90 results on '"Menotti-Raymond M"'
Search Results
2. Mapping of Diabetes Susceptibility Loci in a Domestic Cat Breed with an Unusually High Incidence of Diabetes Mellitus.
- Author
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Balmer, L, O'Leary, CA, Menotti-Raymond, M, David, V, O'Brien, S, Penglis, B, Hendrickson, S, Reeves-Johnson, M, Gottlieb, S, Fleeman, L, Vankan, D, Rand, J, Morahan, G, Balmer, L, O'Leary, CA, Menotti-Raymond, M, David, V, O'Brien, S, Penglis, B, Hendrickson, S, Reeves-Johnson, M, Gottlieb, S, Fleeman, L, Vankan, D, Rand, J, and Morahan, G
- Abstract
Genetic variants that are associated with susceptibility to type 2 diabetes (T2D) are important for identification of individuals at risk and can provide insights into the molecular basis of disease. Analysis of T2D in domestic animals provides both the opportunity to improve veterinary management and breeding programs as well as to identify novel T2D risk genes. Australian-bred Burmese (ABB) cats have a 4-fold increased incidence of type 2 diabetes (T2D) compared to Burmese cats bred in the United States. This is likely attributable to a genetic founder effect. We investigated this by performing a genome-wide association scan on ABB cats. Four SNPs were associated with the ABB T2D phenotype with p values <0.005. All exons and splice junctions of candidate genes near significant single-nucleotide polymorphisms (SNPs) were sequenced, including the genes DGKG, IFG2BP2, SLC8A1, E2F6, ETV5, TRA2B and LIPH. Six candidate polymorphisms were followed up in a larger cohort of ABB cats with or without T2D and also in Burmese cats bred in America, which exhibit low T2D incidence. The original SNPs were confirmed in this cohort as associated with the T2D phenotype, although no novel coding SNPs in any of the seven candidate genes showed association with T2D. The identification of genetic markers associated with T2D susceptibility in ABB cats will enable preventative health strategies and guide breeding programs to reduce the prevalence of T2D in these cats.
- Published
- 2020
3. Tyrosinase and Tyrosinase Related Protein 1 Alleles Specify Domestic Cat Coat Color Phenotypes of the albino and brown Loci
- Author
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Schmidt-Küntzel, A., Eizirik, E., OʼBrien, S. J., and Menotti-Raymond, M.
- Published
- 2005
4. Feline Deafness
- Author
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Ryugo, D.K. and Menotti-Raymond, M.
- Subjects
Hearing Loss, Sensorineural ,Cats ,Evoked Potentials, Auditory, Brain Stem ,Animals ,Ear ,Deafness ,Presbycusis ,Cat Diseases ,Ear Diseases ,Small Animals ,Article - Abstract
Cats have among the best hearing of all mammals in that they are extremely sensitive to a broad range of frequencies. The ear is a highly complex structure that is delicately balanced in terms of its biochemistry, types of receptors, ion channels, mechanical properties, and cellular organization. Sensorineural deafness is caused by "flawed" genes that are inherited from one or both parents. Hearing loss can also be acquired as a result of noise trauma from industrialized environment, viral infection, or blunt trauma. To date, it is not practical to intervene and attempt to correct these forms of deafness in cats.
- Published
- 2012
5. Second-generation integrated genetic linkage/radiation hybrid maps of the domestic cat (Felis catus)
- Author
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Menotti-Raymond, M., David, V. A., Chen, Z. Q., Menotti, K. A., Sun, S., Schaffer, A. A., Agarwala, R., Tomlin, J. F., O'Brien, S. J., and Murphy, W. J.
- Subjects
Heredity -- Genetic aspects ,Heredity -- Research ,Cats -- Genetic aspects ,Genetic research -- Analysis ,Radiation -- Physiological aspects ,Chromosome mapping -- Analysis ,Biological sciences - Abstract
Research has been conducted on genetic linkage in domestic cats. The authors report the construction of the second-generation integrated genetic linkage and radiation hybrid maps in domestic cats with marker concordance and near-full genome coverage.
- Published
- 2003
6. The population origins and expansion of feral cats in Australia
- Author
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Spencer, P.B.S., Yurchenko, A.A., David, V.A., Scott, R., Koepfli, K-P, Driscoll, C., O’Brien, S.J., Menotti-Raymond, M., Spencer, P.B.S., Yurchenko, A.A., David, V.A., Scott, R., Koepfli, K-P, Driscoll, C., O’Brien, S.J., and Menotti-Raymond, M.
- Abstract
The historical literature suggests that in Australia, the domestic cat (Felis catus) had a European origin [similar to 200 years before present (ybp)], but it is unclear if cats arrived from across the Asian land bridge contemporaneously with the dingo (4000 ybp), or perhaps immigrated similar to 40 000 ybp in association with Aboriginal settlement from Asia. The origin of cats in Australia is important because the continent has a complex and ancient faunal assemblage that is dominated by endemic rodents and marsupials and lacks the large placental carnivores found on other large continents. Cats are now ubiquitous across the entire Australian continent and have been implicit in the range contraction or extinction of its small to medium sized (<3.5 kg) mammals. We analyzed the population structure of 830 cats using 15 short tandem repeat (STR) genomic markers. Their origin appears to come exclusively from European founders. Feral cats in continental Australia exhibit high genetic diversity in comparison with the low diversity found in populations of feral cats living on islands. The genetic structure is consistent with a rapid westerly expansion from eastern Australia and a limited expansion in coastal Western Australia. Australian cats show modest if any population structure and a close genetic alignment with European feral cats as compared to cats from Asia, the Christmas and Cocos (Keeling) Islands (Indian Ocean), and European wildcats (F. silvestris silvestris).
- Published
- 2016
7. The Near Eastern Origin of Cat Domestication
- Author
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Driscoll, C.A., Menotti-Raymond, M., Roca, A.L., Hupe, K., Johnson, W.E., Geffen, E., Harley, E.H., Delibes, M., Pontier, D., Kitchener, A.C., Yamaguchi, N., O'Brien, S.J., Macdonald, D.W., Ecoépidémiologie évolutionniste, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT] - Published
- 2007
8. Development of MHC-Linked Microsatellite Markers in the Domestic Cat and Their Use to Evaluate MHC Diversity in Domestic Cats, Cheetahs, and Gir Lions
- Author
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Morris, K. M., primary, Kirby, K., additional, Beatty, J. A., additional, Barrs, V. R., additional, Cattley, S., additional, David, V., additional, O'Brien, S. J., additional, Menotti-Raymond, M., additional, and Belov, K., additional
- Published
- 2014
- Full Text
- View/download PDF
9. Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome
- Author
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Menotti-Raymond, M., primary, David, V.A., additional, Agarwala, R., additional, Schäffer, A.A., additional, Stephens, R., additional, O’Brien, S.J., additional, and Murphy, W.J., additional
- Published
- 2003
- Full Text
- View/download PDF
10. Evolutionary Conservation of Ten Microsatellite Loci in Four Species of Felidae
- Author
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Menotti-Raymond, M. A., primary and O'Brien, S. J., additional
- Published
- 1995
- Full Text
- View/download PDF
11. Dating the genetic bottleneck of the African cheetah.
- Author
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Menotti-Raymond, M, primary and O'Brien, S J, additional
- Published
- 1993
- Full Text
- View/download PDF
12. Characterization of the structure and evolution of the Adh region of Drosophila hydei.
- Author
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Menotti-Raymond, M, primary, Starmer, W T, additional, and Sullivan, D T, additional
- Published
- 1991
- Full Text
- View/download PDF
13. Tyrosinase and Tyrosinase Related Protein I Alleles Specify Domestic Cat Coat Color Phenotypes of the albino and brown Loci.
- Author
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Schmidt-Küntzel, A., Eizirik, E., O'Brien, S. J., Menotti-Raymond, M., and O'Brien, Stephen J.
- Subjects
PHENOL oxidase ,ANIMAL coloration ,NUCLEOTIDE sequence ,GENETIC code ,CHROMOSOMES ,CATS - Abstract
The genes encoding enzymes of the tyrosinase family are strong candidates for coat color variation in mammals. To investigate their influence in domestic cat coat color, we determined the complete nucleotide coding sequence of the domestic cat genes tyrosinase (TYR)--a plausible candidate gene for the albino (C) locus, and tyrosinase related protein 1 (TYRP1)--a candidate gene for the brown (B) locus. Sequence variants between individuals exhibiting variation in pigmentation were submitted to association studies. In TYR, two nonsynonymous substitutions encoding TYR-G301R and TYR-G227W were associated with the siamese and burmese phenotypes of the albino locus, respectively. TYRP1 was mapped on chromosome D4 within 5 cM of a highly polymorphic microsatellite, previously found to be fixed in a cat breed selected for the chocolate (b) allele of the B locus, which reinforced TYRP1 as a candidate gene for the B locus in the domestic cat. Two DNA polymorphisms, one leading to a TYRP1-A3G substitution in the signal peptide and another to an in-frame insertion TYRP1-421ins17/18 caused by a donor splice site mutation in intron 6, were associated with the chocolate (b) allele. A premature UAG stop codon at position 100 of TYRP1 was associated with a second allele of the B locus, cinnamon (b¹). The results provide very strong evidence that the specific nucleotide variants of feline TYR (chromosome D1) are causative of the siamese (c
s ) and burmese (cb ) alleles of the albino locus, as well as nucleotide variants of TYRP1 (chromosome D4) as specifying the chocolate (b) and cinnamon (b¹) alleles of the B locus. [ABSTRACT FROM AUTHOR]- Published
- 2005
- Full Text
- View/download PDF
14. A radiation hybrid map of the cat genome: implications for comparative mapping.
- Author
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Murphy, W J, Sun, S, Chen, Z, Yuhki, N, Hirschmann, D, Menotti-Raymond, M, and O'Brien, S J
- Abstract
Ordered gene maps of mammalian species are becoming increasingly valued in assigning gene variants to function in human and animal models, as well as recapitulating the natural history of genome organization. To extend this power to the domestic cat, a radiation hybrid (RH) map of the cat was constructed integrating 424 Type I-coding genes with 176 microsatellite markers, providing coverage over all 20 feline chromosomes. Alignment of parallel RH maps of human and cat reveal 100 conserved segments ordered (CSOs) between the species, nearly three times the number observed with reciprocal chromosome painting analyses. The observed number is equivalent to theoretical predictions of the number of conserved segments to be found between cat and human, implying that 300-400 Type I gene markers is sufficient to reveal nearly all conserved segments for species that exhibit the most frequently observed "slow" rate of genome reorganization. The cat-human RH map comparisons provide a new genomic tool for comparative gene mapping in the cat and related Felidae, and provide confirmation that the cat genome organization is remarkably conserved compared with human. These data demonstrate that ordered RH-based gene maps provide the most precise assessment of comparing genomes, short of contig construction or full-sequence determination.
- Published
- 2000
15. Unusual molecular evolution of an Adh pseudogene in Drosophila.
- Author
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Sullivan, D T, Starmer, W T, Curtiss, S W, Menotti-Raymond, M, and Yum, J
- Abstract
The Adh locus in Drosophila species which are members of the repleta group contains products of one or two duplication events. In all species examined to date one of the Adh genes is now a pseudogene, since mutations have rendered these genes incapable of being translated into a functional alcohol dehydrogenase. These pseudogenes contain introns in the standard Adh gene position; hence, their origin is not by retrotransposition. Comparison of the sequences of the Adh-psi from representatives of each of the subgroups of the repleta group reveal that the Adh pseudogene is present in each subgroup and that mutations at codon 2 and a deletion in the region immediately 5' to Adh-psi are common to all species. Therefore, it is likely that the translational inactivation event that resulted in a pseudogene occurred before the divergence of the species that make up the repleta group. We have investigated the transcription of Adh-psi of D. hydei and have found that the transcription has a developmental profile dissimilar from any known Adh gene, does not utilize an Adh promoter, and is initiated at a point almost 12 kb upstream. Comparison of sequence divergence of Adh-psi within species of the repleta group reveals that rates of evolution of the exons of Adh-psi are substantially slower than intergenic regions and are only slightly faster than those of exons of functional Adh genes. Second, retention of codon bias is found in the Adh-psi of most species, and substitution at synonymous coding positions substantially exceeds substitution at nonsynonymous coding positions. Comparison of the evolution of other putative pseudogenes with repleta group Adh pseudogenes suggests that at least some pseudogene sequences in Drosophila may be evolving through mechanisms and/or under influences not presently understood.
- Published
- 1994
- Full Text
- View/download PDF
16. Genetic Individualization of Domestic Cats Using Feline STR Loci for Forensic Applications
- Author
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Menotti-Raymond, M, David, VA, Stephens, JC, Lyons, LA, and O'Brien, SJ
- Abstract
A group of ten short tandem repeat (STR) loci suitable for PCR typing from DNA of domestic cats is evaluated for genetic individualization using blinded samples of eight putative feline blood specimens. The ten loci were also typed in a 70 member cat pedigree to demonstrate Mendelian inheritance and independent assortment. A “match window” or measurement precision estimate was empirically established by determining the maximum gel migration difference among alleles identical by descent in different individuals of the pedigree. Hardy-Weinberg equilibrium and abundant heterozygosity was observed for each locus in cat population samples from Canada and the USA. The probabilities of two unrelated individuals matching by chance (Pm) at all ten loci was estimated as 1.35 × 10−10. We present a conservative approach to compute, for forensic consideration, the mathematical likelihood of a chance genotypic match between DNA evidence from a crime scene and the suspect composite STR genotypes for species or populations when genotype frequency information is not available.
- Published
- 1997
- Full Text
- View/download PDF
17. Validation of a short tandem repeat multiplex typing system for genetic individualization of domestic cat samples
- Author
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Coomber, N., David, V. A., O Brien, S. J., and Menotti-Raymond, M.
18. Quantitative polymerase chain reaction-based assay for estimating DNA yield extracted from domestic cat specimens
- Author
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Menotti-Raymond, M., David, V., Wachter, L., Yuhki, N., and O Brien, S. J.
19. Genome maps 10. Comparative genomics. Mammalian radiations. Wall chart
- Author
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O Brien, S. J., Eisenberg, J. F., Miyamoto, M., Hedges, S. B., Kumar, S., Wilson, D. E., Menotti-Raymond, M., Murphy, W. J., Nash, W. G., Lyons, L. A., Menninger, J. C., Roscoe Stanyon, Wienberg, J., Copeland, N. G., Jenkins, N. A., Gellin, J., Yerle, M., Andersson, L., Womack, J., Broad, T., Postlethwait, J., Serov, O., Bailey, E., James, M. R., and Marshall Graves, J. A.
- Subjects
Mammals ,Genome ,Base Sequence ,Genome, Human ,Animals ,Chromosome Mapping ,Humans ,Nucleic Acid Hybridization ,Phylogeny ,Chromosome Painting
20. Mapping of Diabetes Susceptibility Loci in a Domestic Cat Breed with an Unusually High Incidence of Diabetes Mellitus.
- Author
-
Balmer L, O'Leary CA, Menotti-Raymond M, David V, O'Brien S, Penglis B, Hendrickson S, Reeves-Johnson M, Gottlieb S, Fleeman L, Vankan D, Rand J, and Morahan G
- Subjects
- Animals, Australia, Case-Control Studies, Cats, Diabetes Mellitus, Type 2 genetics, Female, Genetic Markers, Genetic Predisposition to Disease, Genome-Wide Association Study, Male, United States, Cat Diseases genetics, Diabetes Mellitus, Type 2 veterinary, Polymorphism, Single Nucleotide
- Abstract
Genetic variants that are associated with susceptibility to type 2 diabetes (T2D) are important for identification of individuals at risk and can provide insights into the molecular basis of disease. Analysis of T2D in domestic animals provides both the opportunity to improve veterinary management and breeding programs as well as to identify novel T2D risk genes. Australian-bred Burmese (ABB) cats have a 4-fold increased incidence of type 2 diabetes (T2D) compared to Burmese cats bred in the United States. This is likely attributable to a genetic founder effect. We investigated this by performing a genome-wide association scan on ABB cats. Four SNPs were associated with the ABB T2D phenotype with p values <0.005. All exons and splice junctions of candidate genes near significant single-nucleotide polymorphisms (SNPs) were sequenced, including the genes DGKG, IFG2BP2, SLC8A1, E2F6, ETV5, TRA2B and LIPH . Six candidate polymorphisms were followed up in a larger cohort of ABB cats with or without T2D and also in Burmese cats bred in America, which exhibit low T2D incidence. The original SNPs were confirmed in this cohort as associated with the T2D phenotype, although no novel coding SNPs in any of the seven candidate genes showed association with T2D. The identification of genetic markers associated with T2D susceptibility in ABB cats will enable preventative health strategies and guide breeding programs to reduce the prevalence of T2D in these cats.
- Published
- 2020
- Full Text
- View/download PDF
21. Correction: A Mutation in LTBP2 Causes Congenital Glaucoma in Domestic Cats (Felis catus).
- Author
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Kuehn MH, Lipsett KA, Menotti-Raymond M, Whitmore SS, Scheetz TE, David VA, O'Brien SJ, Zhao Z, Jens JK, Snella EM, Ellinwood NM, and McLellan GJ
- Abstract
[This corrects the article DOI: 10.1371/journal.pone.0154412.].
- Published
- 2016
- Full Text
- View/download PDF
22. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination.
- Author
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Li G, Hillier LW, Grahn RA, Zimin AV, David VA, Menotti-Raymond M, Middleton R, Hannah S, Hendrickson S, Makunin A, O'Brien SJ, Minx P, Wilson RK, Lyons LA, Warren WC, and Murphy WJ
- Subjects
- Animals, Cats, Chromosomes, Computational Biology methods, Female, Genome-Wide Association Study, Male, Microsatellite Repeats, Translocation, Genetic, Chromosome Mapping, Genetic Linkage, Genome, Genomics methods, Polymorphism, Single Nucleotide, Recombination, Genetic
- Abstract
High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catus v8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location., (Copyright © 2016 Li et al.)
- Published
- 2016
- Full Text
- View/download PDF
23. A Mutation in LTBP2 Causes Congenital Glaucoma in Domestic Cats (Felis catus).
- Author
-
Kuehn MH, Lipsett KA, Menotti-Raymond M, Whitmore SS, Scheetz TE, David VA, O'Brien SJ, Zhao Z, Jens JK, Snella EM, Ellinwood NM, and McLellan GJ
- Subjects
- Animals, Aqueous Humor physiology, Cat Diseases congenital, Cats, Female, Genetic Linkage, Glaucoma congenital, Glaucoma genetics, Intraocular Pressure genetics, Latent TGF-beta Binding Proteins physiology, Male, Mutation genetics, Pedigree, Phenotype, Retinal Ganglion Cells pathology, Cat Diseases genetics, Glaucoma veterinary, Latent TGF-beta Binding Proteins genetics
- Abstract
The glaucomas are a group of diseases characterized by optic nerve damage that together represent a leading cause of blindness in the human population and in domestic animals. Here we report a mutation in LTBP2 that causes primary congenital glaucoma (PCG) in domestic cats. We identified a spontaneous form of PCG in cats and established a breeding colony segregating for PCG consistent with fully penetrant, autosomal recessive inheritance of the trait. Elevated intraocular pressure, globe enlargement and elongated ciliary processes were consistently observed in all affected cats by 8 weeks of age. Varying degrees of optic nerve damage resulted by 6 months of age. Although subtle lens zonular instability was a common feature in this cohort, pronounced ectopia lentis was identified in less than 10% of cats examined. Thus, glaucoma in this pedigree is attributed to histologically confirmed arrest in the early post-natal development of the aqueous humor outflow pathways in the anterior segment of the eyes of affected animals. Using a candidate gene approach, significant linkage was established on cat chromosome B3 (LOD 18.38, θ = 0.00) using tightly linked short tandem repeat (STR) loci to the candidate gene, LTBP2. A 4 base-pair insertion was identified in exon 8 of LTBP2 in affected individuals that generates a frame shift that completely alters the downstream open reading frame and eliminates functional domains. Thus, we describe the first spontaneous and highly penetrant non-rodent model of PCG identifying a valuable animal model for primary glaucoma that closely resembles the human disease, providing valuable insights into mechanisms underlying the disease and a valuable animal model for testing therapies.
- Published
- 2016
- Full Text
- View/download PDF
24. The Population Origins and Expansion of Feral Cats in Australia.
- Author
-
Spencer PB, Yurchenko AA, David VA, Scott R, Koepfli KP, Driscoll C, O'Brien SJ, and Menotti-Raymond M
- Subjects
- Animals, Australia, Gene Frequency, Microsatellite Repeats, Cats genetics, Genetic Variation, Genetics, Population
- Abstract
The historical literature suggests that in Australia, the domestic cat (Felis catus) had a European origin [~200 years before present (ybp)], but it is unclear if cats arrived from across the Asian land bridge contemporaneously with the dingo (4000 ybp), or perhaps immigrated ~40000 ybp in association with Aboriginal settlement from Asia. The origin of cats in Australia is important because the continent has a complex and ancient faunal assemblage that is dominated by endemic rodents and marsupials and lacks the large placental carnivores found on other large continents. Cats are now ubiquitous across the entire Australian continent and have been implicit in the range contraction or extinction of its small to medium sized (<3.5kg) mammals. We analyzed the population structure of 830 cats using 15 short tandem repeat (STR) genomic markers. Their origin appears to come exclusively from European founders. Feral cats in continental Australia exhibit high genetic diversity in comparison with the low diversity found in populations of feral cats living on islands. The genetic structure is consistent with a rapid westerly expansion from eastern Australia and a limited expansion in coastal Western Australia. Australian cats show modest if any population structure and a close genetic alignment with European feral cats as compared to cats from Asia, the Christmas and Cocos (Keeling) Islands (Indian Ocean), and European wildcats (F. silvestris silvestris)., (© The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2016
- Full Text
- View/download PDF
25. Recurrent evolution of melanism in South American felids.
- Author
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Schneider A, Henegar C, Day K, Absher D, Napolitano C, Silveira L, David VA, O'Brien SJ, Menotti-Raymond M, Barsh GS, and Eizirik E
- Subjects
- Animals, Cats, Genetic Variation, Genetics, Population, Haplotypes, Mutation, Phylogeny, South America, Species Specificity, Agouti Signaling Protein genetics, Evolution, Molecular, Melanosis genetics, Receptor, Melanocortin, Type 1 genetics, Selection, Genetic genetics
- Abstract
Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics, but some of the most interesting questions involve non-model organisms that lack well annotated reference genomes. Many felid species exhibit polymorphism for melanism but the relative roles played by genetic drift, natural selection, and interspecies hybridization remain uncertain. We identify mutations of Agouti signaling protein (ASIP) or the Melanocortin 1 receptor (MC1R) as independent causes of melanism in three closely related South American species: the pampas cat (Leopardus colocolo), the kodkod (Leopardus guigna), and Geoffroy's cat (Leopardus geoffroyi). To assess population level variation in the regions surrounding the causative mutations we apply genomic resources from the domestic cat to carry out clone-based capture and targeted resequencing of 299 kb and 251 kb segments that contain ASIP and MC1R, respectively, from 54 individuals (13-21 per species), achieving enrichment of ~500-2500-fold and ~150x coverage. Our analysis points to unique evolutionary histories for each of the three species, with a strong selective sweep in the pampas cat, a distinctive but short melanism-specific haplotype in the Geoffroy's cat, and reduced nucleotide diversity for both ancestral and melanism-bearing chromosomes in the kodkod. These results reveal an important role for natural selection in a trait of longstanding interest to ecologists, geneticists, and the lay community, and provide a platform for comparative studies of morphological variation in other natural populations.
- Published
- 2015
- Full Text
- View/download PDF
26. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.
- Author
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Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, Minx P, Hillier LW, Koboldt DC, Davis BW, Driscoll CA, Barr CS, Blackistone K, Quilez J, Lorente-Galdos B, Marques-Bonet T, Alkan C, Thomas GW, Hahn MW, Menotti-Raymond M, O'Brien SJ, Wilson RK, Lyons LA, Murphy WJ, and Warren WC
- Subjects
- Adaptation, Physiological genetics, Amino Acid Sequence, Animals, Carnivory, Cats classification, Chromosome Mapping, DNA Copy Number Variations, Dogs, Female, Gene Deletion, Gene Duplication, Male, Membrane Transport Proteins classification, Membrane Transport Proteins genetics, Molecular Sequence Data, Phylogeny, Selection, Genetic genetics, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Species Specificity, Animals, Domestic genetics, Animals, Wild genetics, Cats genetics, Genome genetics, Genomics methods
- Abstract
Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae.
- Published
- 2014
- Full Text
- View/download PDF
27. Annotated features of domestic cat - Felis catus genome.
- Author
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Tamazian G, Simonov S, Dobrynin P, Makunin A, Logachev A, Komissarov A, Shevchenko A, Brukhin V, Cherkasov N, Svitin A, Koepfli KP, Pontius J, Driscoll CA, Blackistone K, Barr C, Goldman D, Antunes A, Quilez J, Lorente-Galdos B, Alkan C, Marques-Bonet T, Menotti-Raymond M, David VA, Narfström K, and O'Brien SJ
- Abstract
Background: Domestic cats enjoy an extensive veterinary medical surveillance which has described nearly 250 genetic diseases analogous to human disorders. Feline infectious agents offer powerful natural models of deadly human diseases, which include feline immunodeficiency virus, feline sarcoma virus and feline leukemia virus. A rich veterinary literature of feline disease pathogenesis and the demonstration of a highly conserved ancestral mammal genome organization make the cat genome annotation a highly informative resource that facilitates multifaceted research endeavors., Findings: Here we report a preliminary annotation of the whole genome sequence of Cinnamon, a domestic cat living in Columbia (MO, USA), bisulfite sequencing of Boris, a male cat from St. Petersburg (Russia), and light 30× sequencing of Sylvester, a European wildcat progenitor of cat domestication. The annotation includes 21,865 protein-coding genes identified by a comparative approach, 217 loci of endogenous retrovirus-like elements, repetitive elements which comprise about 55.7% of the whole genome, 99,494 new SNVs, 8,355 new indels, 743,326 evolutionary constrained elements, and 3,182 microRNA homologues. The methylation sites study shows that 10.5% of cat genome cytosines are methylated. An assisted assembly of a European wildcat, Felis silvestris silvestris, was performed; variants between F. silvestris and F. catus genomes were derived and compared to F. catus., Conclusions: The presented genome annotation extends beyond earlier ones by closing gaps of sequence that were unavoidable with previous low-coverage shotgun genome sequencing. The assembly and its annotation offer an important resource for connecting the rich veterinary and natural history of cats to genome discovery.
- Published
- 2014
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28. Endogenous retrovirus insertion in the KIT oncogene determines white and white spotting in domestic cats.
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David VA, Menotti-Raymond M, Wallace AC, Roelke M, Kehler J, Leighty R, Eizirik E, Hannah SS, Nelson G, Schäffer AA, Connelly CJ, O'Brien SJ, and Ryugo DK
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- Animals, Breeding, Cats, Genetic Linkage, Genetics, Population, Genotype, Hearing Loss pathology, Hearing Loss veterinary, Hematopoietic Stem Cells metabolism, Introns, Mast Cells metabolism, Pedigree, Phenotype, Proto-Oncogene Proteins c-kit metabolism, Retroelements genetics, Sequence Analysis, RNA, Terminal Repeat Sequences genetics, Endogenous Retroviruses genetics, Pigmentation genetics, Proto-Oncogene Proteins c-kit genetics
- Abstract
The Dominant White locus (W) in the domestic cat demonstrates pleiotropic effects exhibiting complete penetrance for absence of coat pigmentation and incomplete penetrance for deafness and iris hypopigmentation. We performed linkage analysis using a pedigree segregating White to identify KIT (Chr. B1) as the feline W locus. Segregation and sequence analysis of the KIT gene in two pedigrees (P1 and P2) revealed the remarkable retrotransposition and evolution of a feline endogenous retrovirus (FERV1) as responsible for two distinct phenotypes of the W locus, Dominant White, and white spotting. A full-length (7125 bp) FERV1 element is associated with white spotting, whereas a FERV1 long terminal repeat (LTR) is associated with all Dominant White individuals. For purposes of statistical analysis, the alternatives of wild-type sequence, FERV1 element, and LTR-only define a triallelic marker. Taking into account pedigree relationships, deafness is genetically linked and associated with this marker; estimated P values for association are in the range of 0.007 to 0.10. The retrotransposition interrupts a DNAase I hypersensitive site in KIT intron 1 that is highly conserved across mammals and was previously demonstrated to regulate temporal and tissue-specific expression of KIT in murine hematopoietic and melanocytic cells. A large-population genetic survey of cats (n = 270), representing 30 cat breeds, supports our findings and demonstrates statistical significance of the FERV1 LTR and full-length element with Dominant White/blue iris (P < 0.0001) and white spotting (P < 0.0001), respectively., (Copyright © 2014 David et al.)
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- 2014
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29. Cats: a gold mine for ophthalmology.
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Narfström K, Deckman KH, and Menotti-Raymond M
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- Animals, Cat Diseases genetics, Cats, Eye Diseases pathology, Eye Diseases, Hereditary pathology, Eye Diseases, Hereditary veterinary, Genetic Predisposition to Disease, Humans, Cat Diseases pathology, Eye anatomy & histology, Eye Diseases veterinary, Ocular Physiological Phenomena
- Abstract
Over 200 hereditary diseases have been identified and reported in the cat, several of which affect the eye, with homology to human hereditary disease. Compared with traditional murine models, the cat demonstrates more features in common with humans, including many anatomic and physiologic similarities, longer life span, increased size, and a genetically more heterogeneous background. The development of genomic resources in the cat has facilitated mapping and further characterization of feline models. During recent years, the wealth of knowledge in feline ophthalmology and neurophysiology has been extended to include new diseases of significant interest for comparative ophthalmology. This makes the cat an extremely valuable animal species to utilize for further research into disease processes affecting both cats and humans. This is especially true in the advancement and study of new treatment regimens and for extended therapeutic trials. Groups of feline eye diseases reviewed in the following are lysosomal storage disorders, congenital glaucoma, and neuroretinal degenerations. Each has important implications for human ophthalmic research.
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- 2013
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30. Specifying and sustaining pigmentation patterns in domestic and wild cats.
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Kaelin CB, Xu X, Hong LZ, David VA, McGowan KA, Schmidt-Küntzel A, Roelke ME, Pino J, Pontius J, Cooper GM, Manuel H, Swanson WF, Marker L, Harper CK, van Dyk A, Yue B, Mullikin JC, Warren WC, Eizirik E, Kos L, O'Brien SJ, Barsh GS, and Menotti-Raymond M
- Subjects
- Acinonyx genetics, Acinonyx metabolism, Alleles, Aminopeptidases chemistry, Aminopeptidases metabolism, Animals, Cats embryology, Cats growth & development, Cats metabolism, Endothelin-3 metabolism, Epistasis, Genetic, Felidae growth & development, Felidae metabolism, Gene Expression Regulation, Gene Frequency, Genetic Variation, Hair embryology, Hair growth & development, Hair Follicle embryology, Haplotypes, Metalloproteases chemistry, Metalloproteases metabolism, Mice, Mice, Transgenic, Panthera genetics, Panthera metabolism, Phenotype, Polymorphism, Single Nucleotide, Skin anatomy & histology, Skin embryology, Species Specificity, Aminopeptidases genetics, Cats genetics, Endothelin-3 genetics, Felidae genetics, Hair Color genetics, Metalloproteases genetics, Skin metabolism
- Abstract
Color markings among felid species display both a remarkable diversity and a common underlying periodicity. A similar range of patterns in domestic cats suggests a conserved mechanism whose appearance can be altered by selection. We identified the gene responsible for tabby pattern variation in domestic cats as Transmembrane aminopeptidase Q (Taqpep), which encodes a membrane-bound metalloprotease. Analyzing 31 other felid species, we identified Taqpep as the cause of the rare king cheetah phenotype, in which spots coalesce into blotches and stripes. Histologic, genomic expression, and transgenic mouse studies indicate that paracrine expression of Endothelin3 (Edn3) coordinates localized color differences. We propose a two-stage model in which Taqpep helps to establish a periodic pre-pattern during skin development that is later implemented by differential expression of Edn3.
- Published
- 2012
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31. A population genetic database of cat breeds developed in coordination with a domestic cat STR multiplex.
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Menotti-Raymond M, David VA, Weir BS, and O'Brien SJ
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- Animals, Cats, Female, Gene Frequency, Genotype, Heterozygote, Male, Polymerase Chain Reaction, Y Chromosome, DNA Fingerprinting, Databases, Nucleic Acid, Genetics, Population, Microsatellite Repeats
- Abstract
A simple tandem repeat (STR) PCR-based typing system developed for the genetic individualization of domestic cat samples has been used to generate a population genetic database of domestic cat breeds. A panel of 10 tetranucleotide STR loci and a gender-identifying sequence tagged site (STS) were co-amplified in genomic DNA of 1043 individuals representing 38 cat breeds. The STR panel exhibits relatively high heterozygosity in cat breeds, with an average 10-locus heterozygosity of 0.71, which represents an average of 38 breed-specific heterozygosities for the 10-member panel. When the entire set of breed individuals was analyzed as a single population, a heterozygosity of 0.87 was observed. Heterozygosities obtained for the 10 loci range from 0.72 to 0.96. The power for genetic individualization of domestic cat samples of the multiplex is high, with a probability of match (p(m)) of 6.2E-14, using a conservative θ = 0.05., (© 2012 American Academy of Forensic Sciences.)
- Published
- 2012
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32. How the leopard hides its spots: ASIP mutations and melanism in wild cats.
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Schneider A, David VA, Johnson WE, O'Brien SJ, Barsh GS, Menotti-Raymond M, and Eizirik E
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- Agouti Signaling Protein metabolism, Animals, Biological Evolution, Felis metabolism, Molecular Sequence Data, Mutation, Panthera metabolism, Phenotype, Species Specificity, Agouti Signaling Protein genetics, Felis genetics, Panthera genetics, Pigmentation genetics
- Abstract
The occurrence of melanism (darkening of the background coloration) is documented in 13 felid species, in some cases reaching high frequencies at the population level. Recent analyses have indicated that it arose multiple times in the Felidae, with three different species exhibiting unique mutations associated with this trait. The causative mutations in the remaining species have so far not been identified, precluding a broader assessment of the evolutionary dynamics of melanism in the Felidae. Among these, the leopard (Panthera pardus) is a particularly important target for research, given the iconic status of the 'black panther' and the extremely high frequency of melanism observed in some Asian populations. Another felid species from the same region, the Asian golden cat (Pardofelis temminckii), also exhibits frequent records of melanism in some areas. We have sequenced the coding region of the Agouti Signaling Protein (ASIP) gene in multiple leopard and Asian golden cat individuals, and identified distinct mutations strongly associated with melanism in each of them. The single nucleotide polymorphism (SNP) detected among the P. pardus individuals was caused by a nonsense mutation predicted to completely ablate ASIP function. A different SNP was identified in P. temminckii, causing a predicted amino acid change that should also induce loss of function. Our results reveal two additional cases of species-specific mutations implicated in melanism in the Felidae, and indicate that ASIP mutations may play an important role in naturally-occurring coloration polymorphism.
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- 2012
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33. Characterization of feline hereditary retinal dystrophies using clinical, functional, structural and molecular genetic studies.
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Narfström K, Menotti Raymond M, and Seeliger M
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- Animals, Cat Diseases pathology, Cat Diseases physiopathology, Cats, Electroretinography, Genetic Predisposition to Disease genetics, Retina pathology, Retina physiopathology, Retinal Dystrophies genetics, Retinal Dystrophies pathology, Retinal Dystrophies physiopathology, Cat Diseases genetics, Retinal Dystrophies veterinary
- Abstract
Only in recent years have specific mutations been elucidated for feline hereditary retinal dystrophies. Molecular genetic characterization of feline diseases has so far been a slow process but with a full genome sequence for the cat recently completed and the development of a feline single nucleotide polymorphism chip, the characterization of feline monogenic disorders will be significantly simplified. This review summarizes current knowledge with regard to specific hereditary retinal dystrophies in cats and gives an overview of how cats can be used as models in translational research., (© 2011 American College of Veterinary Ophthalmologists.)
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- 2011
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34. The domestic cat as a large animal model for characterization of disease and therapeutic intervention in hereditary retinal blindness.
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Narfström K, Holland Deckman K, and Menotti-Raymond M
- Abstract
Large mammals, including canids and felids, are affected by spontaneously occurring hereditary retinal diseases with similarities to those of humans. The large mammal models may be used for thorough clinical characterization of disease processes, understanding the effects of specific mutations, elucidation of disease mechanisms, and for development of therapeutic intervention. Two well-characterized feline models are addressed in this paper. The first model is the autosomal recessive, slowly progressive, late-onset, rod-cone degenerative disease caused by a mutation in the CEP290 gene. The second model addressed in this paper is the autosomal dominant early onset rod cone dysplasia, putatively caused by the mutation found in the CRX gene. Therapeutic trials have been performed mainly in the former type including stem cell therapy, retinal transplantation, and development of ocular prosthetics. Domestic cats, having large human-like eyes with comparable spontaneous retinal diseases, are also considered useful for gene replacement therapy, thus functioning as effective model systems for further research.
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- 2011
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35. Mutation discovered in a feline model of human congenital retinal blinding disease.
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Menotti-Raymond M, Deckman KH, David V, Myrkalo J, O'Brien SJ, and Narfström K
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- Amino Acid Sequence, Animals, Base Sequence, Cat Diseases pathology, Cats, Chromosome Mapping, DNA Mutational Analysis veterinary, Dark Adaptation, Electroretinography veterinary, Exons genetics, Female, Male, Molecular Sequence Data, Pedigree, Phenotype, Retinal Dysplasia genetics, Retinal Dysplasia pathology, Sequence Homology, Amino Acid, Cat Diseases genetics, Codon, Nonsense, Disease Models, Animal, Homeodomain Proteins genetics, Photoreceptor Cells, Vertebrate pathology, Retinal Dysplasia veterinary, Trans-Activators genetics
- Abstract
Purpose: To elucidate the gene defect in a pedigree of cats segregating for autosomal dominant rod-cone dysplasia (Rdy), a retinopathy characterized extensively from a clinical perspective. Disease expression in Rdy cats is comparable to that in young patients with congenital blindness (Leber congenital amaurosis [LCA] or retinitis pigmentosa [RP])., Methods: A pedigree segregating for Rdy was generated and phenotyped by clinical ophthalmic examination methods including ophthalmoscopy and full-field flash electroretinography. Short tandem repeat loci tightly linked to candidate genes for autosomal dominant retinitis pigmentosa in humans were genotyped in the pedigree., Results: Significant linkage was established to the candidate gene CRX (LOD = 5.56, = 0) on cat chromosome E2. A single base pair deletion was identified in exon 4 (n.546delC) in affected individuals but not in unaffected littermates. This mutation generates a frame shift in the transcript, introducing a premature stop codon truncating the putative CRX peptide, which would eliminate the critical transcriptional activation region. Clinical observations corroborate previously reported clinical reports about Rdy. Results show that the cone photoreceptor system was more severely affected than the rods in the early disease process., Conclusions: A putative mutation causative of the Rdy phenotype has been described as a single base pair deletion in exon 4 of the CRX gene, thus identifying the first animal model for CRX-linked disease that closely resembles the human disease. As such, it will provide valuable insights into the mechanisms underlying these diseases and their variable presentation, as well as providing a suitable model for testing therapies for these diseases.
- Published
- 2010
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36. Defining and mapping mammalian coat pattern genes: multiple genomic regions implicated in domestic cat stripes and spots.
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Eizirik E, David VA, Buckley-Beason V, Roelke ME, Schäffer AA, Hannah SS, Narfström K, O'Brien SJ, and Menotti-Raymond M
- Subjects
- Animals, Dogs, Epistasis, Genetic, Female, Genes, Dominant, Genetic Loci genetics, Genomics, Genotype, Humans, Male, Pedigree, Phenotype, Cats anatomy & histology, Cats genetics, Chromosome Mapping, Genome genetics, Hair, Pigmentation genetics
- Abstract
Mammalian coat patterns (e.g., spots, stripes) are hypothesized to play important roles in camouflage and other relevant processes, yet the genetic and developmental bases for these phenotypes are completely unknown. The domestic cat, with its diversity of coat patterns, is an excellent model organism to investigate these phenomena. We have established three independent pedigrees to map the four recognized pattern variants classically considered to be specified by a single locus, Tabby; in order of dominance, these are the unpatterned agouti form called "Abyssinian" or "ticked" (T(a)), followed by Spotted (T(s)), Mackerel (T(M)), and Blotched (t(b)). We demonstrate that at least three different loci control the coat markings of the domestic cat. One locus, responsible for the Abyssinian form (herein termed the Ticked locus), maps to an approximately 3.8-Mb region on cat chromosome B1. A second locus controls the Tabby alleles T(M) and t(b), and maps to an approximately 5-Mb genomic region on cat chromosome A1. One or more additional loci act as modifiers and create a spotted coat by altering mackerel stripes. On the basis of our results and associated observations, we hypothesize that mammalian patterned coats are formed by two distinct processes: a spatially oriented developmental mechanism that lays down a species-specific pattern of skin cell differentiation and a pigmentation-oriented mechanism that uses information from the preestablished pattern to regulate the synthesis of melanin profiles.
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- 2010
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37. Retinal degeneration in the Abyssinian and Somali cat (rdAc): correlation between genotype and phenotype and rdAc allele frequency in two continents.
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Narfström K, David V, Jarret O, Beatty J, Barrs V, Wilkie D, O'Brien S, and Menotti-Raymond M
- Subjects
- Animals, Australia, Cats, Europe, Gene Frequency genetics, Genotype, Phenotype, Retinal Degeneration genetics, Cat Diseases genetics, Retinal Degeneration veterinary
- Abstract
Objective: To characterize hereditary retinal degeneration in the Abyssinian cat (rdAc) in a recently established closed colony segregating for the rdAc mutation, and evaluate possible differences in the age of onset and progression of disease phenotype since the initial description of rdAc 25 years ago. The sample size of an earlier study was increased in order to determine the allele frequency in Abyssinian and Somali cats on a worldwide basis., Animals Studied: Twenty rdAc affected cats from the closed animal facility, 87 Abyssinian and Somali cats for study of genotype-phenotype concordance, and DNA from 131 Abyssinian and Somali cats from Scandinavia, the UK and Australia for evaluation of the rdAc allele frequency., Procedures: DNA was extracted from blood and buccal swabs using commercially available kits, followed by genotyping. Ophthalmic examinations were performed in the USA and Sweden by two board-certified veterinary ophthalmologists., Results: A greater variation in the age of onset and progression of the disease was observed compared to that previously described. An excellent correlation between genotype and phenotype was observed. A population genetic survey revealed that the rdAc allele is in moderate abundance in the Abyssinian breed in Europe and Australia. Surprisingly, homozygosity for the mutant allele was observed in a Siamese cat with ophthalmoscopic findings similar to those originally described for affected rdAc individuals., Conclusions: Alertness to the potential of rdAc is needed on the part of the veterinary ophthalmology community, not only in Abyssinian and Somali cats but possibly also in other related cat breeds.
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- 2009
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38. Mapping of the domestic cat "SILVER" coat color locus identifies a unique genomic location for silver in mammals.
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Menotti-Raymond M, David VA, Eizirik E, Roelke ME, Ghaffari H, and O'Brien SJ
- Subjects
- Animals, Cats, Chromosome Mapping veterinary, Chromosomes, Mammalian, Female, Genetic Linkage, Male, Melanins genetics, Microsatellite Repeats genetics, Pedigree, Hair Color genetics
- 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.
- Published
- 2009
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39. A domestic cat X chromosome linkage map and the sex-linked orange locus: mapping of orange, multiple origins and epistasis over nonagouti.
- Author
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Schmidt-Küntzel A, Nelson G, David VA, Schäffer AA, Eizirik E, Roelke ME, Kehler JS, Hannah SS, O'Brien SJ, and Menotti-Raymond M
- Subjects
- Animals, Chromosome Mapping, Genetics, Population, Microsatellite Repeats, Quantitative Trait Loci, Agouti Signaling Protein genetics, Cats genetics, Epistasis, Genetic physiology, Evolution, Molecular, Hair Color genetics, X Chromosome genetics
- Abstract
A comprehensive genetic linkage map of the domestic cat X chromosome was generated with the goal of localizing the genomic position of the classic X-linked orange (O) locus. Microsatellite markers with an average spacing of 3 Mb were selected from sequence traces of the cat 1.9x whole genome sequence (WGS), including the pseudoautosomal region 1 (PAR1). Extreme variation in recombination rates (centimorgans per megabase) was observed along the X chromosome, ranging from a virtual absence of recombination events in a region estimated to be >30 Mb to recombination frequencies of 15.7 cM/Mb in a segment estimated to be <0.3 Mb. This detailed linkage map was applied to position the X-linked orange gene, placing this locus on the q arm of the X chromosome, as opposed to a previously reported location on the p arm. Fine mapping placed the locus between markers at positions 106 and 116.8 Mb in the current 1.9x-coverage sequence assembly of the cat genome. Haplotype analysis revealed potential recombination events that could reduce the size of the candidate region to 3.5 Mb and suggested multiple origins for the orange phenotype in the domestic cat. Furthermore, epistasis of orange over nonagouti was demonstrated at the genetic level.
- Published
- 2009
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40. An autosomal genetic linkage map of the domestic cat, Felis silvestris catus.
- Author
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Menotti-Raymond M, David VA, Schäffer AA, Tomlin JF, Eizirik E, Phillip C, Wells D, Pontius JU, Hannah SS, and O'Brien SJ
- Subjects
- Animals, Chromosome Mapping, Chromosomes genetics, Genetic Markers, Genome, Genotype, Pedigree, Radiation Hybrid Mapping, Cats genetics, Genetic Linkage
- Abstract
We report on the completion of an autosomal genetic linkage (GL) map of the domestic cat (Felis silvestris catus). Unlike two previous linkage maps of the cat constructed with a hybrid pedigree between the domestic cat and the Asian leopard cat, this map was generated entirely with domestic cats, using a large multi-generational pedigree (n=256) maintained by the Nestlé Purina PetCare Company. Four hundred eighty-three simple tandem repeat (STR) loci have been assigned to linkage groups on the cat's 18 autosomes. A single linkage group spans each autosome. The length of the cat map, estimated at 4370 cM, is long relative to most reported mammalian maps. A high degree of concordance in marker order was observed between the third-generation map and the 1.5 Mb-resolution radiation hybrid (RH) map of the cat. Using the cat 1.9x whole-genome sequence, we identified map coordinates for 85% of the loci in the cat assembly, with high concordance observed in marker order between the linkage map and the cat sequence assembly. The present version represents a marked improvement over previous cat linkage maps as it (i) nearly doubles the number of markers that were present in the second-generation linkage map in the cat, (ii) provides a linkage map generated in a domestic cat pedigree which will more accurately reflect recombination distances than previous maps generated in a hybrid pedigree, and (iii) provides single linkage groups spanning each autosome. Marker order was largely consistent between this and the previous maps, though the use of a hybrid pedigree in the earlier versions appears to have contributed to some suppression of recombination. The improved linkage map will provide an added resource for the mapping of phenotypic variation in the domestic cat and the use of this species as a model system for biological research.
- Published
- 2009
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41. State of cat genomics.
- Author
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O'Brien SJ, Johnson W, Driscoll C, Pontius J, Pecon-Slattery J, and Menotti-Raymond M
- Subjects
- Animals, Animals, Domestic genetics, Animals, Domestic physiology, Genome, Genomics trends, Geography, Phylogeny, Sequence Analysis, DNA, Cats genetics, Felidae genetics
- Abstract
Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.
- Published
- 2008
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42. Patterns of molecular genetic variation among cat breeds.
- Author
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Menotti-Raymond M, David VA, Pflueger SM, Lindblad-Toh K, Wade CM, O'Brien SJ, and Johnson WE
- Subjects
- Animals, Crosses, Genetic, Algorithms, Breeding, Cats genetics, Phylogeny, Polymorphism, Single Nucleotide, Sequence Analysis, DNA
- Abstract
Genetic variation in cat breeds was assessed utilizing a panel of short tandem repeat (STR) loci genotyped in 38 cat breeds and 284 single-nucleotide polymorphisms (SNPs) genotyped in 24 breeds. Population structure in cat breeds generally reflects their recent ancestry and absence of strong breed barriers between some breeds. There is a wide range in the robustness of population definition, from breeds demonstrating high definition to breeds with as little as a third of their genetic variation partitioning into a single population. Utilizing the STRUCTURE algorithm, there was no clear demarcation of the number of population subdivisions; 16 breeds could not be resolved into independent populations, the consequence of outcrossing in established breeds to recently developed breeds with common ancestry. These 16 breeds were divided into 6 populations. Ninety-six percent of cats in a sample set of 1040 were correctly assigned to their classified breed or breed group/population. Average breed STR heterozygosities ranged from moderate (0.53; Havana, Korat) to high (0.85; Norwegian Forest Cat, Manx). Most of the variation in cat breeds was observed within a breed population (83.7%), versus 16.3% of the variation observed between populations. The hierarchical relationships of cat breeds is poorly defined as demonstrated by phylogenetic trees generated from both STR and SNP data, though phylogeographic grouping of breeds derived completely or in part from Southeast Asian ancestors was apparent.
- Published
- 2008
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43. Initial sequence and comparative analysis of the cat genome.
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Pontius JU, Mullikin JC, Smith DR, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schäffer AA, Agarwala R, Narfström K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G, and O'Brien SJ
- Subjects
- Animals, Dogs, Humans, Mice, MicroRNAs, Microsatellite Repeats, Models, Genetic, Polymorphism, Single Nucleotide, Rats, Repetitive Sequences, Nucleic Acid, Cats genetics, Genome, Genomics
- Abstract
The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing approximately 65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence.
- Published
- 2007
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44. Four independent mutations in the feline fibroblast growth factor 5 gene determine the long-haired phenotype in domestic cats.
- Author
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Kehler JS, David VA, Schäffer AA, Bajema K, Eizirik E, Ryugo DK, Hannah SS, O'Brien SJ, and Menotti-Raymond M
- Subjects
- Amino Acid Sequence, Animals, Chromosome Mapping, Female, Genetic Markers, Genome, Male, Molecular Sequence Data, Pedigree, Phenotype, Species Specificity, Cats genetics, Fibroblast Growth Factor 5 genetics, Hair physiology, Mutation
- Abstract
To determine the genetic regulation of "hair length" in the domestic cat, a whole-genome scan was performed in a multigenerational pedigree in which the "long-haired" phenotype was segregating. The 2 markers that demonstrated the greatest linkage to the long-haired trait (log of the odds > or = 6) flanked an estimated 10-Mb region on cat chromosome B1 containing the Fibroblast Growth Factor 5 (FGF5) gene, a candidate gene implicated in regulating hair follicle growth cycle in other species. Sequence analyses of FGF5 in 26 cat breeds and 2 pedigrees of nonbreed cats revealed 4 separate mutations predicted to disrupt the biological activity of the FGF5 protein. Pedigree analyses demonstrated that different combinations of paired mutant FGF5 alleles segregated with the long-haired phenotype in an autosomal recessive manner. Association analyses of more than 380 genotyped breed and nonbreed cats were consistent with mutations in the FGF5 gene causing the long-haired phenotype in an autosomal recessive manner. In combination, these genomic approaches demonstrated that FGF5 is the major genetic determinant of hair length in the domestic cat.
- Published
- 2007
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45. Validation of a short tandem repeat multiplex typing system for genetic individualization of domestic cat samples.
- Author
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Coomber N, David VA, O'Brien SJ, and Menotti-Raymond M
- Subjects
- Animals, Cats genetics, DNA Fingerprinting, Microsatellite Repeats
- Abstract
Aim: To conduct developmental validation studies on a polymerase chain reaction (PCR) based short tandem repeat (STR) multiplex typing system, developed for the purpose of genetic individualization and parentage testing in domestic cat samples., Methods: To evaluate reproducibility of the typing system, the multiplex was amplified using DNA extracted from hair, blood, and buccal samples obtained from the same individual (n=13). Additional studies were performed to evaluate the system's species' specificity, using 26 North American mammalian species and two prokaryotes Sacchromyces and Escherichia coli, sensitivity, and ability to identify DNA mixtures. Patterns of Mendelian inheritance and mutation rates for the 11 loci were directly examined in a large multi-generation domestic cat pedigree (n=263)., Results: Our studies confirm that the multiplex system was species-specific for feline DNA and amplified robustly with as little as 125 picograms of genomic template DNA, demonstrating good product balance. The multiplex generated all components of a two DNA mixture when the minor component was one tenth of the major component at a threshold of 50 relative fluorescence units. The multiplex was reproducible in multiple tissue types of the same individual. Mutation rates for the 11 STR were within the range of sex averaged rates observed for Combined DNA Index System (CODIS) loci., Conclusion: The cat STR multiplex typing system is a robust and reliable tool for the use of forensic DNA analysis of domestic cat samples.
- Published
- 2007
46. The Near Eastern origin of cat domestication.
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Driscoll CA, Menotti-Raymond M, Roca AL, Hupe K, Johnson WE, Geffen E, Harley EH, Delibes M, Pontier D, Kitchener AC, Yamaguchi N, O'brien SJ, and Macdonald DW
- Subjects
- Africa, Animals, Animals, Wild genetics, DNA, Mitochondrial genetics, Europe, Haplotypes, Hybridization, Genetic, Microsatellite Repeats, Middle East, Molecular Sequence Data, Time, Animals, Domestic genetics, Cats classification, Cats genetics, Phylogeny
- Abstract
The world's domestic cats carry patterns of sequence variation in their genome that reflect a history of domestication and breed development. A genetic assessment of 979 domestic cats and their wild progenitors-Felis silvestris silvestris (European wildcat), F. s. lybica (Near Eastern wildcat), F. s. ornata (central Asian wildcat), F. s. cafra (southern African wildcat), and F. s. bieti (Chinese desert cat)-indicated that each wild group represents a distinctive subspecies of Felis silvestris. Further analysis revealed that cats were domesticated in the Near East, probably coincident with agricultural village development in the Fertile Crescent. Domestic cats derive from at least five founders from across this region, whose descendants were transported across the world by human assistance.
- Published
- 2007
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47. Mutation in CEP290 discovered for cat model of human retinal degeneration.
- Author
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Menotti-Raymond M, David VA, Schäffer AA, Stephens R, Wells D, Kumar-Singh R, O'Brien SJ, and Narfström K
- Subjects
- Animals, Cats, Cell Cycle Proteins, Cytoskeletal Proteins, DNA, Complementary, Humans, Polymorphism, Single Nucleotide, RNA, Messenger genetics, Species Specificity, Antigens, Neoplasm genetics, Models, Animal, Mutation, Neoplasm Proteins genetics, Retinal Degeneration genetics
- Abstract
A mutation in the CEP290 gene is reported in a cat pedigree segregating for autosomal recessive (AR) late-onset photoreceptor degeneration (rdAc). An initial screen of 39 candidate genes and genomic locations failed to detect linkage to cat rdAc. Linkage was ultimately established on cat B4 with 15 simple tandem repeat markers (logarithm of odds [LOD] range 4.83-15.53, Theta = 0.0), in a region demonstrating conserved synteny to human chromosome 12, 84.9-90.63 Mb. The sequence of 10 genes with feline retinal expression was examined in affected and unaffected individuals. A single-nucleotide polymorphism was characterized in intron 50 of CEP290 (IVS50 + 9T>G) that creates a strong canonical splice donor site, resulting in a 4-bp insertion and frameshift in the mRNA transcript, with subsequent introduction of a stop codon and premature truncation of the protein. A population genetic survey of 136 cats demonstrated that the rdAc mutation is in low frequency in Abyssinian populations (0.13, Sweden; 0.07, United States) and absent in breeds of non-Abyssinian heritage. Mutations in CEP290 have recently been shown to cause two human diseases, Joubert syndrome, a syndromic retinal degeneration, and Leber's congenital amaurosis, an AR early-onset retinal dystrophy. Human AR retinitis pigmentosa is among the most common causes of retinal degeneration and blindness, with no therapeutic intervention available. This identification of a large animal model for human retinal blindness offers considerable promise in developing gene-based therapies.
- Published
- 2007
- Full Text
- View/download PDF
48. A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes.
- Author
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Murphy WJ, Davis B, David VA, Agarwala R, Schäffer AA, Pearks Wilkerson AJ, Neelam B, O'Brien SJ, and Menotti-Raymond M
- Subjects
- Animals, Biological Evolution, Chromosomes, Human, X genetics, Dogs genetics, Genetic Markers, Genome, Genome, Human, Genomics, Humans, Microsatellite Repeats, Species Specificity, X Chromosome genetics, Cats genetics, Radiation Hybrid Mapping
- Abstract
We report the construction of a 1.5-Mb-resolution radiation hybrid map of the domestic cat genome. This new map includes novel microsatellite loci and markers derived from the 2X genome sequence that target previous gaps in the feline-human comparative map. Ninety-six percent of the 1793 cat markers we mapped have identifiable orthologues in the canine and human genome sequences. The updated autosomal and X-chromosome comparative maps identify 152 cat-human and 134 cat-dog homologous synteny blocks. Comparative analysis shows the marked change in chromosomal evolution in the canid lineage relative to the felid lineage since divergence from their carnivoran ancestor. The canid lineage has a 30-fold difference in the number of interchromosomal rearrangements relative to felids, while the felid lineage has primarily undergone intrachromosomal rearrangements. We have also refined the pseudoautosomal region and boundary in the cat and show that it is markedly longer than those of human or mouse. This improved RH comparative map provides a useful tool to facilitate positional cloning studies in the feline model.
- Published
- 2007
- Full Text
- View/download PDF
49. Development of Y chromosome intraspecific polymorphic markers in the Felidae.
- Author
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Luo SJ, Johnson WE, David VA, Menotti-Raymond M, Stanyon R, Cai QX, Beck T, Yuhki N, Pecon-Slattery J, Smith JL, and O'Brien SJ
- Subjects
- Animals, Base Sequence, Chromosome Mapping, DNA Primers, In Situ Hybridization, Fluorescence, Male, Microsatellite Repeats, Cats genetics, Felidae genetics, Polymorphism, Genetic, Polymorphism, Single Nucleotide, Y Chromosome
- Abstract
Y chromosome haplotyping based on microsatellites and single nucleotide polymorphisms (SNPs) has proved to be a powerful tool for population genetic studies of humans. However, the promise of the approach is hampered in the majority of nonhuman mammals by the lack of Y-specific polymorphic markers. We were able to identify new male-specific polymorphisms in the domestic cat Felis catus and 6 additional Felidae species with a combination of molecular genetic and cytogenetic approaches including 1) identifying domestic cat male-specific microsatellites from markers generated from a male cat microsatellite-enriched genomic library, a flow-sorted Y cosmid library, or a Y-specific cat bacteria artificial chromosome (BAC) clone, (2) constructing microsatellite-enriched libraries from flow-sorted Y chromosomes isolated directly from focal wildcat species, and (3) screening Y chromosome conserved anchored tagged sequences primers in Felidae species. Forty-one male-specific microsatellites were identified, but only 6 were single-copy loci, consistent with the repetitive nature of the Y chromosome. Nucleotide diversity (pi) of Y-linked intron sequences (2.1 kbp) was in the range of 0 (tiger) to 9.95 x 10(-4) (marbled cat), and the number of SNPs ranged from none in the tiger to 7 in the Asian leopard cat. The Y haplotyping system described here, consisting of 4 introns (SMCY3, SMCY7, UTY11, and DBY7) and 1 polymorphic microsatellite (SMCY-STR), represents the first available markers for tracking intraspecific male lineage polymorphisms in Felidae species and promises to provide significant insights to evolutionary and population genetic studies of the species.
- Published
- 2007
- Full Text
- View/download PDF
50. A homozygous single-base deletion in MLPH causes the dilute coat color phenotype in the domestic cat.
- Author
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Ishida Y, David VA, Eizirik E, Schäffer AA, Neelam BA, Roelke ME, Hannah SS, O'Brien SJ, and Menotti-Raymond M
- Subjects
- Animals, Animals, Domestic genetics, Base Sequence, Homozygote, Introns genetics, Microsatellite Repeats genetics, Molecular Sequence Data, Phenotype, Adaptor Proteins, Signal Transducing genetics, Cats genetics, Chromosome Mapping veterinary, Gene Deletion, Hair Color genetics
- Abstract
Three proteins have been described in humans and mice as being essential for even distribution, transport, and translocation of pigment granules, with defects in these molecules giving rise to lighter skin/coat color. The dilute phenotype in domestic cats affects both eumelanin and phaeomelanin pigment pathways; for example, black pigmentation combined with dilute appears gray and orange pigments appear cream. The dilute pigmentation segregates as a fully penetrant, autosomal recessive trait. We conducted classical linkage mapping with microsatellites in a large multigeneration pedigree of domestic cats and detected tight linkage for dilute on cat chromosome C1 (theta=0.08, LOD=10.81). Fine-mapping identified a genomic region exhibiting conserved synteny to human chromosome 2, which included one of the three dilute candidate genes, melanophilin (MLPH). Sequence analysis in dilute cats identified a single base pair deletion in exon 2 of MLPH transcripts that introduces a stop codon 11 amino acids downstream, resulting in the truncation of the bulk of the MLPH protein. The occurrence of this homozygous variant in 97 unrelated dilute cats representing 26 cat breeds and random-bred cats, along with 89 unrelated wild-type cats representing 29 breeds and random-bred cats, supports the finding that dilute is caused by this single mutation in MLPH (p<0.00001). Single-nucleotide polymorphism analyses in dilute individuals identified a single haplotype in dilute cats, suggesting that a single mutation event in MLPH gave rise to dilute in domestic cats.
- Published
- 2006
- Full Text
- View/download PDF
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