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Jaito W, Singchat W, Patta C, Thatukan C, Kumnan N, Chalermwong P, Budi T, Panthum T, Wongloet W, Wattanadilokchatkun P, Thong T, Muangmai N, Han K, Duengkae P, Phatcharakullawarawat R, Srikulnath K. Shared alleles and genetic structures in different Thai domestic cat breeds: the possible influence of common racial origins. Genomics Inform 2024; 22:12. [PMID: 39085978 PMCID: PMC11292921 DOI: 10.1186/s44342-024-00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024] Open
Abstract
Over hundreds of years, cats have been domesticated and selectively bred, resulting in numerous pedigreed breeds expedited by recent cat shows and breeding associations. Concerns have been raised about the limited breeding options and the genetic implications of inbreeding, indicating challenges in maintaining genetic diversity and accurate identification in purebred cats. In this study, genetic variability and structure were examined in 5 Thai domestic cat breeds using 15 microsatellite markers and mitochondrial DNA (mtDNA) D-loop sequencing. In total, 184 samples representing the Wichien Maat (WCM), Suphalak (SL), Khao-Manee (KM), Korat (KR), and Konja (KJ) breeds were analyzed. High genetic diversity (Ho and He > 0.5) was observed in all breeds, and mtDNA analysis revealed two primary haplogroups (A and B) that were shared among all domestic cat breeds in Thailand and globally. However, minor differences were observed between Thai domestic cat breeds based on clustering analyses, in which a distinct genetic structure was observed in the WCM breed. This suggests that allele fixation for distinctive morphological traits has occurred in Thai domestic cat breeds that emerged in isolated regions with shared racial origins. Analysis of relationships among individuals within the breed revealed high identification efficiency in Thai domestic cat breeds (P(ID)sibs < 10-4). Additionally, diverse and effective individual identification can be ensured by optimizing marker efficiency by using only nine loci. This comprehensive genetic characterization provides valuable insights into conservation strategies and breeding practices for Thai domestic cat breeds.
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Grants
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- 3/2564 Thailand Science Research and Innovation (TSRI) grant through the Kasetsart University Reinventing University Program 2021
- 3/2564 Thailand Science Research and Innovation (TSRI) grant through the Kasetsart University Reinventing University Program 2021
- Higher Education for Industry Consortium (Hi–FI)
- International SciKU Branding (ISB), Faculty of Science, Kasetsart University
- High-Quality Research Graduate Development Cooperation Project between Kasetsart University and the National Science and Technology Development Agency (NSTDA)
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Affiliation(s)
- Wattanawan Jaito
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
| | - Chananya Patta
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Chadaphon Thatukan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Nichakorn Kumnan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Microbiology, Dankook University, Cheonan, 31116, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, 31116, Korea
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | | | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, 10900, Thailand.
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2
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Patterson EC, Lall GM, Neumann R, Ottolini B, Sacchini F, Foster AP, Jobling MA, Wetton JH. Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing. Forensic Sci Int Genet 2023; 67:102944. [PMID: 37820546 DOI: 10.1016/j.fsigen.2023.102944] [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: 06/24/2023] [Revised: 09/14/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
Hair shed by domestic cats is a potentially useful source of forensic evidence. Analysable hair DNA is predominantly mitochondrial, but the recent domestication history of cats means that mtDNA diversity is low. A 402-bp control region segment is usually sequenced, defining only a small number of distinct haplotypes in populations. Previously, we used a long-amplicon approach to sequence whole mitogenomes in a sample of blood DNAs from 119 UK cats, greatly increasing observed diversity and reducing random match probabilities. To exploit this variation for forensic analysis, we here describe a multiplex system that amplifies the cat mitogenome in 60 overlapping amplicons of mean length 360 bp, followed by Nanopore sequencing. Variants detected in multiplex sequence data from unrooted hair completely mirror those from long-amplicon data from blood from the same individuals. However, applying the multiplex to matched blood DNA reveals additional sequence variants which derive from the major feline nuclear mitochondrial insertion sequence (numt), which covers 7.9 kb of the 17-kb mitogenome and exists in multiple tandem copies. We use long-amplicon Nanopore sequencing to investigate numt variation in a set of cats, together with an analysis of published genome sequences, and show that numt arrays are variable in both structure and sequence, thus providing a potential source of uncertainty when nuclear DNA predominates in a sample. Forensic application of the multiplex was demonstrated by matching hairs from a cat with skeletal remains from its putative mother, both of which shared a globally common haplotype at the control region. The random match probability in this case with the CR 402-bp segment was 0.21 and this decreased to 0.03 when considering the whole mitogenome. The developed multiplex and sequencing approach, when applied to cat hair where nuclear DNA is scarce, can provide a reliable and highly discriminating source of forensic genetic evidence from a single hair. The confounding effect of numt co-amplification in degraded samples where mixed sequences are observed can be mitigated by variant phasing, and by comparison with numt sequence diversity data, such as those presented here.
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Affiliation(s)
- Emily C Patterson
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Gurdeep Matharu Lall
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Barbara Ottolini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Federico Sacchini
- IDEXX Laboratories Italia S.r.l., Via Guglielmo Silva, 36-20149 Milano (MI), Italy
| | - Aiden P Foster
- Bristol Veterinary School, University of Bristol, Langford House, Langford, North Somerset BS40 5DU, UK
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK.
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3
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Liang HM, Yang KT, Cheng YT, Chang SC, Lin CY, Tsai MY, Lin DY, Hung KH. Genetic Diversity and Population Structure in Captive Populations of Formosan Sambar Deer ( Rusa unicolor swinhoei). Animals (Basel) 2023; 13:3106. [PMID: 37835712 PMCID: PMC10571969 DOI: 10.3390/ani13193106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Formosan sambar deer (Rusa unicolor swinhoei) are of great economic significance in Taiwan, resulting in a substantial increase in deer farming to meet the high demand for velvet antlers. Inbreeding depression and reduced genetic variability can lead to the deterioration of captive populations. In this study, 239 Formosan sambar deer were genotyped using 13 microsatellites to analyze their genetic diversity and population genetic structure. Our results indicate a high-resolution power of these microsatellites in individual discrimination and parentage analysis. However, captive populations exhibit a low level of genetic diversity, likely because of inbreeding and bottleneck effects. Both principal coordinate analysis (PCoA) and STRUCTURE analyses revealed two distinct and segregated genetic groups within the captive populations and indicated no clear population genetic structure among the captive populations. Introducing new genetic material from the wild through translocation offers a potential solution for mitigating the impact of inbreeding and enhancing genetic diversity. The comprehensive information obtained from these genetic analyses is crucial for the development of effective breeding strategies aimed at preserving and enhancing Formosan sambar deer populations.
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Affiliation(s)
- Hsiao-Mei Liang
- Southern Region Branch, Livestock Research Institute, Ministry of Agriculture, Pingtung 912013, Taiwan; (H.-M.L.); (S.-C.C.)
| | - Kuo-Tai Yang
- Department of Animal Science, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Yu-Tzu Cheng
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Shen-Chang Chang
- Southern Region Branch, Livestock Research Institute, Ministry of Agriculture, Pingtung 912013, Taiwan; (H.-M.L.); (S.-C.C.)
| | - Cheng-Yung Lin
- Livestock Management Division, Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan; (C.-Y.L.); (M.-Y.T.)
| | - Ming-Yang Tsai
- Livestock Management Division, Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan; (C.-Y.L.); (M.-Y.T.)
| | - Der-Yuh Lin
- Genetics and Physiology Division, Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan;
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
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4
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Ueno H, Itoh T, Nasuno T, Konno W, Kondo A, Konishi I, Inukai H, Kokubo D, Isaka M, Islam MS, Yamato O. Pyruvate kinase deficiency mutant gene carriage in stray cats and rescued cats from animal hoarding in Hokkaido, Japan. J Vet Med Sci 2023; 85:972-976. [PMID: 37495518 PMCID: PMC10539810 DOI: 10.1292/jvms.23-0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023] Open
Abstract
The mutant allele frequency of the Pyruvate kinase (PK) gene has been investigated mostly in pure breed cats. We investigated the PK mutant gene in stray and animal hoarding mongrel cats in Hokkaido, Japan. We also investigated the kinship of individuals carrying the mutant gene. Genotyping was conducted using the previously reported real-time PCR method. Fourteen microsatellite markers were used to identify the parents and offspring of cats carrying the PK mutant gene, and some kinship such as parent-offspring and siblings was observed. Some stray and animal hoarding cats carried the PK mutation gene and that consanguinity was confirmed among these cats indicated that the PK mutation gene was spread by unregulated interbreeding.
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Affiliation(s)
- Hiroshi Ueno
- Department of Companion Animal Clinical Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan
- National BioResource Project Japanese Macaques, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Aichi, Japan
| | - Tomohito Itoh
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Gumma, Japan
| | | | - Wataru Konno
- Department of Companion Animal Clinical Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan
| | | | | | | | - Daiki Kokubo
- Department of Companion Animal Clinical Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan
| | - Mitsuhiro Isaka
- Department of Companion Animal Clinical Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan
| | - Md Shafiqul Islam
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Osamu Yamato
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
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5
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Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Nagata SI. Construction of an individual identification panel for horses using insertion and deletion markers. J Equine Sci 2023; 34:83-92. [PMID: 37781568 PMCID: PMC10534061 DOI: 10.1294/jes.34.83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/21/2023] [Indexed: 10/03/2023] Open
Abstract
Individual identification and paternity testing are important for avoiding inbreeding in the management of small populations of wild and domestic animals. In horse racing industries, they are extremely important for identifying and registering individuals and doping control to ensure fair competition. In this study, we constructed an individual identification panel for horses by using insertion and deletion (INDEL) markers. The panel included 39 INDEL markers selected from a whole-genome INDEL database. Genotyping of 89 Thoroughbreds showed polymorphisms with minor allele frequencies (MAFs) of 0.180-0.489 in all markers. The total probability of exclusion for paternity testing, power of discrimination, and probability of identity were 0.9994271269, >0.9999999999, and 0.9999999987, respectively. The panel was applied to 13 trios (sires, dams, and foals), and no contradictions were observed in genetic inheritance among the trios. When this panel was applied to the trios (52 trios) containing false fathers, an average of 7.3 markers excluded parentage relationships. In addition, genomic DNA extracted from the urine of six horses was partially genotyped for 39 markers, and 6-28 markers were successfully genotyped. The newly constructed panel has two advantages: a low marker mutation rate compared with short tandem repeats and a genotyping procedure that is as simple as short tandem repeat typing compared with single nucleotide variant typing. This panel can be applied for individual identification, paternity determination, and urine-sample identification in Thoroughbred horses.
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Affiliation(s)
- Teruaki Tozaki
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
| | - Aoi Ohnuma
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
| | - Mio Kikuchi
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
| | - Taichiro Ishige
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
| | - Hironaga Kakoi
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
| | - Kei-ichi Hirota
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
| | - Shun-ichi Nagata
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
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de Groot M, Anderson H, Bauer H, Bauguil C, Bellone RR, Brugidou R, Buckley RM, Dovč P, Forman O, Grahn RA, Kock L, Longeri M, Mouysset‐Geniez S, Qiu J, Sofronidis G, van der Goor LHP, Lyons LA. Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus). Anim Genet 2021; 52:675-682. [PMID: 34143521 PMCID: PMC8519126 DOI: 10.1111/age.13100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2021] [Indexed: 01/02/2023]
Abstract
The domestic cat (Felis silvestris catus) is a valued companion animal throughout the world. Over 60 different cat breeds are accepted for competition by the cat fancy registries in different countries. Genetic markers, including short tandem repeats and SNPs, are available to evaluate and manage levels of inbreeding and genetic diversity, population and breed structure relationships, and individual identification for forensic and registration purposes. The International Society of Animal Genetics (ISAG) hosts the Applied Genetics in Companion Animals Workshop, which supports the standardization of genetic marker panels and genotyping for the identification of cats via comparison testing. SNP panels have been in development for many species, including the domestic cat. An ISAG approved core panel of SNPs for use in cat identification and parentage analyses is presented. SNPs (n = 121) were evaluated by different university-based and commercial laboratories using 20 DNA samples as part of the ISAG comparison testing procedures. Different SNP genotyping technologies were examined, including DNA arrays, genotyping-by-sequencing and mass spectroscopy, to select a robust and efficient panel of 101 SNPs as the ISAG core panel for cats. The SNPs are distributed across all chromosomes including two on the X chromosome and an XY pseudo-autosomal sexing marker (zinc-finger XY; ZFXY). A population study demonstrated that the markers have an average polymorphic information content of 0.354 and a power of exclusion greater than 0.9999. The SNP panel should keep testing affordable while also allowing for the development of additional panels to monitor health, phenotypic traits, hybrid cats and highly inbred cats.
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Affiliation(s)
- M. de Groot
- MolGenTraverse 2VeenendaalUtrecht3905NLThe Netherlands
| | | | - H. Bauer
- Laboklin GMBH & Co. KGBad Kissingen97688Germany
| | | | - R. R. Bellone
- Veterinary Genetics LaboratorySchool of Veterinary MedicineUniversity of CaliforniaDavisCA95616USA
- Population Health and ReproductionSchool of Veterinary MedicineUniversity of CaliforniaDavisCA95616USA
| | | | - R. M. Buckley
- Department of Veterinary Medicine and SurgeryCollege of Veterinary MedicineUniversity of MissouriColumbiaMO65211USA
| | - P. Dovč
- Department of Animal ScienceBiotechnical FacultyUniversity of LjubljanaLjubljana1000Slovenia
| | | | - R. A. Grahn
- Veterinary Genetics LaboratorySchool of Veterinary MedicineUniversity of CaliforniaDavisCA95616USA
| | - L. Kock
- Neogen GenomicsLincolnNE68504USA
| | - M. Longeri
- Department of Veterinary MedicineUniversity of MilanMilan20133Italy
| | | | - J. Qiu
- Neogen GenomicsLincolnNE68504USA
| | - G. Sofronidis
- Orivet Genetic Pet CareSuite St. KildaMelbourneVic.3182Australia
| | | | - L. A. Lyons
- Department of Veterinary Medicine and SurgeryCollege of Veterinary MedicineUniversity of MissouriColumbiaMO65211USA
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van der Zwan H, van der Sluis R. Polly Wants a Genome: The Lack of Genetic Testing for Pet Parrot Species. Genes (Basel) 2021; 12:1097. [PMID: 34356113 PMCID: PMC8307168 DOI: 10.3390/genes12071097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/04/2022] Open
Abstract
Parrots are considered the third most popular pet species, after dogs and cats, in the United States of America. Popular birds include budgerigars, lovebirds and cockatiels and are known for their plumage and vocal learning abilities. Plumage colour variation remains the main driving force behind breeder selection. Despite the birds' popularity, only two molecular genetic tests-bird sexing and pathogen screening-are commercially available to breeders. For a limited number of species, parentage verification tests are available, but are mainly used in conservation and not for breeding purposes. No plumage colour genotyping test is available for any of the species. Due to the fact that there isn't any commercial plumage genotype screening or parentage verification tests available, breeders mate close relatives to ensure recessive colour alleles are passed to the next generation. This, in turn, leads to inbreeding depression and decreased fertility, lower hatchability and smaller clutch sizes, all important traits in commercial breeding systems. This review highlights the research carried out in the field of pet parrot genomics and points out the areas where future research can make a vital contribution to understanding how parrot breeding can be improved to breed healthy, genetically diverse birds.
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Affiliation(s)
- Henriëtte van der Zwan
- Focus Area for Human Metabolomics, North-West University, Potchefstroom 2531, South Africa;
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8
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Kim SM, Yun SW, Cho GJ. Assessment of genetic diversity using microsatellite markers to compare donkeys (Equus asinus) with horses (Equus caballus). Anim Biosci 2021; 34:1460-1465. [PMID: 33902168 PMCID: PMC8495341 DOI: 10.5713/ab.20.0860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/20/2021] [Indexed: 11/29/2022] Open
Abstract
Objective The study aimed to evaluate the diversity of donkey populations by comparing with the diversity of Thoroughbred and Jeju Halla horses; identified breeding backgrounds can contribute to management and conservation of donkeys in South Korea. Methods A total of 100 horse (50 Thoroughbreds and 50 Jeju Halla horses) and 79 donkeys samples were genotyped with 15 microsatellite markers (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3, and VHL20), to identify genetic diversity and relationships among horses and donkeys. Results The observed number of alleles per locus ranged from 1 (ASB17, HMS1) to 14 (AHT5), with a mean value of 4.87, 8.00, and 5.87 in Thoroughbreds, Jeju Halla horses, and donkeys, respectively. Of the 15 markers, AHT4, AHT5, ASB23, CA425, HMS2, HMS3, HTG4, HTG10, and LEX3 loci had relatively high polymorphism information content (PIC) values (PIC>0.5) in these three populations. Mean levels of genetic variation were HE = 0.6721 and HO = 0.6600 in Thoroughbreds, HE = 0.7898 and HO = 0.7100 in Jeju Halla horses, and HE = 0.5635 and HO = 0.4861 in donkeys. Of the 15 loci in donkeys, three loci had negative inbreeding coefficients (FIS), with a moderate mean FIS (0.138). The FIS estimate for the HTG4 marker was highest (0.531) and HMS6 marker was lowest (−0.001). The total probability of exclusion value of 15 microsatellite loci was 0.9996 in donkeys. Conclusion Genetic cluster analysis showed that the genetic relationship among 79 donkeys was generally consistent with pedigree records. Among the three breeds, donkeys and Thoroughbred horses formed clearly different groups, but the group of Jeju Halla horses overlapped with that of Thoroughbred horses, suggesting that the loci would be suitable for donkey parentage testing. Therefore, the results of this study are a valid tool for genetic study and conservation of donkeys.
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Affiliation(s)
- Su-Min Kim
- College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea
| | - Sung Wook Yun
- College of Veterinary Medicine and Institute of Equine Medicine, Kyungpook National University, Daegu 41566, Korea
| | - Gil-Jae Cho
- College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea.,College of Veterinary Medicine and Institute of Equine Medicine, Kyungpook National University, Daegu 41566, Korea
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9
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Lyons LA, Buckley RM. Direct-to-Consumer Genetic Testing for Domestic Cats. Vet Clin North Am Small Anim Pract 2020; 50:991-1000. [PMID: 32665138 DOI: 10.1016/j.cvsm.2020.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The era of precision/genomic medicine has arrived, including its application within veterinary medicine for the health care of companion animals. The plummeting costs of assaying large groups of genetic tests into one panel has led many laboratories offering direct-to-consumer (DTC) genetic testing for animals, including cats. However, proper education of the consumer and the veterinarian is lacking, causing a significant lack of genetic counseling pertaining to the results of the genetic tests. This article addresses the current state of DTC testing in domestic cats and the implications for veterinary care.
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Affiliation(s)
- Leslie A Lyons
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri - Columbia, E109 Vet Med Building, 825 East Campus Loop, Columbia, MO 65211, USA.
| | - Reuben M Buckley
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri - Columbia, E109 Vet Med Building, 825 East Campus Loop, Columbia, MO 65211, USA
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10
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Buckley RM, Gandolfi B, Creighton EK, Pyne CA, Bouhan DM, LeRoy ML, Senter DA, Gobble JR, Abitbol M, Lyons LA. Werewolf, There Wolf: Variants in Hairless Associated with Hypotrichia and Roaning in the Lykoi Cat Breed. Genes (Basel) 2020; 11:E682. [PMID: 32580512 PMCID: PMC7348984 DOI: 10.3390/genes11060682] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 12/22/2022] Open
Abstract
A variety of cat breeds have been developed via novelty selection on aesthetic, dermatological traits, such as coat colors and fur types. A recently developed breed, the lykoi (a.k.a. werewolf cat), was bred from cats with a sparse hair coat with roaning, implying full color and all white hairs. The lykoi phenotype is a form of hypotrichia, presenting as a significant reduction in the average numbers of follicles per hair follicle group as compared to domestic shorthair cats, a mild to severe perifollicular to mural lymphocytic infiltration in 77% of observed hair follicle groups, and the follicles are often miniaturized, dilated, and dysplastic. Whole genome sequencing was conducted on a single lykoi cat that was a cross between two independently ascertained lineages. Comparison to the 99 Lives dataset of 194 non-lykoi cats suggested two variants in the cat homolog for Hairless (HR) (HR lysine demethylase and nuclear receptor corepressor) as candidate causal gene variants. The lykoi cat was a compound heterozygote for two loss of function variants in HR, an exon 3 c.1255_1256dupGT (chrB1:36040783), which should produce a stop codon at amino acid 420 (p.Gln420Serfs*100) and, an exon 18 c.3389insGACA (chrB1:36051555), which should produce a stop codon at amino acid position 1130 (p.Ser1130Argfs*29). Ascertainment of 14 additional cats from founder lineages from Canada, France and different areas of the USA identified four additional loss of function HR variants likely causing the highly similar phenotypic hair coat across the diverse cats. The novel variants in HR for cat hypotrichia can now be established between minor differences in the phenotypic presentations.
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Affiliation(s)
- Reuben M. Buckley
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
| | - Barbara Gandolfi
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
| | - Erica K. Creighton
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
| | - Connor A. Pyne
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
| | - Delia M. Bouhan
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
| | - Michelle L. LeRoy
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
- Veterinary Allergy and Dermatology Clinic, LLC., Overland Park, KS 66210, USA
| | - David A. Senter
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
- Veterinary Allergy and Dermatology Clinic, LLC., Overland Park, KS 66210, USA
| | | | - Marie Abitbol
- NeuroMyoGène Institute, CNRS UMR 5310, INSERM U1217, Faculty of Medicine, Rockefeller, Claude Bernard Lyon I University, 69008 Lyon, France;
- VetAgro Sup, University of Lyon, Marcy-l’Etoile, 69280 Lyon, France
| | - Leslie A. Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (R.M.B.); (B.G.); (E.K.C.); (C.A.P.); (D.M.B.); (M.L.L.); (D.A.S.)
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11
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Yu Y, Creighton EK, Buckley RM, Lyons LA. A Deletion in GDF7 is Associated with a Heritable Forebrain Commissural Malformation Concurrent with Ventriculomegaly and Interhemispheric Cysts in Cats. Genes (Basel) 2020; 11:E672. [PMID: 32575532 PMCID: PMC7349246 DOI: 10.3390/genes11060672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022] Open
Abstract
An inherited neurologic syndrome in a family of mixed-breed Oriental cats has been characterized as forebrain commissural malformation, concurrent with ventriculomegaly and interhemispheric cysts. However, the genetic basis for this autosomal recessive syndrome in cats is unknown. Forty-three cats were genotyped on the Illumina Infinium Feline 63K iSelect DNA Array and used for analyses. Genome-wide association studies, including a sib-transmission disequilibrium test and a case-control association analysis, and homozygosity mapping, identified a critical region on cat chromosome A3. Short-read whole genome sequencing was completed for a cat trio segregating with the syndrome. A homozygous 7 bp deletion in growth differentiation factor 7 (GDF7) (c.221_227delGCCGCGC [p.Arg74Profs]) was identified in affected cats, by comparison to the 99 Lives Cat variant dataset, validated using Sanger sequencing and genotyped by fragment analyses. This variant was not identified in 192 unaffected cats in the 99 Lives dataset. The variant segregated concordantly in an extended pedigree. In mice, GDF7 mRNA is expressed within the roof plate when commissural axons initiate ventrally-directed growth. This finding emphasized the importance of GDF7 in the neurodevelopmental process in the mammalian brain. A genetic test can be developed for use by cat breeders to eradicate this variant.
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Affiliation(s)
- Yoshihiko Yu
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (Y.Y.); (E.K.C.); (R.M.B.)
- Laboratory of Veterinary Radiology, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Erica K. Creighton
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (Y.Y.); (E.K.C.); (R.M.B.)
| | - Reuben M. Buckley
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (Y.Y.); (E.K.C.); (R.M.B.)
| | - Leslie A. Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (Y.Y.); (E.K.C.); (R.M.B.)
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12
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Jaraud A, Bossé P, Dufaure de Citres C, Tiret L, Gache V, Abitbol M. Feline chimerism revealed by DNA profiling. Anim Genet 2020; 51:631-633. [PMID: 32452546 DOI: 10.1111/age.12957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 04/29/2020] [Accepted: 05/02/2020] [Indexed: 11/27/2022]
Abstract
In dogs and cats, unusual coat colour phenotypes may result from various phenomena, including chimerism. In the domestic cat, the tortoiseshell coat colour that combines red and non-red hairs is the most obvious way to identify chimeras in males. Several cases of tortoiseshell males have been reported, some of which were diagnosed as chimeras without any molecular confirmation. Here, we report the case of a female feline chimera identified thanks to its coat colour and confirmed through DNA profiling and a coat colour test. We ruled out the hypothesis of mosaicism and aneuploidy. All the data were consistent with a natural case of female chimerism.
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Affiliation(s)
- Ambre Jaraud
- U955 - IMRB - Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS , École nationale vétérinaire d'Alfort, Maisons-Alfort, France
| | - Philippe Bossé
- U955 - IMRB - Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS , École nationale vétérinaire d'Alfort, Maisons-Alfort, France
| | | | - Laurent Tiret
- U955 - IMRB - Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS , École nationale vétérinaire d'Alfort, Maisons-Alfort, France
| | - Vincent Gache
- Univ Lyon, Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon I, Lyon, France
| | - Marie Abitbol
- Univ Lyon, Institut NeuroMyoGène, CNRS UMR5310, INSERM U1217, Faculté de Médecine Rockefeller, Université Claude Bernard Lyon I, Lyon, France.,Univ Lyon, VetAgro Sup, Marcy-l'Etoile, France
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13
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Longeri M, Chiodi A, Brilli M, Piazza A, Lyons LA, Sofronidis G, Cozzi MC, Bazzocchi C. Targeted genotyping by sequencing: a new way to genome profile the cat. Anim Genet 2019; 50:718-725. [PMID: 31512748 PMCID: PMC6899796 DOI: 10.1111/age.12838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2019] [Indexed: 01/01/2023]
Abstract
Targeted GBS is a recent approach for obtaining an effective characterization for hundreds to thousands of markers. The high throughput of next-generation sequencing technologies, moreover, allows sample multiplexing. The aims of this study were to (i) define a panel of single nucleotide polymorphisms (SNPs) in the cat, (ii) use GBS for profiling 16 cats, and (iii) evaluate the performance with respect to the inference using standard approaches at different coverage thresholds, thereby providing useful information for designing similar experiments. Probes for sequencing 230 variants were designed based on the Felis_catus_8.0. 8.0 genome. The regions comprised anonymous and non-anonymous SNPs. Sixteen cat samples were analysed, some of which had already been genotyped in a large group of loci and one having been whole-genome sequenced in the 99_Lives Cat Genome Sequencing Project. The accuracy of the method was assessed by comparing the GBS results with the genotypes already available. Overall, GBS achieved good performance, with 92-96% correct assignments, depending on the coverage threshold used to define the set of trustable genotypes. Analyses confirmed that (i) the reliability of the inference of each genotype depends on the coverage at that locus and (ii) the fraction of target loci whose genotype can be inferred correctly is a function of the total coverage. GBS proves to be a valid alternative to other methods. Data suggested a depth of less than 11× is required for greater than 95% accuracy. However, sequencing depth must be adapted to the total size of the targets to ensure proper genotype inference.
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Affiliation(s)
- M. Longeri
- Department of Veterinary MedicineUniversity of MilanMilano20133Italy
| | - A. Chiodi
- Department of Earth and Environmental SciencesUniversity of PaviaPavia27100Italy
| | - M. Brilli
- Department of BiosciencesUniversity of MilanMilano20133Italy
- Paediatric Clinical Research Centre “Romeo ed Enrica Invernizzi”University of MilanMilano20157Italy
| | - A. Piazza
- Paediatric Clinical Research Centre “Romeo ed Enrica Invernizzi”University of MilanMilano20157Italy
- Department of Biomedical and Clinical Sciences “L. Sacco”University of MilanMilano20157Italy
| | - L. A. Lyons
- Department of Veterinary Medicine and SurgeryCollege of Veterinary MedicineUniversity of MissouriColumbiaMO65211USA
| | - G. Sofronidis
- Orivet Genetic Pet CareSuite 102/163-169 Inkerman StreetSt. KildaVic.3182Australia
| | - M. C. Cozzi
- Department of Veterinary MedicineUniversity of MilanMilano20133Italy
| | - C. Bazzocchi
- Department of Veterinary MedicineUniversity of MilanMilano20133Italy
- Paediatric Clinical Research Centre “Romeo ed Enrica Invernizzi”University of MilanMilano20157Italy
- Coordinated Research Centre “EpiSoMI”University of MilanMilano20133Italy
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14
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de Groot M, van Haeringen WA. An evaluation of the International Society for Animal Genetics recommended parentage and identification panel for the domestic pigeon (Columba livia domestica
). Anim Genet 2017; 48:431-435. [DOI: 10.1111/age.12555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2017] [Indexed: 11/29/2022]
Affiliation(s)
- M. de Groot
- VHLGenetics; Agro Business Park 100 NL 6708 PW Wageningen The Netherlands
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15
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Keating MK, Sturges BK, Sisó S, Wisner ER, Creighton EK, Lyons LA. Characterization of an Inherited Neurologic Syndrome in Toyger Cats with Forebrain Commissural Malformations, Ventriculomegaly and Interhemispheric Cysts. J Vet Intern Med 2016; 30:617-26. [PMID: 26846816 PMCID: PMC4913598 DOI: 10.1111/jvim.13836] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/16/2015] [Accepted: 01/05/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In children, frequent congenital malformations with concomitant agenesis of the corpus callosum are diagnosed by neuroimaging in association with other cerebral malformations, including interhemispheric cysts and ventriculomegaly. Similar studies providing full characterization of brain defects by in vivo magnetic resonance imaging (MRI), and correlations with the pertinent anatomic pathologic examinations are absent in veterinary medicine. HYPOTHESIS/OBJECTIVES Congenital brain defects underlie the neurologic signs observed in Toyger cats selectively bred for a short ear phenotype. ANIMALS Using proper pedigree analysis and genetic evaluations, 20 related Oriental-derived crossbred Toyger cats were evaluated. Seven clinically healthy (carrier) cats and 13 clinically affected cats that had neurologic signs, short ear phenotype and concomitant complex brain anomalies were studied. METHODS Complete physical and neurologic examinations and MRI were performed in all clinically healthy and affected cats. Postmortem and histopathologic examinations were performed in 8 affected cats and 5 healthy cats. RESULTS Neurologic and MRI investigations confirmed 13 clinically affected cats with structural brain abnormalities. Ventriculomegaly with frequent concomitant supratentorial interhemispheric, communicating ventricular type-1b cysts and multiple midline and callosal malformations were detected in all cats displaying neurologic signs. Genetic analysis confirmed autosomal recessive mode of inheritance with no chromosomal abnormalities. CONCLUSIONS AND CLINICAL IMPORTANCE Neuroanatomic dissections and histopathology were helpful for evaluation of abnormalities in midline brain structures, and for the full characterization of cysts. However, MRI was more sensitive for detection of small cysts. In this feline model, MRI diagnosis had extremely good correlation with pathologic abnormalities noted in the subset of animals that were examined by both modalities.
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Affiliation(s)
- M K Keating
- William R. Prichard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California - Davis, Davis, CA
| | - B K Sturges
- William R. Prichard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California - Davis, Davis, CA.,Department of Surgical & Radiological Sciences, School of Veterinary Medicine, University of California - Davis, Davis, CA
| | - S Sisó
- William R. Prichard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California - Davis, Davis, CA.,Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA
| | - E R Wisner
- William R. Prichard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California - Davis, Davis, CA.,Department of Surgical & Radiological Sciences, School of Veterinary Medicine, University of California - Davis, Davis, CA
| | - E K Creighton
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA.,Department of Medicine & Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO
| | - L A Lyons
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA.,Department of Medicine & Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO
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16
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Brooks A, Creighton EK, Gandolfi B, Khan R, Grahn RA, Lyons LA. SNP Miniplexes for Individual Identification of Random-Bred Domestic Cats. J Forensic Sci 2016; 61:594-606. [PMID: 27122395 PMCID: PMC5019183 DOI: 10.1111/1556-4029.13026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 03/13/2015] [Accepted: 06/06/2015] [Indexed: 11/30/2022]
Abstract
Phenotypic and genotypic characteristics of the cat can be obtained from single nucleotide polymorphisms (SNPs) analyses of fur. This study developed miniplexes using SNPs with high discriminating power for random‐bred domestic cats, focusing on individual and phenotypic identification. Seventy‐eight SNPs were investigated using a multiplex PCR followed by a fluorescently labeled single base extension (SBE) technique (SNaPshot®). The SNP miniplexes were evaluated for reliability, reproducibility, sensitivity, species specificity, detection limitations, and assignment accuracy. Six SNPplexes were developed containing 39 intergenic SNPs and 26 phenotypic SNPs, including a sex identification marker, ZFXY. The combined random match probability (cRMP) was 6.58 × 10−19 across all Western cat populations and the likelihood ratio was 1.52 × 1018. These SNPplexes can distinguish individual cats and their phenotypic traits, which could provide insight into crime reconstructions. A SNP database of 237 cats from 13 worldwide populations is now available for forensic applications.
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Affiliation(s)
- Ashley Brooks
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616
| | - Erica K Creighton
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, 1600 East Rollins Street, Columbia, MO, 65211
| | - Barbara Gandolfi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616.,Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, 1600 East Rollins Street, Columbia, MO, 65211
| | - Razib Khan
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616
| | - Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616.,Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, 1600 East Rollins Street, Columbia, MO, 65211
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17
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Lyons LA, Erdman CA, Grahn RA, Hamilton MJ, Carter MJ, Helps CR, Alhaddad H, Gandolfi B. Aristaless-Like Homeobox protein 1 (ALX1) variant associated with craniofacial structure and frontonasal dysplasia in Burmese cats. Dev Biol 2015; 409:451-8. [PMID: 26610632 DOI: 10.1016/j.ydbio.2015.11.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/03/2015] [Accepted: 11/20/2015] [Indexed: 10/22/2022]
Abstract
Frontonasal dysplasia (FND) can have severe presentations that are medically and socially debilitating. Several genes are implicated in FND conditions, including Aristaless-Like Homeobox 1 (ALX1), which is associated with FND3. Breeds of cats are selected and bred for extremes in craniofacial morphologies. In particular, a lineage of Burmese cats with severe brachycephyla is extremely popular and is termed Contemporary Burmese. Genetic studies demonstrated that the brachycephyla of the Contemporary Burmese is a simple co-dominant trait, however, the homozygous cats have a severe craniofacial defect that is incompatible with life. The craniofacial defect of the Burmese was genetically analyzed over a 20 year period, using various genetic analysis techniques. Family-based linkage analysis localized the trait to cat chromosome B4. Genome-wide association studies and other genetic analyses of SNP data refined a critical region. Sequence analysis identified a 12bp in frame deletion in ALX1, c.496delCTCTCAGGACTG, which is 100% concordant with the craniofacial defect and not found in cats not related to the Contemporary Burmese.
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Affiliation(s)
- Leslie A Lyons
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, MO 65211, USA; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95776, USA.
| | - Carolyn A Erdman
- Department of Psychiatry, University of California-San Francisco, San Francisco, CA 94143, USA; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95776, USA
| | - Robert A Grahn
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 96516, USA; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95776, USA
| | - Michael J Hamilton
- Department of Cell Biology and Neuroscience, Institute for Integrative Genome Biology, Center for Disease Vector Research, University of California-Riverside, Riverside, CA 92521, USA; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95776, USA
| | - Michael J Carter
- MDxHealth Inc, 15279 Alton Parkway, Suite #100, Irvine, CA 92618, USA; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95776, USA
| | | | | | - Barbara Gandolfi
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, MO 65211, USA; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95776, USA
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18
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Pollard RE, Koehne AL, Peterson CB, Lyons LA. Japanese Bobtail: vertebral morphology and genetic characterization of an established cat breed. J Feline Med Surg 2015; 17:719-26. [PMID: 25488973 PMCID: PMC11104057 DOI: 10.1177/1098612x14558147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Several cat breeds are defined by morphological variation of the tail. The Japanese Bobtail is a breed that has been accepted for registration only within the past 50 years; however, the congenital kinked tail variants defining this breed were documented in the Far East centuries ago and the cats are considered 'good luck' in several Asian cultures. The recent discovery of the mutation for the tailless Manx phenotype has demonstrated that the Japanese Bobtail does not have a causative mutation in the same gene (T-Box). Here, a simple segregation analysis of cats bred from a pedigreed Japanese Bobtail demonstrated a simple autosomal dominant mode of inheritance with variable expression of the tail length and kink placement. Unexpectedly, radiological examinations of the entire vertebral column of kink-tailed cats indicated variation from the normal vertebral feline formula (C7, T13, L7, S3, Cd20-24), including cats with mostly one reduction of thoracic vertebrae (C7, T12, L7, S3), and an average of 15.8 caudal vertebrae. A few cats had variation in the number of cervical vertebrae. Several transitional vertebrae and anomalous ribs were noted. One cat had a bifid vertebra in the tail. Most cats had hemivertebrae that were usually included in the tail kink, one of which was demonstrated by gross pathology and histopathology. The abnormal vertebral formula or the placement of the kink in the tail did not coincide with morbidity or mortality.
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Affiliation(s)
- Rachel E Pollard
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Amanda L Koehne
- Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Carlyn B Peterson
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA
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Malik R, Musca FJ, Gunew MN, Menrath VH, Simpson C, Culvenor J, Grahn RA, Helps C, Lyons LA, Gandolfi B. Periodic hypokalaemic polymyopathy in Burmese and closely related cats: a review including the latest genetic data. J Feline Med Surg 2015; 17:417-26. [PMID: 25896241 PMCID: PMC10816241 DOI: 10.1177/1098612x15581135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GLOBAL IMPORTANCE Hypokalaemic polymyopathy is a genetic disease of Burmese cats that has been encountered in Australasia, Europe and South Africa. CLINICAL FEATURES Affected cats usually present with signs of muscle weakness and muscle pain in the first year of life. Although certain clinical features, such as ventroflexion of the head and neck, are especially characteristic, some cats do not display these signs. Usually weakness is periodic or episodic, but occasionally it is incessant. DIAGNOSTIC CHALLENGES In the past, diagnosis was problematic in that clinical signs and a lowered serum potassium concentration were not always observed synchronously. This necessitated serial serum potassium concentration determinations, testing of serum creatine kinase activity and exclusion of other potential causes of muscle disease in cats (including muscular dystrophies, Toxoplasma myositis, immune-mediated polymyositis, organophosphorus intoxication and envenomations). Signs in affected cats often waxed and waned, possibly in response to changes in dietary factors and stress, and some cats could apparently 'grow out of' the condition. RECENT ADVANCES AND FUTURE PROSPECTS Recent molecular genetics research has identified a single nonsense mutation in the gene (WNK4) coding for lysine-deficient 4 protein kinase, an enzyme present primarily in the distal nephron. The underlying pathomechanism in affected cats is therefore likely to be a potassium wasting nephropathy, as this enzyme is involved in complex sodium/potassium exchange mechanisms in the kidney. Additional functional characterisation of the condition is warranted to define precisely how, why and when the serum potassium concentration declines. The diagnosis of Burmese hypokalaemia is now straightforward, as an inexpensive PCR test can identify affected homozygous individuals, as well as carriers. The elimination of this condition from the Burmese breed, and also from pedigree cats infused with Burmese lines, such as the Bombay, Tonkinese and Tiffanie breeds, should therefore be possible.
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Affiliation(s)
- Richard Malik
- Centre for Veterinary Education, B22, The University of Sydney, New South Wales, Australia
| | - Fran J Musca
- The Cat Clinic, Creek Road, Mount Gravatt, Queensland, Australia
| | - Marcus N Gunew
- The Cat Clinic, Creek Road, Mount Gravatt, Queensland, Australia
| | - Victor H Menrath
- The Cat Clinic, Creek Road, Mount Gravatt, Queensland, Australia
| | - Christopher Simpson
- Southern Animal Referral Centre and Emergency Centre, 248 Wickham Road, Highett, Victoria, Australia
| | - John Culvenor
- North Shore Veterinary Specialist Centre, 64 Atchison Street, Crows Nest, New South Wales, Australia
| | - Robert A Grahn
- Veterinary Genetics Laboratory, 980 Old Davis Road, University of California, Davis, CA, USA
| | | | - Leslie A Lyons
- College of Veterinary Medicine, University of Missouri, USA
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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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Lyons LA, Grahn RA, Kun TJ, Netzel LR, Wictum EE, Halverson JL. Acceptance of domestic cat mitochondrial DNA in a criminal proceeding. Forensic Sci Int Genet 2014; 13:61-7. [PMID: 25086413 DOI: 10.1016/j.fsigen.2014.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 06/20/2014] [Accepted: 07/07/2014] [Indexed: 02/06/2023]
Abstract
Shed hair from domestic animals readily adheres to clothing and other contact items, providing a source of transfer evidence for criminal investigations. Mitochondrial DNA is often the only option for DNA analysis of shed hair. Human mitochondrial DNA analysis has been accepted in the US court system since 1996. The murder trial of the State of Missouri versus Henry L. Polk, Jr. represents the first legal proceeding where cat mitochondrial DNA analysis was introduced into evidence. The mitochondrial DNA evidence was initially considered inadmissible due to concerns about the cat dataset and the scientific acceptance of the marker. Those concerns were subsequently addressed, and the evidence was deemed admissible. This report reviews the case in regards to the cat biological evidence and its ultimate admission as generally accepted and reliable. Expansion and saturation analysis of the cat mitochondrial DNA control region dataset supported the initial interpretation of the evidence.
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Affiliation(s)
- Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States.
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States; Forensics Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Teri J Kun
- Forensics Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Linda R Netzel
- Kansas City Police Crime Laboratory, 6633 Troost Avenue, Kansas City, MO 64131, United States
| | - Elizabeth E Wictum
- Forensics Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Joy L Halverson
- Zoogen Services, 1046 Olive Drive Suite 1, Davis, CA 95616, United States
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Schury N, Schleenbecker U, Hellmann AP. Forensic animal DNA typing: Allele nomenclature and standardization of 14 feline STR markers. Forensic Sci Int Genet 2014; 12:42-59. [PMID: 24893348 DOI: 10.1016/j.fsigen.2014.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/29/2014] [Accepted: 05/01/2014] [Indexed: 11/19/2022]
Abstract
Since the domestic cat (Felis catus) has become one of the most popular pets and owners usually develop a close relationship to their cats, it is necessary to take traces of cats into account for forensic casework. For this purpose feline short tandem (STR) repeat markers have been investigated in several earlier studies, but no detailed description of sequence data, allelic variations or a repeat-based nomenclature is available. The aim of the study was to provide a suggestion for the allele nomenclature of 14 cat STR markers according to the recommendations of the International Society for Forensic Genetics (ISFG) for human DNA typing and to present a standardized system for a secure DNA typing of samples. Samples of 122 unrelated cats from a local animal shelter and private owners in Germany were used to generate a population database with allele frequencies and to analyze the tandemly repeated sequence variations within the alleles of each STR marker. These markers could be grouped into two STR classes: simple repeat STRs and complex STRs (some with the supplement highly complex), consisting of di- and tetranucleotide repeat motifs. After analyzing the repeat structure and elaborating a repeat based nomenclature, allelic ladders of common and rarely occurring alleles for each marker were designed to enable accurate typing of alleles that differ in fragment length and to facilitate data exchange.
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Affiliation(s)
- N Schury
- Bundeskriminalamt, Forensic Science Institute, KT32, Äppelallee 45, 65203 Wiesbaden, Germany; Johannes Gutenberg University Mainz, Institute of Legal Medicine - Medical University, Molecular Biology, Am Pulverturm 3, 55131 Mainz, Germany
| | - U Schleenbecker
- Bundeskriminalamt, Forensic Science Institute, KT32, Äppelallee 45, 65203 Wiesbaden, Germany
| | - A P Hellmann
- Bundeskriminalamt, Forensic Science Institute, KT32, Äppelallee 45, 65203 Wiesbaden, Germany.
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Lambo CA, Grahn RA, Lyons LA, Bateman HL, Newsom J, Swanson WF. Comparative fertility of freshly collected vs frozen-thawed semen with laparoscopic oviductal artificial insemination in domestic cats. Reprod Domest Anim 2013; 47 Suppl 6:284-8. [PMID: 23279520 DOI: 10.1111/rda.12038] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 06/21/2012] [Indexed: 11/29/2022]
Abstract
Artificial insemination (AI) is potentially invaluable as an adjunct to natural breeding for the conservation management of non-domestic felid populations. The efficacy of AI, however, must be substantially improved for applied use, especially when using frozen semen. Our recent advances in using laparoscopic oviductal AI (LO-AI) with low sperm numbers and freezing of cat semen in a soy lecithin-based cryoprotectant medium suggest that combining these two approaches might improve pregnancy outcomes with frozen-thawed spermatozoa. In this study, our objectives were to (i) assess the effect of two gonadotropin dosages (100 vs 150 IU eCG) on ovarian response in domestic cats and (ii) compare the relative fertility of frozen-thawed and fresh semen in vivo following LO-AI. All 16 females ovulated after gonadotropin treatment and were inseminated with fresh semen from one male and frozen-thawed semen from a second male. There were no differences between gonadotropin dosages in CL number, pregnancy percentage or litter size. Half (8/16) of the females conceived, with seven females giving birth to a total of 36 offspring. Paternity analysis showed that more kittens resulted from LO-AI with fresh (28/36, 78%) than frozen-thawed (8/36, 22%) semen, possibly due to impaired motility and longevity of thawed sperm. These results demonstrated that viable offspring can be produced by AI using semen frozen in a soy lecithin-based medium. Insemination with greater numbers of frozen-thawed spermatozoa, combined with further refinement of cat sperm cryopreservation methods, may be necessary to optimize pregnancy success with LO-AI in domestic and nondomestic cats.
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Affiliation(s)
- C A Lambo
- Center for Conservation and Research of Endangered Wildlife, Cincinnati Zoo and Botanical Gardens, Cincinnati, OH 45220, USA.
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24
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Rosa A, Sardina M, Mastrangelo S, Tolone M, Portolano B. Parentage verification of Valle del Belice dairy sheep using multiplex microsatellite panel. Small Rumin Res 2013. [DOI: 10.1016/j.smallrumres.2013.03.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Lee-Montero I, Navarro A, Borrell Y, García-Celdrán M, Martín N, Negrín-Báez D, Blanco G, Armero E, Berbel C, Zamorano MJ, Sánchez JJ, Estévez A, Ramis G, Manchado M, Afonso JM. Development of the first standardised panel of two new microsatellite multiplex PCRs for gilthead seabream (Sparus aurata L.). Anim Genet 2013; 44:533-46. [PMID: 23574152 DOI: 10.1111/age.12037] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2013] [Indexed: 11/30/2022]
Abstract
The high number of multiplex PCRs developed for gilthead seabream (Sparus aurata L.) from many different microsatellite markers does not allow comparison among populations. This highlights the need for developing a reproducible panel of markers, which can be used with safety and reliability by all users. In this study, the first standardised panel of two new microsatellite multiplex PCRs was developed for this species. Primers of 138 specific microsatellites from the genetic linkage map were redesigned and evaluated according to their genetic variability, allele size range and genotyping reliability. A protocol to identify and classify genotyping errors or potential errors was proposed to assess the reliability of each marker. Two new multiplex PCRs from the best assessed markers were designed with 11 markers in each, named SMsa1 and SMsa2 (SuperMultiplex Sparus aurata). Three broodstocks (59, 47 and 98 breeders) from different Spanish companies, and a sample of 80 offspring from each one, were analysed to validate the usefulness of these multiplexes in the parental assignation. It was possible to assign each offspring to a single parent pair (100% success) using the exclusion method with SMsa1 and/or SMsa2. In each genotyped a reference sample (Ref-sa) was used, and its DNA is available on request similar to the kits of bin set to genotype by genemapper (v.3.7) software (kit-SMsa1 and kit-SMsa2). This will be a robust and effective tool for pedigree analysis or characterisation of populations and will be proposed as an international panel for this species.
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Affiliation(s)
- I Lee-Montero
- Grupo de Investigación en Acuicultura, Instituto Universitario de Sanidad Animal y Seguridad Alimentaria, Instituto Canario de Ciencias Marinas, Universidad de Las Palmas de Gran Canaria, Carretera Trasmontaña s/n, Arucas, Las Palmas, Spain
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26
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Gandolfi B, Gruffydd-Jones TJ, Malik R, Cortes A, Jones BR, Helps CR, Prinzenberg EM, Erhardt G, Lyons LA. First WNK4-hypokalemia animal model identified by genome-wide association in Burmese cats. PLoS One 2012; 7:e53173. [PMID: 23285264 PMCID: PMC3532348 DOI: 10.1371/journal.pone.0053173] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 11/26/2012] [Indexed: 11/18/2022] Open
Abstract
Burmese is an old and popular cat breed, however, several health concerns, such as hypokalemia and a craniofacial defect, are prevalent, endangering the general health of the breed. Hypokalemia, a subnormal serum potassium ion concentration ([K+]), most often occurs as a secondary problem but can occur as a primary problem, such as hypokalaemic periodic paralysis in humans, and as feline hypokalaemic periodic polymyopathy primarily in Burmese. The most characteristic clinical sign of hypokalemia in Burmese is a skeletal muscle weakness that is frequently episodic in nature, either generalized, or sometimes localized to the cervical and thoracic limb girdle muscles. Burmese hypokalemia is suspected to be a single locus autosomal recessive trait. A genome wide case-control study using the illumina Infinium Feline 63K iSelect DNA array was performed using 35 cases and 25 controls from the Burmese breed that identified a locus on chromosome E1 associated with hypokalemia. Within approximately 1.2 Mb of the highest associated SNP, two candidate genes were identified, KCNH4 and WNK4. Direct sequencing of the genes revealed a nonsense mutation, producing a premature stop codon within WNK4 (c.2899C>T), leading to a truncated protein that lacks the C-terminal coiled-coil domain and the highly conserved Akt1/SGK phosphorylation site. All cases were homozygous for the mutation. Although the exact mechanism causing hypokalemia has not been determined, extrapolation from the homologous human and mouse genes suggests the mechanism may involve a potassium-losing nephropathy. A genetic test to screen for the genetic defect within the active breeding population has been developed, which should lead to eradication of the mutation and improved general health within the breed. Moreover, the identified mutation may help clarify the role of the protein in K+ regulation and the cat represents the first animal model for WNK4-associated hypokalemia.
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Affiliation(s)
- Barbara Gandolfi
- Department of Population Health and Reproduction, University of California Davis, Davis, California, United States of America
| | | | - Richard Malik
- Centre for Veterinary Education, University of Sydney, Sydney, Australia
| | - Alejandro Cortes
- Department of Population Health and Reproduction, University of California Davis, Davis, California, United States of America
| | - Boyd R. Jones
- Institute of Veterinary, Animal & Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Chris R. Helps
- Molecular Diagnostic Unit, University of Bristol, Langford, Bristol, United Kingdom
| | - Eva M. Prinzenberg
- Institute of Animal Breeding & Genetics, Justus Liebig University, Giessen, Germany
| | - George Erhardt
- Institute of Animal Breeding & Genetics, Justus Liebig University, Giessen, Germany
| | - Leslie A. Lyons
- Department of Population Health and Reproduction, University of California Davis, Davis, California, United States of America
- * E-mail:
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Lyons LA. Genetic testing in domestic cats. Mol Cell Probes 2012; 26:224-30. [PMID: 22546621 PMCID: PMC3541004 DOI: 10.1016/j.mcp.2012.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 04/12/2012] [Accepted: 04/13/2012] [Indexed: 12/29/2022]
Abstract
Varieties of genetic tests are currently available for the domestic cat that support veterinary health care, breed management, species identification, and forensic investigations. Approximately thirty-five genes contain over fifty mutations that cause feline health problems or alterations in the cat's appearance. Specific genes, such as sweet and drug receptors, have been knocked-out of Felidae during evolution and can be used along with mtDNA markers for species identification. Both STR and SNP panels differentiate cat race, breed, and individual identity, as well as gender-specific markers to determine sex of an individual. Cat genetic tests are common offerings for commercial laboratories, allowing both the veterinary clinician and the private owner to obtain DNA test results. This article will review the genetic tests for the domestic cat, and their various applications in different fields of science. Highlighted are genetic tests specific to the individual cat, which are a part of the cat's genome.
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Affiliation(s)
- Leslie A Lyons
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616, USA.
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Kurushima JD, Lipinski MJ, Gandolfi B, Froenicke L, Grahn JC, Grahn RA, Lyons LA. Variation of cats under domestication: genetic assignment of domestic cats to breeds and worldwide random-bred populations. Anim Genet 2012; 44:311-24. [PMID: 23171373 DOI: 10.1111/age.12008] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2012] [Indexed: 02/04/2023]
Abstract
Both cat breeders and the lay public have interests in the origins of their pets, not only in the genetic identity of the purebred individuals, but also in the historical origins of common household cats. The cat fancy is a relatively new institution with over 85% of its 40-50 breeds arising only in the past 75 years, primarily through selection on single-gene aesthetic traits. The short, yet intense cat breed history poses a significant challenge to the development of a genetic marker-based breed identification strategy. Using different breed assignment strategies and methods, 477 cats representing 29 fancy breeds were analysed with 38 short tandem repeats, 148 intergenic and five phenotypic single nucleotide polymorphisms. Results suggest the frequentist method of Paetkau (single nucleotide polymorphisms = 0.78, short tandem repeats = 0.88) surpasses the Bayesian method of Rannala and Mountain (single nucleotide polymorphisms = 0.56, short tandem repeats = 0.83) for accurate assignment of individuals to the correct breed. Additionally, a post-assignment verification step with the five phenotypic single nucleotide polymorphisms accurately identified between 0.31 and 0.58 of the misassigned individuals raising the sensitivity of assignment with the frequentist method to 0.89 and 0.92 for single nucleotide polymorphisms and short tandem repeats respectively. This study provides a novel multistep assignment strategy and suggests that, despite their short breed history and breed family groupings, a majority of cats can be assigned to their proper breed or population of origin, that is, race.
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Affiliation(s)
- J D Kurushima
- Department of Health & Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616, USA
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29
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The plant physical features selected by wildcats as signal posts: an economic approach to fecal marking. Naturwissenschaften 2012; 99:801-9. [DOI: 10.1007/s00114-012-0962-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Revised: 08/09/2012] [Accepted: 08/14/2012] [Indexed: 10/28/2022]
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Filler S, Alhaddad H, Gandolfi B, Kurushima JD, Cortes A, Veit C, Lyons LA, Brem G. Selkirk Rex: morphological and genetic characterization of a new cat breed. ACTA ACUST UNITED AC 2012; 103:727-33. [PMID: 22837475 DOI: 10.1093/jhered/ess039] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Rexoid, curly hair mutations have been selected to develop new domestic cat breeds. The Selkirk Rex is the most recently established curly-coated cat breed originating from a spontaneous mutation that was discovered in the United States in 1987. Unlike the earlier and well-established Cornish and Devon Rex breeds with curly-coat mutations, the Selkirk Rex mutation is suggested as autosomal dominant and has a different curl phenotype. This study provides a genetic analysis of the Selkirk Rex breed. An informal segregation analysis of genetically proven matings supported an autosomal, incomplete dominant expression of the curly trait in the Selkirk Rex. Homozygous curl cats can be distinguished from heterozygous cats by head and body type, as well as the presentation of the hair curl. Bayesian clustering of short tandem repeat (STR) genotypes from 31 cats that represent the future breeding stock supported the close relationship of the Selkirk Rex to the British Shorthair, Scottish Fold, Persian, and Exotic Shorthair, suggesting the Selkirk as part of the Persian breed family. The high heterozygosity of 0.630 and the low mean inbreeding coefficient of 0.057 suggest that Selkirk Rex has a diverse genetic foundation. A new locus for Selkirk autosomal dominant Rex, SADRE, is suggested for the curly trait.
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Affiliation(s)
- Serina Filler
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine Vienna Vienna, Austria
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31
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Ciampolini R, Cecchi F, Bramante A, Tancredi M, Presciuttini S. Towards standardization of canine STRs: a proposed nomenclature for six markers from the ISAG comparison-test panel. Anim Genet 2012; 43:463-7. [PMID: 22497738 DOI: 10.1111/j.1365-2052.2011.02267.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Eight short tandem repeat markers included in the International Society for Animal Genetics panel of 24 loci investigated in canine comparison tests were analysed in a sample of pure-breed dogs, with the purpose of defining an allele nomenclature based on the number of repeats. A regression analysis of the raw data produced by the sequencer, coupled with the direct sequencing of selected alleles, allowed us to propose a system of nomenclature for six of the eight loci (four di-nucleotidic: AHT121, AHTh137, REN169018 and REN64E19, and two tetra-nucleotidic: FH2001 and FH2328). The remaining two loci (INU055 and FH2848) showed a pattern of fragments that did not resolve in a simple allele series. This work may be useful to establish a basis for comparing data across different laboratories for a set of validated canine markers, which can be used in population genetics, forensics and other analyses.
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Affiliation(s)
- R Ciampolini
- Department of Animal Pathology, University of Pisa, Italy
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Rendo F, Iriondo M, Manzano C, Estonba A. Microsatellite based ovine parentage testing to identify the source responsible for the killing of an endangered species. Forensic Sci Int Genet 2010; 5:333-5. [PMID: 20952265 DOI: 10.1016/j.fsigen.2010.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 09/16/2010] [Accepted: 09/20/2010] [Indexed: 10/18/2022]
Abstract
In this study, we present an animal forensic genetics case in which we applied ovine microsatellite based parentage testing to the resolution of an act against protected wildlife. The aim was to identify the origin of the animal responsible for the death of an Egyptian vulture (Neophron percnopterus) that had been poisoned through consumption of a Latxa Blond Face breed lamb. Thus, we carried out a 22 microsatellite based parentage test in order to identify the parents of the lamb in the flock which grazes in the same place where the vulture's remains were found. Multiple parentage analysis revealed two possible parents, one ewe and one ram, with a combined paternity/maternity index (PI) higher than 9.09E9 and a likelihood (W) value of 99.9999%, assuming 50% probability a priori. This result confirmed the flock of origin of the poisoned lamb and shows that the microsatellite panel described herein is a potentially useful tool for the resolution of animal forensic cases.
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Affiliation(s)
- Fernando Rendo
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of Basque Country, E-48940 Bilbao, Spain
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van de Goor LHP, Panneman H, van Haeringen WA. A proposal for standardization in forensic equine DNA typing: allele nomenclature for 17 equine-specific STR loci. Anim Genet 2010; 41:122-7. [DOI: 10.1111/j.1365-2052.2009.01975.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Grahn RA, Kurushima JD, Billings NC, Grahn JC, Halverson JL, Hammer E, Ho CK, Kun TJ, Levy JK, Lipinski MJ, Mwenda JM, Ozpinar H, Schuster RK, Shoorijeh SJ, Tarditi CR, Waly NE, Wictum EJ, Lyons LA. Feline non-repetitive mitochondrial DNA control region database for forensic evidence. Forensic Sci Int Genet 2010; 5:33-42. [PMID: 20457082 DOI: 10.1016/j.fsigen.2010.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Revised: 01/08/2010] [Accepted: 01/20/2010] [Indexed: 01/26/2023]
Abstract
The domestic cat is the one of the most popular pets throughout the world. A by-product of owning, interacting with, or being in a household with a cat is the transfer of shed fur to clothing or personal objects. As trace evidence, transferred cat fur is a relatively untapped resource for forensic scientists. Both phenotypic and genotypic characteristics can be obtained from cat fur, but databases for neither aspect exist. Because cats incessantly groom, cat fur may have nucleated cells, not only in the hair bulb, but also as epithelial cells on the hair shaft deposited during the grooming process, thereby generally providing material for DNA profiling. To effectively exploit cat hair as a resource, representative databases must be established. The current study evaluates 402 bp of the mtDNA control region (CR) from 1394 cats, including cats from 25 distinct worldwide populations and 26 breeds. Eighty-three percent of the cats are represented by 12 major mitotypes. An additional 8.0% are clearly derived from the major mitotypes. Unique sequences are found in 7.5% of the cats. The overall genetic diversity for this data set is 0.8813±0.0046 with a random match probability of 11.8%. This region of the cat mtDNA has discriminatory power suitable for forensic application worldwide.
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Affiliation(s)
- R A Grahn
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
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van de Goor LHP, Panneman H, van Haeringen WA. A proposal for standardization in forensic bovine DNA typing: allele nomenclature of 16 cattle-specific short tandem repeat loci. Anim Genet 2009; 40:630-6. [PMID: 19397508 DOI: 10.1111/j.1365-2052.2009.01891.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, a proposal is presented for the allele nomenclature of 16 polymorphic short tandem repeat (STR) loci (BM1824, BM2113, ETH10, ETH225, INRA023, SPS115, TGLA122, TGLA126, TGLA227, ETH3, TGLA53, BM1818, CSRM60, CSSM66, HAUT27 and ILSTS006) for bovine genotyping (Bos taurus). The nomenclature is based on sequence data of the polymorphic region(s) of the STR loci as recommended by the DNA commission of the International Society of Forensic Genetics for human DNA typing. To cover commonly and rarely occurring alleles, a selection of animals homozygous for the alleles at these STR loci were analysed and subjected to sequence studies. The alleles of the STR loci consisted either of simple or compound dinucleotide repeat patterns. Only a limited number of alleles with the same fragment size showed different repeat structures. The allele designation described here was based on the number of repeats including all variable regions within the amplified fragment. The set of 16 STR markers should be propagated for the use in all bovine applications including forensic analysis.
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Affiliation(s)
- L H P van de Goor
- Dr Van Haeringen Laboratorium BV, Agro Business Park 100, NL 6708 PW Wageningen, The Netherlands.
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Cytidine monophospho-N-acetylneuraminic acid hydroxylase (CMAH) mutations associated with the domestic cat AB blood group. BMC Genet 2007; 8:27. [PMID: 17553163 PMCID: PMC1913925 DOI: 10.1186/1471-2156-8-27] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 06/06/2007] [Indexed: 12/02/2022] Open
Abstract
Background The cat has one common blood group with two major serotypes, blood type A that is dominant to type B. A rare type AB may also be allelic and is suspected to be recessive to A and dominant to B. Cat blood type antigens are defined, N-glycolylneuraminic acid (NeuGc) is associated with type A and N-acetylneuraminic acid (NeuAc) with type B. The enzyme cytidine monophospho-N-acetylneuraminic acid hydroxylase (CMAH) determines the sugar bound to the red cell by converting NeuAc to NeuGc. Thus, mutations in CMAH may cause the A and B blood types. Results Genomic sequence of CMAH from eight cats and the cDNA of four cats representing all blood types were analyzed to identify causative mutations. DNA variants consistent with the blood types were genotyped in over 200 cats. Five SNPs and an indel formed haplotypes that were consistent with each blood type. Conclusion Mutations in type B cats likely disrupt the gene function of CMAH, leading to a predominance of NeuAc. Type AB concordant variants were not identified, however, cDNA species suggest an alternative allele that activates a downstream start site, leading to a CMAH protein that would be altered at the 5' region. The cat AB blood group system is proposed to be designated by three alleles, A > aab > b. The A and b CMAH alleles described herein can distinguish type A and type B cats without blood sample collections. CMAH represents the first blood group gene identified outside of non-human primates and humans.
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