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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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Scott ML, John EE, Bellone RR, Ching JCH, Loewen ME, Sandmeyer LS, Grahn BH, Forsyth GW. Redundant contribution of a Transient Receptor Potential cation channel Member 1 exon 11 single nucleotide polymorphism to equine congenital stationary night blindness. BMC Vet Res 2016; 12:121. [PMID: 27329127 PMCID: PMC4915136 DOI: 10.1186/s12917-016-0745-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 06/14/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Congenital stationary night-blindness (CSNB) is a recessive autosomal defect in low-light vision in Appaloosa and other horse breeds. This condition has been mapped by linkage analysis to a gene coding for the Transient Receptor Potential cation channel Member 1 (TRPM1). TRPM1 is normally expressed in the ON-bipolar cells of the inner nuclear layer of the retina. Down-regulation of TRPM1 expression in CSNB results from a transposon-like insertion in intron 1 of the TRPM1 gene. Stop transcription signals in this transposon significantly reduce TRPM1 primary transcript levels in CSNB horses. This study describes additional contributions by a second mutation of the TRPM1 gene, the ECA1 108,249,293 C > T SNP, to down-regulation of transcription of the TRPM1 gene in night-blind horses. This TRPM1 SNP introduces a consensus binding site for neuro-oncological ventral antigen 1 (Nova-1) protein in the primary transcript. Nova-1 binding disrupts normal splicing signals, producing unstable, non-functional mRNA transcripts. RESULTS Retinal bipolar cells express both TRPM1 and Nova-1 proteins. In vitro addition of Nova-1 protein retards electrophoretic migration of TRPM1 RNA containing the ECA1 108,249,293 C > T SNP. Up-regulating Nova-1 expression in primary cultures of choroidal melanocytes carrying the intron 11 SNP caused an average log 2-fold reduction of ~6 (64-fold) of TRPM1 mRNA expression. CONCLUSIONS These finding suggest that the equine TRPM1 SNP can act independently to reduce survival of TRPM1 mRNA escaping the intron 1 transcriptional stop signals in CSNB horses. Coexistence and co-inheritance of two independent TRPM1 mutations across 1000 equine generations suggests a selective advantage for the apparently deleterious CSNB trait.
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Affiliation(s)
- Michelle L Scott
- Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Emily E John
- Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | | | - John C H Ching
- Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Matthew E Loewen
- Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Lynne S Sandmeyer
- Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Bruce H Grahn
- Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - George W Forsyth
- Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada.
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Ludwig A, Reissmann M, Benecke N, Bellone R, Sandoval-Castellanos E, Cieslak M, Fortes GG, Morales-Muñiz A, Hofreiter M, Pruvost M. Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130386. [PMID: 25487337 DOI: 10.1098/rstb.2013.0386] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Leopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli-Kanligecit (Turkey) dating to 2700-2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times.
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Affiliation(s)
- Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Monika Reissmann
- Department for Crop and Animal Sciences, Humboldt University Berlin, Berlin, Germany
| | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, Berlin, Germany
| | - Rebecca Bellone
- Department of Population Health and Reproduction and the Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
| | | | - Michael Cieslak
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Gloria G Fortes
- Department of Biology, University of York, Heslington, York, UK Instituto Universitario de Xeología (IUX), A Coruña, Spain
| | | | - Michael Hofreiter
- Department of Biology, University of York, Heslington, York, UK Adaptive and Evolutionary Genomics, Institute for Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Strasse 24-24, 14476 Potsdam, Germany
| | - Melanie Pruvost
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany Department of Natural Sciences, German Archaeological Institute, Berlin, Germany Institut Jacques Monod, UMR 7592 CNRS, Université Paris Diderot, Paris, 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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Congenital stationary night blindness: An analysis and update of genotype–phenotype correlations and pathogenic mechanisms. Prog Retin Eye Res 2015; 45:58-110. [DOI: 10.1016/j.preteyeres.2014.09.001] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/25/2014] [Accepted: 09/30/2014] [Indexed: 01/18/2023]
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Fritz KL, Kaese HJ, Valberg SJ, Hendrickson JA, Rendahl AK, Bellone RR, Dynes KM, Wagner ML, Lucio MA, Cuomo FM, Brinkmeyer-Langford CL, Skow LC, Mickelson JR, Rutherford MS, McCue ME. Genetic risk factors for insidious equine recurrent uveitis in Appaloosa horses. Anim Genet 2014; 45:392-9. [PMID: 24467435 DOI: 10.1111/age.12129] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2013] [Indexed: 11/29/2022]
Abstract
Appaloosa horses are predisposed to equine recurrent uveitis (ERU), an immune-mediated disease characterized by recurring inflammation of the uveal tract in the eye, which is the leading cause of blindness in horses. Nine genetic markers from the ECA1 region responsible for the spotted coat color of Appaloosa horses, and 13 microsatellites spanning the equine major histocompatibility complex (ELA) on ECA20, were evaluated for association with ERU in a group of 53 Appaloosa ERU cases and 43 healthy Appaloosa controls. Three markers were significantly associated (corrected P-value <0.05): a SNP within intron 11 of the TRPM1 gene on ECA1, an ELA class I microsatellite located near the boundary of the ELA class III and class II regions and an ELA class II microsatellite located in intron 1 of the DRA gene. Association between these three genetic markers and the ERU phenotype was confirmed in a second population of 24 insidious ERU Appaloosa cases and 16 Appaloosa controls. The relative odds of being an ERU case for each allele of these three markers were estimated by fitting a logistic mixed model with each of the associated markers independently and with all three markers simultaneously. The risk model using these markers classified ~80% of ERU cases and 75% of controls in the second population as moderate or high risk, and low risk respectively. Future studies to refine the associations at ECA1 and ELA loci and identify functional variants could uncover alleles conferring susceptibility to ERU in Appaloosa horses.
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Affiliation(s)
- K L Fritz
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, 55108, USA
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Bellone RR, Holl H, Setaluri V, Devi S, Maddodi N, Archer S, Sandmeyer L, Ludwig A, Foerster D, Pruvost M, Reissmann M, Bortfeldt R, Adelson DL, Lim SL, Nelson J, Haase B, Engensteiner M, Leeb T, Forsyth G, Mienaltowski MJ, Mahadevan P, Hofreiter M, Paijmans JLA, Gonzalez-Fortes G, Grahn B, Brooks SA. Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse. PLoS One 2013; 8:e78280. [PMID: 24167615 PMCID: PMC3805535 DOI: 10.1371/journal.pone.0078280] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/10/2013] [Indexed: 12/21/2022] Open
Abstract
Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ2=1022.00, p<<0.0005), and CSNB, testing 43 horses (χ2=43, p<<0.0005). The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder.
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Affiliation(s)
- Rebecca R. Bellone
- Department of Biology, University of Tampa, Tampa, Florida, United States of America
- * E-mail:
| | - Heather Holl
- Department of Animal Science, Cornell University, Ithaca, New York, United States of America
| | - Vijayasaradhi Setaluri
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Sulochana Devi
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Nityanand Maddodi
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | | | - Lynne Sandmeyer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Daniel Foerster
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Melanie Pruvost
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Epigenomic and Palaeogenomic Group, Institut Jacques Monod, Paris, France
| | - Monika Reissmann
- Department of Breeding Biology and Molecular Genetics, Humboldt University Berlin, Berlin, Germany
| | - Ralf Bortfeldt
- Department of Breeding Biology and Molecular Genetics, Humboldt University Berlin, Berlin, Germany
| | - David L. Adelson
- School of Molecular and Biomedical Science, the University of Adelaide, South Australia, Australia
| | - Sim Lin Lim
- School of Molecular and Biomedical Science, the University of Adelaide, South Australia, Australia
| | - Janelle Nelson
- Department of Biology, University of Tampa, Tampa, Florida, United States of America
| | - Bianca Haase
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | | | - Tosso Leeb
- Institute of Genetics, University of Bern, Bern, Switzerland
| | - George Forsyth
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Michael J. Mienaltowski
- Department of Molecular Pharmacology & Physiology, College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Padmanabhan Mahadevan
- Department of Biology, University of Tampa, Tampa, Florida, United States of America
| | | | | | | | - Bruce Grahn
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Samantha A. Brooks
- Department of Animal Science, Cornell University, Ithaca, New York, United States of America
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Haase B, Signer-Hasler H, Binns MM, Obexer-Ruff G, Hauswirth R, Bellone RR, Burger D, Rieder S, Wade CM, Leeb T. Accumulating mutations in series of haplotypes at the KIT and MITF loci are major determinants of white markings in Franches-Montagnes horses. PLoS One 2013; 8:e75071. [PMID: 24098679 PMCID: PMC3787084 DOI: 10.1371/journal.pone.0075071] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 07/24/2013] [Indexed: 11/18/2022] Open
Abstract
Coat color and pattern variations in domestic animals are frequently inherited as simple monogenic traits, but a number are known to have a complex genetic basis. While the analysis of complex trait data remains a challenge in all species, we can use the reduced haplotypic diversity in domestic animal populations to gain insight into the genomic interactions underlying complex phenotypes. White face and leg markings are examples of complex traits in horses where little is known of the underlying genetics. In this study, Franches-Montagnes (FM) horses were scored for the occurrence of white facial and leg markings using a standardized scoring system. A genome-wide association study (GWAS) was performed for several white patterning traits in 1,077 FM horses. Seven quantitative trait loci (QTL) affecting the white marking score with p-values p≤10(-4) were identified. Three loci, MC1R and the known white spotting genes, KIT and MITF, were identified as the major loci underlying the extent of white patterning in this breed. Together, the seven loci explain 54% of the genetic variance in total white marking score, while MITF and KIT alone account for 26%. Although MITF and KIT are the major loci controlling white patterning, their influence varies according to the basic coat color of the horse and the specific body location of the white patterning. Fine mapping across the MITF and KIT loci was used to characterize haplotypes present. Phylogenetic relationships among haplotypes were calculated to assess their selective and evolutionary influences on the extent of white patterning. This novel approach shows that KIT and MITF act in an additive manner and that accumulating mutations at these loci progressively increase the extent of white markings.
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Affiliation(s)
- Bianca Haase
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- * E-mail:
| | - Heidi Signer-Hasler
- Department of Agriculture, Forestry, Food Science and Management, Bern University of Applied Science, Zollikofen, Switzerland
| | | | | | - Regula Hauswirth
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rebecca R. Bellone
- Department of Biology, University of Tampa, Tampa, Florida, United States of America
| | - Dominik Burger
- Swiss Institute of Equine Medicine, ALP-Haras and University of Bern, Avenches, Switzerland
| | - Stefan Rieder
- Agroscope ALP-Haras Research Station, Swiss National Stud Farm, Avenches, Switzerland
| | - Claire M. Wade
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
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Sandmeyer LS, Bellone RR, Archer S, Bauer BS, Nelson J, Forsyth G, Grahn BH. Congenital stationary night blindness is associated with the leopard complex in the Miniature Horse. Vet Ophthalmol 2011; 15:18-22. [PMID: 22051042 DOI: 10.1111/j.1463-5224.2011.00903.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To determine if congenital stationary night blindness (CSNB) exists in the Miniature Horse in association with leopard complex spotting patterns (LP), and to investigate if CSNB in the Miniature Horse is associated with three single nucleotide polymorphisms (SNPs) in the region of TRPM1 that are highly associated with CSNB and LP in Appaloosas. ANIMALS STUDIED Three groups of Miniature Horses were studied based on coat patterns suggestive of LP/LP (n=3), LP/lp (n=4), and lp/lp genotype (n=4). PROCEDURES Horses were categorized based on phenotype as well as pedigree analysis as LP/LP, LP/lp, and lp/lp. Neurophthalmic examination, slit-lamp biomicroscopy, indirect ophthalmoscopy, and scotopic flash electroretinography were performed on all horses. Hair samples were processed for DNA analysis. Three SNPs identified and associated with LP and CSNB in the Appaloosa were investigated for association with LP and CSNB in these Miniature Horses. RESULTS All horses in the LP/LP group were affected by CSNB, while none in the LP/lp or lp/lp groups were affected. All three SNPs were completely associated with LP genotype (χ(2) = 22, P << 0.0005) and CSNB status (χ(2) =11, P<0.0005). CONCLUSIONS The Miniature Horse breed is affected by CSNB and it appears to be associated with LP as in the Appaloosa breed. The SNPs tested could be used as a DNA test for CSNB until the causative mutation is determined.
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Affiliation(s)
- Lynne S Sandmeyer
- Department of Small Animal Clinical Sciences, University of Saskatchewan, Quill Lake, Saskatchewan, Canada.
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