Krause J, Boldgiv B, Undrakhbold S, Erdenebaatar D, Lepetz S, Mashkour M, Ludwig A, Wallner B, Merz V, Merz I, Zaibert V, Willerslev E, Librado P, Outram AK, Orlando L. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science 2018; 360:111-114. [DOI: 10.1126/science.aao3297] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/31/2018] [Indexed: 12/28/2022]
Abstract
The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski’s horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.
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22
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Two Variants in SLC24A5 Are Associated with "Tiger-Eye" Iris Pigmentation in Puerto Rican Paso Fino Horses. G3-GENES GENOMES GENETICS 2017; 7:2799-2806. [PMID: 28655738 PMCID: PMC5555483 DOI: 10.1534/g3.117.043786] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A unique eye color, called tiger-eye, segregates in the Puerto Rican Paso Fino (PRPF) horse breed and is characterized by a bright yellow, amber, or orange iris. Pedigree analysis identified a simple autosomal recessive mode of inheritance for this trait. A genome-wide association study (GWAS) with 24 individuals identified a locus on ECA 1 reaching genome-wide significance (Pcorrected = 1.32 × 10−5). This ECA1 locus harbors the candidate gene, Solute Carrier Family 24 (Sodium/Potassium/Calcium Exchanger), Member 5 (SLC24A5), with known roles in pigmentation in humans, mice, and zebrafish. Humans with compound heterozygous mutations in SLC24A5 have oculocutaneous albinism (OCA) type 6 (OCA6), which is characterized by dilute skin, hair, and eye pigmentation, as well as ocular anomalies. Twenty tiger-eye horses were homozygous for a nonsynonymous mutation in exon 2 (p.Phe91Tyr) of SLC24A5 (called here Tiger-eye 1), which is predicted to be deleterious to protein function. Additionally, eight of the remaining 12 tiger-eye horses heterozygous for the p.Phe91Tyr variant were also heterozygous for a 628 bp deletion encompassing all of exon 7 of SLC24A5 (c.875-340_1081+82del), which we will call here the Tiger-eye 2 allele. None of the 122 brown-eyed horses were homozygous for either tiger-eye-associated allele or were compound heterozygotes. Further, neither variant was detected in 196 horses from four related breeds not known to have the tiger-eye phenotype. Here, we propose that two mutations in SLC24A5 affect iris pigmentation in tiger-eye PRPF horses. Further, unlike OCA6 in humans, the Tiger-eye 1 mutation in its homozygous state or as a compound heterozygote (Tiger-eye 1/Tiger-eye 2) does not appear to cause ocular anomalies or a change in coat color in the PRPF horse.
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Lewis SL, Holl HM, Streeter C, Posbergh C, Schanbacher BJ, Place NJ, Mallicote MF, Long MT, Brooks SA. Genomewide association study reveals a risk locus for equine metabolic syndrome in the Arabian horse. J Anim Sci 2017; 95:1071-1079. [PMID: 28380523 DOI: 10.2527/jas.2016.1221] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Equine obesity can cause life-threatening secondary chronic conditions, similar to those in humans and other animal species. Equine metabolic syndrome (EMS), primarily characterized by hyperinsulinemia, is often present in obese horses and ponies. Due to clinical similarities to conditions such as pituitary pars intermedia dysfunction (formerly equine Cushing's disease), conclusive diagnosis of EMS often proves challenging. Aside from changes in diet and exercise, few targeted treatments are available for EMS, emphasizing the need for early identification of at-risk individuals to enable implementation of preventative measures. A genomewide association study (GWAS) using Arabian horses with a history of severe laminitis secondary to EMS revealed significant genetic markers near a single candidate gene () that may play a role in cholesterol homeostasis. The best marker, BIEC2-263524 (chr14:69276814 T > C), was correlated with elevated insulin values and increased frequency of laminitis ( = 0.0024 and = 9.663 × 10, respectively). In a second population of Arabian horses, the BIEC2-263524 marker maintained its associations with higher modified insulin-to-glucose ratio (MIRG) values ( = 0.0056) and BCS ( = 0.0063). Screening of the predicted coding regions by sequencing identified a polymorphic guanine homopolymer and 5 haplotypes in the 3' untranslated region (UTR). An 11 guanine (11-G) allele at was correlated with elevated insulin values in the GWAS population ( = 0.0008) and, in the second population, elevated MIRG and increased BCS > 6.5 ( = 0.0055 and = 0.0162, respectively). The BIEC2-263524-C and the 3' UTR -11(G) polymorphisms were correlated at a 98% frequency, indicating strong linkage disequilibrium across this 150-kb haplotype. Assays for these markers could diagnose horses with a genetic predisposition to develop obesity. Additionally, discovery of FAM174A function may improve our understanding of the etiology of this troubling illness in the horse and warrants investigation of this locus for a role in metabolic- and obesity-related disorders of other species.
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Ji X, Zhao L, Luo H, Zhang X, Jin Y, Liu W. Amino acids suppress the expression of PAT1 on lysosomes via inducing the cleavage of a targeting signal. FEBS Lett 2017; 591:2279-2289. [PMID: 28670736 DOI: 10.1002/1873-3468.12738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/19/2017] [Accepted: 06/21/2017] [Indexed: 11/11/2022]
Abstract
The lysosome-associated transporter proton-coupled amino acid transporter 1 (PAT1) promotes nutrient recycling through releasing luminal amino acids into the cytosol. Using HEK293 cells expressing an EGFP-tagged PAT1 (EGFP-PAT1) as a model, we identified a consensus tyrosine-based targeting signal in the cytosolic N-terminal region of PAT1, which facilitates its expression on the lysosome. Interestingly, this signal can be removed via protein cleavage in an amino acid-sensitive manner. The cleavage is suppressed upon amino acid starvation and is induced by amino acid replenishment. However, amino acid deficiency does not suppress the cleavage of amino acid-binding mutants of EGFP-PAT1. Our data support a mechanism, whereby amino acid binding induces PAT1 cleavage to remove a targeting signal, thus suppressing the expression of PAT1 on the lysosome.
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Affiliation(s)
- Xin Ji
- Key Laboratory of Animal Biotechnology, the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forest University, Yangling, Shaanxi, China
| | - Lingling Zhao
- Key Laboratory of Animal Biotechnology, the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forest University, Yangling, Shaanxi, China
| | - Hongjie Luo
- Key Laboratory of Animal Biotechnology, the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forest University, Yangling, Shaanxi, China
| | - Xiangxiang Zhang
- Key Laboratory of Animal Biotechnology, the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forest University, Yangling, Shaanxi, China
| | - Yaping Jin
- Key Laboratory of Animal Biotechnology, the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forest University, Yangling, Shaanxi, China
| | - Wei Liu
- Key Laboratory of Animal Biotechnology, the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forest University, Yangling, Shaanxi, China
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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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Abstract
Horses are valued for the beauty and variety of colouration and coat patterning. To date, eleven different genes have been characterized that contribute to the variation observed in the horse. Unfortunately, mutations involving pigmentation often lead to deleterious effects in other systems, some of which have been described in the horse. This review focuses on six such pleiotropic effects or associations with pigmentation genes. These include neurological defects (lethal white foal syndrome and lavender foal syndrome), hearing defects, eye disorders (congenital stationary night blindness and multiple congenital ocular anomalies), as well as horse-specific melanoma. The pigmentation phenotype, disorder phenotype, mode of inheritance, genetic or genomic methods utilized to identify the genes involved and, if known, the causative mutations, molecular interactions and other susceptibility loci are discussed. As our understanding of pigmentation in the horse increases, through the use of novel genomic tools, we are likely to unravel yet unknown pleiotropic effects and determine additional interactions between previously discovered loci.
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Affiliation(s)
- R R Bellone
- Department of Biology, University of Tampa, 401 W. Kennedy Blvd., Tampa, FL 33606, USA.
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Jun J, Cho YS, Hu H, Kim HM, Jho S, Gadhvi P, Park KM, Lim J, Paek WK, Han K, Manica A, Edwards JS, Bhak J. Whole genome sequence and analysis of the Marwari horse breed and its genetic origin. BMC Genomics 2014; 15 Suppl 9:S4. [PMID: 25521865 PMCID: PMC4290615 DOI: 10.1186/1471-2164-15-s9-s4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characteristics, including inwardly turned ear tips. It is thought to have originated from the crossbreeding of local Indian ponies with Arabian horses beginning in the 12th century. Results We generated 101 Gb (~30 × coverage) of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. The sequences were mapped to the horse reference genome at a mapping rate of ~98% and with ~95% of the genome having at least 10 × coverage. A total of 5.9 million single nucleotide variations, 0.6 million small insertions or deletions, and 2,569 copy number variation blocks were identified. We confirmed a strong Arabian and Mongolian component in the Marwari genome. Novel variants from the Marwari sequences were annotated, and were found to be enriched in olfactory functions. Additionally, we suggest a potential functional genetic variant in the TSHZ1 gene (p.Ala344>Val) associated with the inward-turning ear tip shape of the Marwari horses. Conclusions Here, we present an analysis of the Marwari horse genome. This is the first genomic data for an Asian breed, and is an invaluable resource for future studies of genetic variation associated with phenotypes and diseases in horses.
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Metzger J, Tonda R, Beltran S, Agueda L, Gut M, Distl O. Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication. BMC Genomics 2014; 15:562. [PMID: 24996778 PMCID: PMC4097168 DOI: 10.1186/1471-2164-15-562] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 06/24/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Domestication has shaped the horse and lead to a group of many different types. Some have been under strong human selection while others developed in close relationship with nature. The aim of our study was to perform next generation sequencing of breed and non-breed horses to provide an insight into genetic influences on selective forces. RESULTS Whole genome sequencing of five horses of four different populations revealed 10,193,421 single nucleotide polymorphisms (SNPs) and 1,361,948 insertion/deletion polymorphisms (indels). In comparison to horse variant databases and previous reports, we were able to identify 3,394,883 novel SNPs and 868,525 novel indels. We analyzed the distribution of individual variants and found significant enrichment of private mutations in coding regions of genes involved in primary metabolic processes, anatomical structures, morphogenesis and cellular components in non-breed horses and in contrast to that private mutations in genes affecting cell communication, lipid metabolic process, neurological system process, muscle contraction, ion transport, developmental processes of the nervous system and ectoderm in breed horses. CONCLUSIONS Our next generation sequencing data constitute an important first step for the characterization of non-breed in comparison to breed horses and provide a large number of novel variants for future analyses. Functional annotations suggest specific variants that could play a role for the characterization of breed or non-breed horses.
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Affiliation(s)
| | | | | | | | | | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany.
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Jensen A, Figueiredo-Larsen M, Holm R, Broberg ML, Brodin B, Nielsen CU. PAT1 (SLC36A1) shows nuclear localization and affects growth of smooth muscle cells from rats. Am J Physiol Endocrinol Metab 2014; 306:E65-74. [PMID: 24222668 DOI: 10.1152/ajpendo.00322.2013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The proton-coupled amino acid transporter 1 (PAT1) is a transporter of amino acids in small intestinal enterocytes. PAT1 is, however, also capable of regulating cell growth and sensing the availability of amino acids in other cell types. The aim of the present study was to investigate the localization and function of PAT1 in smooth muscle cells (SMCs). The PAT1 protein was found in smooth muscles from rat intestine and in the embryonic rat aorta cell line A7r5. Immunolocalization and cellular fractionation studies revealed that the majority of the PAT1 protein located within the cell nucleus of A7r5 cells. These results were confirmed in primary SMCs derived from rat aorta and colon. A 3'-untranslated region of the PAT1 transcript directed the nuclear localization. Neither cellular starvation nor cell division altered the nuclear localization. In agreement, uptake studies of l-proline, a PAT1 substrate, in A7r5 cells suggested an alternative role for PAT1 in SMCs than in transport. To shed light on the function of PAT1 in A7r5 cells, experiments with downregulation of the PAT1 level by use of a siRNA approach were conducted. The growth rates of the cells were evaluated, and knockdown of PAT1 led to induced cellular growth, suggesting a role for PAT1 in regulating cellular proliferation of SMCs.
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MESH Headings
- Amino Acid Transport Systems, Neutral/analysis
- Amino Acid Transport Systems, Neutral/genetics
- Amino Acid Transport Systems, Neutral/physiology
- Animals
- Aorta
- Caco-2 Cells
- Cell Fractionation
- Cell Line
- Cell Nucleus/chemistry
- Cell Proliferation
- Colon
- Embryo, Mammalian
- Gene Expression
- Humans
- Male
- Myocytes, Smooth Muscle/physiology
- Myocytes, Smooth Muscle/ultrastructure
- Proline/metabolism
- RNA, Messenger/analysis
- RNA, Small Interfering/genetics
- RNA, Small Interfering/pharmacology
- Rats
- Rats, Wistar
- Symporters/analysis
- Symporters/genetics
- Symporters/physiology
- Transfection
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Affiliation(s)
- Anne Jensen
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; and
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Petersen JL, Mickelson JR, Rendahl AK, Valberg SJ, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Capomaccio S, Cappelli K, Cothran EG, Distl O, Fox-Clipsham L, Graves KT, Guérin G, Haase B, Hasegawa T, Hemmann K, Hill EW, Leeb T, Lindgren G, Lohi H, Lopes MS, McGivney BA, Mikko S, Orr N, Penedo MCT, Piercy RJ, Raekallio M, Rieder S, Røed KH, Swinburne J, Tozaki T, Vaudin M, Wade CM, McCue ME. Genome-wide analysis reveals selection for important traits in domestic horse breeds. PLoS Genet 2013; 9:e1003211. [PMID: 23349635 PMCID: PMC3547851 DOI: 10.1371/journal.pgen.1003211] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/15/2012] [Indexed: 02/04/2023] Open
Abstract
Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.
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Affiliation(s)
- Jessica L Petersen
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA.
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Thwaites DT, Anderson CMH. The SLC36 family of proton-coupled amino acid transporters and their potential role in drug transport. Br J Pharmacol 2012; 164:1802-16. [PMID: 21501141 DOI: 10.1111/j.1476-5381.2011.01438.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Members of the solute carrier (SLC) 36 family are involved in transmembrane movement of amino acids and derivatives. SLC36 consists of four members. SLC36A1 and SLC36A2 both function as H(+) -coupled amino acid symporters. SLC36A1 is expressed at the luminal surface of the small intestine but is also commonly found in lysosomes in many cell types (including neurones), suggesting that it is a multipurpose carrier with distinct roles in different cells including absorption in the small intestine and as an efflux pathway following intralysosomal protein breakdown. SLC36A1 has a relatively low affinity (K(m) 1-10 mM) for its substrates, which include zwitterionic amino and imino acids, heterocyclic amino acids and amino acid-based drugs and derivatives used experimentally and/or clinically to treat epilepsy, schizophrenia, bacterial infections, hyperglycaemia and cancer. SLC36A2 is expressed at the apical surface of the human renal proximal tubule where it functions in the reabsorption of glycine, proline and hydroxyproline. SLC36A2 also transports amino acid derivatives but has a narrower substrate selectivity and higher affinity (K(m) 0.1-0.7 mM) than SLC36A1. Mutations in SLC36A2 lead to hyperglycinuria and iminoglycinuria. SLC36A3 is expressed only in testes and is an orphan transporter with no known function. SLC36A4 is widely distributed at the mRNA level and is a high-affinity (K(m) 2-3 µM) transporter for proline and tryptophan. We have much to learn about this family of transporters, but from current knowledge, it seems likely that their function will influence the pharmacokinetic profiles of amino acid-based drugs by mediating transport in both the small intestine and kidney.
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Affiliation(s)
- David T Thwaites
- Epithelial Research Group, Institute for Cell & Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
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Doan R, Cohen ND, Sawyer J, Ghaffari N, Johnson CD, Dindot SV. Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare. BMC Genomics 2012; 13:78. [PMID: 22340285 PMCID: PMC3309927 DOI: 10.1186/1471-2164-13-78] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 02/17/2012] [Indexed: 11/24/2022] Open
Abstract
Background The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. Results Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse's genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. Conclusions This is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids.
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Affiliation(s)
- Ryan Doan
- Department of Veterinary Pathobiology, Texas A&M University College of Veterinary Medicine and Biomedical Sciences, College Station, TX, USA
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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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Abstract
Amino acids are essential building blocks of all mammalian cells. In addition to their role in protein synthesis, amino acids play an important role as energy fuels, precursors for a variety of metabolites and as signalling molecules. Disorders associated with the malfunction of amino acid transporters reflect the variety of roles that they fulfil in human physiology. Mutations of brain amino acid transporters affect neuronal excitability. Mutations of renal and intestinal amino acid transporters affect whole-body homoeostasis, resulting in malabsorption and renal problems. Amino acid transporters that are integral parts of metabolic pathways reduce the function of these pathways. Finally, amino acid uptake is essential for cell growth, thereby explaining their role in tumour progression. The present review summarizes the involvement of amino acid transporters in these roles as illustrated by diseases resulting from transporter malfunction.
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Greenwood AK, Jones FC, Chan YF, Brady SD, Absher DM, Grimwood J, Schmutz J, Myers RM, Kingsley DM, Peichel CL. The genetic basis of divergent pigment patterns in juvenile threespine sticklebacks. Heredity (Edinb) 2011; 107:155-66. [PMID: 21304547 DOI: 10.1038/hdy.2011.1] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Animal pigment patterns are important for a range of functions, including camouflage and communication. Repeating pigment patterns, such as stripes, bars and spots have been of particular interest to developmental and theoretical biologists, but the genetic basis of natural variation in such patterns is largely unexplored. In this study, we identify a difference in a periodic pigment pattern among juvenile threespine sticklebacks (Gasterosteus aculeatus) from different environments. Freshwater sticklebacks exhibit prominent vertical bars that visually break up the body shape, but sticklebacks from marine populations do not. We hypothesize that these distinct pigment patterns are tuned to provide crypsis in different habitats. This phenotypic difference is widespread and appears in most of the freshwater populations that we sampled. We used quantitative trait locus (QTL) mapping in freshwater-marine F2 hybrids to elucidate the genetic architecture underlying divergence in this pigmentation pattern. We identified two QTL that were significantly associated with variation in barring. Interestingly, these QTL were associated with two distinct aspects of the pigment pattern: melanophore number and overall pigment level. We compared the QTL locations with positions of known pigment candidate genes in the stickleback genome. We also identified two major QTL for juvenile body size, providing new insights into the genetic basis of juvenile growth rates in natural populations. In summary, although there is a growing literature describing simple genetic bases for adaptive coloration differences, this study emphasizes that pigment patterns can also possess a more complex genetic architecture.
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Affiliation(s)
- A K Greenwood
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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Goberdhan DCI. Intracellular amino acid sensing and mTORC1-regulated growth: new ways to block an old target? CURRENT OPINION IN INVESTIGATIONAL DRUGS (LONDON, ENGLAND : 2000) 2010; 11:1360-1367. [PMID: 21154118 PMCID: PMC3044466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Mammalian target of rapamycin (mTOR) complex 1 (mTORC1) is a multicomponent, nutrient-sensitive protein that is implicated in a wide range of major human diseases. mTORC1 responds to both growth factors and changes in local amino acid levels. Until recently, the intracellular amino acid-sensing mechanism that regulates mTORC1 had remained unexplored. However, studies in human cells in culture have demonstrated that in response to amino acid stimulation, mTOR (a conserved member of the PI3K superfamily) is shuttled to late endosomal and lysosomal compartments, where it binds the Ragulator-Rag complex and is assembled into active mTORC1. Members of the proton-assisted amino acid transporter (PAT/SLC36) family have been identified as critical components of the amino acid-sensing system that regulates mTORC1 present in endosomal and lysosomal membranes. These discoveries not only highlight several new potential drug targets that could impact selectively on mTORC1 activity in cancer cells, but also provide novel insights into the strategies used by such cells to outcompete their neighbors in growth factor- and nutrient-depleted conditions. In this review, recent mechanistic insights into how mTORC1 activity is controlled by amino acids and the potential for the selective targeting this regulatory input are discussed.
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Affiliation(s)
- Deborah C I Goberdhan
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, UK.
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Yang H, Ma YH, Li B, Dugarjaviin M. [Progress on horse genome project]. YI CHUAN = HEREDITAS 2010; 32:211-8. [PMID: 20233697 DOI: 10.3724/sp.j.1005.2010.00211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
There is unique genetic information belonging to various kinds of living beings. Understanding of the formation process of organisms and a variety of vital movement is associated with the achievements of genome study. As horse has a notable health condition and great record of the genealogy in the world, thus it becomes a valuable model animal for studying life science. Despite of a late start, the map of the horse genome has undergone unprecedented expansion during the last few years. The current progresses of the horse genome, including genetic map, physical map, comparative genomic map, and functional genomics, were reviewed in this paper. The maps are currently used worldwide to discover genes associated with various traits of significance in horse including general health, disease resistance, reproduction, fertility, athletic performance, phenotypic characteristics like coat color, etc. The results are believed to provide new ideas and approaches for prevention, diagnostics, and therapeutic for horses, and also better foundation of breed selection and equine genetic breeding.
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Affiliation(s)
- Hong Yang
- College of Animal Science and Animal Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China.
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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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Characterization of equine and other vertebrate TLR3, TLR7, and TLR8 genes. Immunogenetics 2009; 61:529-39. [DOI: 10.1007/s00251-009-0381-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Accepted: 06/08/2009] [Indexed: 01/15/2023]
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Menotti-Raymond M, David VA, Eizirik E, Roelke ME, Ghaffari H, O'Brien SJ. Mapping of the domestic cat "SILVER" coat color locus identifies a unique genomic location for silver in mammals. J Hered 2009; 100 Suppl 1:S8-13. [PMID: 19398491 PMCID: PMC3307065 DOI: 10.1093/jhered/esp018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2008] [Revised: 03/06/2009] [Accepted: 03/16/2009] [Indexed: 11/12/2022] Open
Abstract
The SILVER locus has been mapped in the domestic cat, identifying a unique genomic location distinct from that of any known reported gene associated with silver or hypopigmentation in mammals. A demonstrated lack of linkage to SILV, the strong candidate gene for silver, led to the initiation of a genome scan utilizing 2 pedigrees segregating for silver coat color. Linkage mapping defined a genomic region for SILVER as a 3.3-Mb region, (95.87-99.21 Mb) on chromosome D2, (peak logarithm of the odds = 10.5, = 0), which displays conserved synteny to a genomic interval between 118.58 and 121.85 Mb on chromosome 10 in the human genome. In the domestic cat, mutations at the SILVER locus suppress the development of pigment in the hair, but in contrast to other mammalian silver variants, there is an apparently greater influence on the production of pheomelanin than eumelanin pigment. The mapping of a novel locus for SILVER offers much promise in identifying a gene that may help elucidate aspects of pheomelanogenesis, a pathway that has been very elusive, and illustrates the promise of the cat genome project in increasing our understanding of basic biological processes of general relevance for mammals.
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Affiliation(s)
- Marilyn Menotti-Raymond
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MD 21702, USA.
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He L, Vasiliou K, Nebert DW. Analysis and update of the human solute carrier (SLC) gene superfamily. Hum Genomics 2009; 3:195-206. [PMID: 19164095 PMCID: PMC2752037 DOI: 10.1186/1479-7364-3-2-195] [Citation(s) in RCA: 233] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The solute-carrier gene (SLC) superfamily encodes membrane-bound transporters. The SLC superfamily comprises 55 gene families having at least 362 putatively functional protein-coding genes. The gene products include passive transporters, symporters and antiporters, located in all cellular and organelle membranes, except, perhaps, the nuclear membrane. Transport substrates include amino acids and oligopeptides, glucose and other sugars, inorganic cations and anions (H+, HCO3-, Cl-, Na+, K+, Ca2+, Mg2+, PO43-, HPO42-, H2PO4-, SO42-, C2O42-, OH-,CO32-), bile salts, carboxylate and other organic anions, acetyl coenzyme A, essential metals, biogenic amines, neurotransmitters, vitamins, fatty acids and lipids, nucleosides, ammonium, choline, thyroid hormone and urea. Contrary to gene nomenclature commonly assigned on the basis of evolutionary divergence http://www.genenames.org/, the SLC gene superfamily has been named based largely on transporter function by proteins having multiple transmembrane domains. Whereas all the transporters exist for endogenous substrates, it is likely that drugs, non-essential metals and many other environmental toxicants are able to 'hitch-hike' on one or another of these transporters, thereby enabling these moieties to enter (or leave) the cell. Understanding and characterising the functions of these transporters is relevant to medicine, genetics, developmental biology, pharmacology and cancer chemotherapy.
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Affiliation(s)
- Lei He
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA 02114, USA
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