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Murphy WJ, Harris AJ. Toward telomere-to-telomere cat genomes for precision medicine and conservation biology. Genome Res 2024; 34:655-664. [PMID: 38849156 DOI: 10.1101/gr.278546.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Genomic data from species of the cat family Felidae promise to stimulate veterinary and human medical advances, and clarify the coherence of genome organization. We describe how interspecies hybrids have been instrumental in the genetic analysis of cats, from the first genetic maps to propelling cat genomes toward the T2T standard set by the human genome project. Genotype-to-phenotype mapping in cat models has revealed dozens of health-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natural and captive populations across the cat family tree will increase our understanding of the genetic architecture of traits, population dynamics, and guide a future of genome-enabled biodiversity conservation.
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Affiliation(s)
- William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA;
- Department of Biology, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
| | - Andrew J Harris
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
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Kaelin CB, McGowan KA, Hutcherson AD, Delay JM, Li JH, Kiener S, Jagannathan V, Leeb T, Murphy WJ, Barsh GS. Ancestry dynamics and trait selection in a designer cat breed. Curr Biol 2024; 34:1506-1518.e7. [PMID: 38531359 PMCID: PMC11162505 DOI: 10.1016/j.cub.2024.02.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/10/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
The Bengal cat breed was developed from intercrosses between the Asian leopard cat, Prionailurus bengalensis, and the domestic cat, Felis catus, with a last common ancestor approximately 6 million years ago. Predicted to derive ∼94% of their genome from domestic cats, regions of the leopard cat genome are thought to account for the unique pelage traits and ornate color patterns of the Bengal breed, which are similar to those of ocelots and jaguars. We explore ancestry distribution and selection signatures in the Bengal breed by using reduced representation and whole-genome sequencing from 947 cats. The mean proportion of leopard cat DNA in the Bengal breed is 3.48%, lower than predicted from breed history, and is broadly distributed, covering 93% of the Bengal genome. Overall, leopard cat introgressions do not show strong signatures of selection across the Bengal breed. However, two popular color traits in Bengal cats, charcoal and pheomelanin intensity, are explained by selection of leopard cat genes whose expression is reduced in a domestic cat background, consistent with genetic incompatibility resulting from hybridization. We characterize several selective sweeps in the Bengal genome that harbor candidate genes for pelage and color pattern and that are associated with domestic, rather than leopard, cat haplotypes. We identify the molecular and phenotypic basis of one selective sweep as reduced expression of the Fgfr2 gene, which underlies glitter, a trait desired by breeders that affects hair texture and light reflectivity.
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Affiliation(s)
- Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kelly A McGowan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - John M Delay
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Sarah Kiener
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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3
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Tensen L, Power J, Camacho G, Godinho R, Jansen van Vuuren B, Fischer K. Molecular tracking and prevalence of the red colour morph restricted to a harvested leopard population in South Africa. Evol Appl 2022; 15:1028-1041. [PMID: 35782007 PMCID: PMC9234631 DOI: 10.1111/eva.13423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 12/02/2022] Open
Abstract
The red leopard (Panthera pardus) colour morph is a colour variant that occurs only in South Africa, where it is confined to the Central Bushveld bioregion. Red leopards have been spreading over the past 40 years, which raises the speculation that the prevalence of this phenotype is related to low dispersal of young individuals owing to high off‐take in the region. Intensive selective hunting tends to remove large resident male leopards from the breeding population, which gives young male leopards the chance to mate with resident female leopards that are more likely to be their relatives, eventually increasing the frequency of rare genetic variants. To investigate the genetic mechanisms underlying the red coat colour morph in leopards, and whether its prevalence in South Africa relates to an increase in genetic relatedness in the population, we sequenced exons of six coat colour‐associated genes and 20 microsatellite loci in twenty Wild‐type and four red leopards. The results were combined with demographic data available from our study sites. We found that red leopards own a haplotype in homozygosity identified by two SNPs and a 1 bp deletion that causes a frameshift in the tyrosinase‐related protein 1 (TYRP1), a gene known to be involved in the biosynthesis of melanin. Microsatellite analyses indicate clear signs of a population bottleneck and a relatedness of 0.11 among all pairwise relationships, eventually supporting our hypothesis that a rare colour morph in the wild has increased its local frequency due to low natal dispersal, while subject to high human‐induced mortality rate.
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Affiliation(s)
- Laura Tensen
- Institute for Integrated Natural Sciences University of Koblenz‐ Landau Germany
- Department of Zoology University of Johannesburg South Africa
| | - John Power
- Directorate of Biodiversity Management, Department of Economic Development, Environment, Conservation and Tourism North West Provincial Government South Africa
| | | | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto Vairão Portugal
- Department of Zoology University of Johannesburg South Africa
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão Vairão Portugal
| | | | - Klaus Fischer
- Institute for Integrated Natural Sciences University of Koblenz‐ Landau Germany
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Sagar V, Kaelin CB, Natesh M, Reddy PA, Mohapatra RK, Chhattani H, Thatte P, Vaidyanathan S, Biswas S, Bhatt S, Paul S, Jhala YV, Verma MM, Pandav B, Mondol S, Barsh GS, Swain D, Ramakrishnan U. High frequency of an otherwise rare phenotype in a small and isolated tiger population. Proc Natl Acad Sci U S A 2021; 118:e2025273118. [PMID: 34518374 PMCID: PMC8488692 DOI: 10.1073/pnas.2025273118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2021] [Indexed: 11/18/2022] Open
Abstract
Most endangered species exist today in small populations, many of which are isolated. Evolution in such populations is largely governed by genetic drift. Empirical evidence for drift affecting striking phenotypes based on substantial genetic data are rare. Approximately 37% of tigers (Panthera tigris) in the Similipal Tiger Reserve (in eastern India) are pseudomelanistic, characterized by wide, merged stripes. Camera trap data across the tiger range revealed the presence of pseudomelanistic tigers only in Similipal. We investigated the genetic basis for pseudomelanism and examined the role of drift in driving this phenotype's frequency. Whole-genome data and pedigree-based association analyses from captive tigers revealed that pseudomelanism cosegregates with a conserved and functionally important coding alteration in Transmembrane Aminopeptidase Q (Taqpep), a gene responsible for similar traits in other felid species. Noninvasive sampling of tigers revealed a high frequency of the Taqpep p.H454Y mutation in Similipal (12 individuals, allele frequency = 0.58) and absence from all other tiger populations (395 individuals). Population genetic analyses confirmed few (minimal number) tigers in Similipal, and its genetic isolation, with poor geneflow. Pairwise FST (0.33) at the mutation site was high but not an outlier. Similipal tigers had low diversity at 81 single nucleotide polymorphisms (mean heterozygosity = 0.28, SD = 0.27). Simulations were consistent with founding events and drift as possible drivers for the observed stark difference of allele frequency. Our results highlight the role of stochastic processes in the evolution of rare phenotypes. We highlight an unusual evolutionary trajectory in a small and isolated population of an endangered species.
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Affiliation(s)
- Vinay Sagar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
| | - Christopher B Kaelin
- Department of Genetics, Stanford University, Palo Alto, CA 94309
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Meghana Natesh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Biology Department, Indian Institute of Science Education and Research, Tirupati 411008, India
| | - P Anuradha Reddy
- Laboratory for Conservation of Endangered Species, Center for Cellular & Molecular Biology, Hyderabad 500048, India
| | | | - Himanshu Chhattani
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Prachi Thatte
- World Wide Fund for Nature - India, New Delhi 110003 India
| | - Srinivas Vaidyanathan
- Foundation for Ecological Research, Advocacy and Learning, Auroville Post, Tamil Nadu 605101 India
| | | | | | - Shashi Paul
- Odisha Forest Department, Bhubaneswar 751023, India
| | - Yadavendradev V Jhala
- Wildlife Institute of India, Dehradun 248001, India
- National Tiger Conservation Authority, Wildlife Institute of India Tiger Cell, Wildlife Institute of India, Dehradun 248001, India
| | | | | | | | - Gregory S Barsh
- Department of Genetics, Stanford University, Palo Alto, CA 94309
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Debabrata Swain
- Former Member Secretary, National Tiger Conservation Authority, New Delhi 110003, India
- Former Principal Chief Conservator of Forest and Head of Forest Force, Indian Forest Service, Bhubaneswar 751023, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
- DBT - Wellcome Trust India Alliance, Hyderabad 500034, India
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A domestic cat whole exome sequencing resource for trait discovery. Sci Rep 2021; 11:7159. [PMID: 33785770 PMCID: PMC8009874 DOI: 10.1038/s41598-021-86200-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
Over 94 million domestic cats are susceptible to cancers and other common and rare diseases. Whole exome sequencing (WES) is a proven strategy to study these disease-causing variants. Presented is a 35.7 Mb exome capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of the cat genome. Whole exome sequencing was conducted on 41 cats with known and unknown genetic diseases and traits, of which ten cats had matching whole genome sequence (WGS) data available, used to validate WES performance. At 80 × mean exome depth of coverage, 96.4% of on-target base coverage had a sequencing depth > 20-fold, while over 98% of single nucleotide variants (SNVs) identified by WGS were also identified by WES. Platform-specific SNVs were restricted to sex chromosomes and a small number of olfactory receptor genes. Within the 41 cats, we identified 31 previously known causal variants and discovered new gene candidate variants, including novel missense variance for polycystic kidney disease and atrichia in the Peterbald cat. These results show the utility of WES to identify novel gene candidate alleles for diseases and traits for the first time in a feline model.
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Behavior and health issues in Bengal cats as perceived by their owners: A descriptive study. J Vet Behav 2021. [DOI: 10.1016/j.jveb.2020.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Brashear WA, Raudsepp T, Murphy WJ. Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation. Genome Res 2018; 28:1841-1851. [PMID: 30381290 PMCID: PMC6280758 DOI: 10.1101/gr.237586.118] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/27/2018] [Indexed: 12/20/2022]
Abstract
Despite claims that the mammalian Y Chromosome is on a path to extinction, comparative sequence analysis of primate Y Chromosomes has shown the decay of the ancestral single-copy genes has all but ceased in this eutherian lineage. The suite of single-copy Y-linked genes is highly conserved among the majority of eutherian Y Chromosomes due to strong purifying selection to retain dosage-sensitive genes. In contrast, the ampliconic regions of the Y Chromosome, which contain testis-specific genes that encode the majority of the transcripts on eutherian Y Chromosomes, are rapidly evolving and are thought to undergo species-specific turnover. However, ampliconic genes are known from only a handful of species, limiting insights into their long-term evolutionary dynamics. We used a clone-based sequencing approach employing both long- and short-read sequencing technologies to assemble ∼2.4 Mb of representative ampliconic sequence dispersed across the domestic cat Y Chromosome, and identified the major ampliconic gene families and repeat units. We analyzed fluorescence in situ hybridization, qPCR, and whole-genome sequence data from 20 cat species and revealed that ampliconic gene families are conserved across the cat family Felidae but show high transcript diversity, copy number variation, and structural rearrangement. Our analysis of ampliconic gene evolution unveils a complex pattern of long-term gene content stability despite extensive structural variation on a nonrecombining background.
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Affiliation(s)
- Wesley A Brashear
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
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Arahori M, Chijiiwa H, Takagi S, Bucher B, Abe H, Inoue-Murayama M, Fujita K. Microsatellite Polymorphisms Adjacent to the Oxytocin Receptor Gene in Domestic Cats: Association with Personality? Front Psychol 2017; 8:2165. [PMID: 29326623 PMCID: PMC5741686 DOI: 10.3389/fpsyg.2017.02165] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 11/28/2017] [Indexed: 01/06/2023] Open
Abstract
A growing number of studies have explored the oxytocin system in humans and non-human animals, and some have found important genetic polymorphisms in the oxytocin receptor gene (OXTR) associated with the bonding system, social behaviors, and personality in several species. Although single nucleotide polymorphisms in OXTR have been well-examined in various species, microsatellites (or short tandem repeats) adjacent to OXTR have rarely been studied, despite some suggestions that microsatellite polymorphisms near genes might play a role in genetic transcription and translation. In this study, we surveyed microsatellites in the upstream, intron, and downstream regions of OXTR in domestic cats (Felis catus). We succeeded in amplifying 5 out of 10 regions, and recognized these five regions as polymorphic. We compared allele frequencies in these five regions between mongrel cats in Japan (n = 100) and cats of 10 pure breeds (n = 40). There were significant differences in allele frequencies between the two populations in all microsatellite regions. Additionally, the owners of mongrel cats answered a comprehensive personality questionnaire, and factor analysis extracted four factors (Openness, Friendliness, Roughness, and Neuroticism). We examined the association between the microsatellite genotypes, age, sex, neutering status, and personality scores. Compared to their counterparts, younger cats tended to score higher on Openness, male cats scored higher on Friendliness, and female and neutered cats scored higher on Roughness. When we divided the sample into three groups depending on the length of alleles, we found a marginally significant association between Friendliness and MS3. Additionally, we found a sex-mediated effect of genotypes in MS4 on Friendliness, resulting in different effects on females and males. Our findings that mongrel cats had longer alleles in MS3 and MS4 than purebred cats, and that those cats tended to score higher on Friendliness, supported the previous findings. However, future studies such as comparison between purebred cats with apparently different origin or personality are required to determine the association of genetic variants in the OXTR with personality.
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Affiliation(s)
- Minori Arahori
- Department of Psychology, Graduate School of Letters, Kyoto University, Kyoto, Japan.,Japan Society for the Promotion of Science, Tokyo, Japan
| | - Hitomi Chijiiwa
- Department of Psychology, Graduate School of Letters, Kyoto University, Kyoto, Japan.,Japan Society for the Promotion of Science, Tokyo, Japan
| | - Saho Takagi
- Department of Psychology, Graduate School of Letters, Kyoto University, Kyoto, Japan.,Japan Society for the Promotion of Science, Tokyo, Japan
| | - Benoit Bucher
- Department of Psychology, Graduate School of Letters, Kyoto University, Kyoto, Japan.,Japan Society for the Promotion of Science, Tokyo, Japan
| | - Hideaki Abe
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Tsukuba, Japan
| | - Kazuo Fujita
- Department of Psychology, Graduate School of Letters, Kyoto University, Kyoto, Japan
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Bourguet A, Chaudieu G, Briatta A, Guyonnet A, Abitbol M, Chahory S. Cataracts in a population of Bengal cats in France. Vet Ophthalmol 2017; 21:10-18. [PMID: 28444876 DOI: 10.1111/vop.12470] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To document the clinical appearance and prevalence of cataracts in a French population of Bengal cats. METHODS Two distinct populations of Bengal cats were examined as follows: (i) 51 animals recruited for evaluation of national prevalence of ocular diseases in an observational study conducted between October 2014 and November 2016 at the Alfort ophthalmology unit; (ii) 12 patients referred for cataract diagnosis examined at a veterinary eye clinic located in central France, between December 2014 and February 2016. Buccal swabs or blood samples for DNA analysis were collected from all patients. The pedigrees of the examined Bengal cats were also investigated. RESULTS Cataracts were diagnosed in 23 of 51 (45%) cats in the observational study and in all cats in the referral population, mostly bilaterally. Visual impairment was never reported. Age of subjects affected by cataracts ranged from 3 months to 9.6 years (median: 1.9 years). Cataracts were classified as nuclear cataracts (14 of 23 in the observational group and 12 of 12 in the referral group) with a focal, perinuclear, posterior, or complete nuclear pattern, or posterior polar subcapsular cataracts (10 of 23 only in the observational group). An inherited congenital origin appears to be the most likely hypothesis. The pedigree analysis suggests a hereditary component of cataract formation, but further analyses in a larger population or test matings are needed to determine the exact mode of inheritance. CONCLUSION Presumed inherited cataracts appear to have a high prevalence in Bengal cats in France. The main manifestations are nuclear or subcapsular form, mostly bilateral, symmetrical, and apparently nonprogressive.
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Affiliation(s)
- Aurélie Bourguet
- Ophthalmology Unit, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, 7 Avenue du Général de Gaulle, 94700, Maisons-Alfort Cedex, France
| | - Gilles Chaudieu
- Clinique Vétérinaire, 52 boulevard M. Pourchon, Clermont-Ferrand, 63100, France
| | - Alice Briatta
- Ophthalmology Unit, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, 7 Avenue du Général de Gaulle, 94700, Maisons-Alfort Cedex, France
| | - Alexandre Guyonnet
- Ophthalmology Unit, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, 7 Avenue du Général de Gaulle, 94700, Maisons-Alfort Cedex, France
| | - Marie Abitbol
- INSERM U955-E10, IMRB, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est Créteil, Maisons-Alfort Cedex, France
| | - Sabine Chahory
- Ophthalmology Unit, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, 7 Avenue du Général de Gaulle, 94700, Maisons-Alfort Cedex, France
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Martin PM, Palhière I, Ricard A, Tosser-Klopp G, Rupp R. Genome Wide Association Study Identifies New Loci Associated with Undesired Coat Color Phenotypes in Saanen Goats. PLoS One 2016; 11:e0152426. [PMID: 27030980 PMCID: PMC4816504 DOI: 10.1371/journal.pone.0152426] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/14/2016] [Indexed: 11/18/2022] Open
Abstract
This paper reports a quantitative genetics and genomic analysis of undesirable coat color patterns in goats. Two undesirable coat colors have routinely been recorded for the past 15 years in French Saanen goats. One fifth of Saanen females have been phenotyped “pink” (8.0%) or “pink neck” (11.5%) and consequently have not been included in the breeding program as elite animals. Heritability of the binary “pink” and “pink neck” phenotype, estimated from 103,443 females was 0.26 for “pink” and 0.21 for “pink neck”. Genome wide association studies (using haplotypes or single SNPs) were implemented using a daughter design of 810 Saanen goats sired by 9 Artificial Insemination bucks genotyped with the goatSNP50 chip. A highly significant signal (-log10pvalue = 10.2) was associated with the “pink neck” phenotype on chromosome 11, suggesting the presence of a major gene. Highly significant signals for the “pink” phenotype were found on chromosomes 5 and 13 (-log10p values of 7.2 and, 7.7 respectively). The most significant SNP on chromosome 13 was in the ASIP gene region, well known for its association with coat color phenotypes. Nine significant signals were also found for both traits. The highest signal for each trait was detected by both single SNP and haplotype approaches, whereas the smaller signals were not consistently detected by the two methods. Altogether these results demonstrated a strong genetic control of the “pink” and “pink neck” phenotypes in French Saanen goats suggesting that SNP information could be used to identify and remove undesired colored animals from the breeding program.
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Affiliation(s)
- Pauline Marie Martin
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
- * E-mail:
| | - Isabelle Palhière
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Anne Ricard
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Gwenola Tosser-Klopp
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Rachel Rupp
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
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Abstract
PRACTICAL RELEVANCE The health of the cat is a complex interaction between its environment (nurture) and its genetics (nature). Over 70 genetic mutations (variants) have been defined in the cat, many involving diseases, structural abnormalities and clinically relevant health concerns. As more of the cat's genome is deciphered, less commonly will the term 'idiopathic' be used regarding the diagnosis of diseases and unique health conditions. State-of-the-art health care will include DNA profiling of the individual cat, and perhaps its tumor, to establish the best treatment approaches. Genetic testing and eventually whole genome sequencing should become routine diagnostics for feline health care. GLOBAL IMPORTANCE Cat breeds have disseminated around the world. Thus, practitioners should be aware of the breeds common to their region and the mutations found in those regional populations. Specific random-bred populations can also have defined genetic characteristics and mutations. AUDIENCE This review of 'the good, the bad and the ugly' DNA variants provides the current state of knowledge for genetic testing and genetic health management for cats. It is aimed at feline and general practitioners wanting to update and review the basics of genetics, what tests are available for cats and sources for genetic testing. The tables are intended to be used as references in the clinic. Practitioners with a high proportion of cat breeder clientele will especially benefit from the review. EVIDENCE BASE The data presented is extracted from peer-reviewed publications pertaining to mutation identification, and relevant articles concerning the heritable trait and/or disease. The author also draws upon personal experience and expertise in feline genetics.
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Affiliation(s)
- Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO 65201, USA
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