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Sandoval-Castellanos E, Hare AJ, Lin AT, Dimopoulos EA, Daly KG, Geiger S, Mullin VE, Wiechmann I, Mattiangeli V, Lühken G, Zinovieva NA, Zidarov P, Çakırlar C, Stoddart S, Orton D, Bulatović J, Mashkour M, Sauer EW, Horwitz LK, Horejs B, Atici L, Özkaya V, Mullville J, Parker Pearson M, Mainland I, Card N, Brown L, Sharples N, Griffiths D, Allen D, Arbuckle B, Abell JT, Duru G, Mentzer SM, Munro ND, Uzdurum M, Gülçur S, Buitenhuis H, Gladyr E, Stiner MC, Pöllath N, Özbaşaran M, Krebs S, Burger J, Frantz L, Medugorac I, Bradley DG, Peters J. Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep ( Ovis aries). Sci Adv 2024; 10:eadj0954. [PMID: 38608027 PMCID: PMC11014441 DOI: 10.1126/sciadv.adj0954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024]
Abstract
Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Aşıklı Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Aşıklı Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Aşıklı Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.
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Affiliation(s)
- Edson Sandoval-Castellanos
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Andrew J. Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Audrey T. Lin
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560 USA
| | - Evangelos A. Dimopoulos
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Kevin G. Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Sheila Geiger
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Victoria E. Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Ingrid Wiechmann
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University of Gießen, Ludwigstr. 21, 35390 Gießen, Germany
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region, Russia
| | - Petar Zidarov
- Institute of Prehistory, Early History and Medieval Archaeology, Tübingen University, Tübingen, Germany
| | - Canan Çakırlar
- Institute of Archaeology, University of Groningen, 9712 ER Groningen, Netherlands
| | - Simon Stoddart
- Magdalene College, University of Cambridge, Cambridge CB3 0AG, UK
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK
| | - Jelena Bulatović
- Department of Historical Studies, University of Gothenburg, BOX 200, 40530 Gothenburg, Sweden
| | - Marjan Mashkour
- Unité Archéozoologie, Archéobotanique, Sociétés Pratiques et Environnements (AASPE), CNRS, Muséum National d’Histoire Naturelle, 75020 Paris, France
| | - Eberhard W. Sauer
- School of History, Classics and Archaeology, University of Edinburgh, Old Medical School, Teviot Place, Edinburgh EH8 9AG, UK
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Barbara Horejs
- OeAI, Austrian Academy of Sciences and HEAS, University of Vienna, Vienna, Austria
| | - Levent Atici
- Department of Anthropology, University of Nevada, Las Vegas, NV 89154, USA
| | - Vecihi Özkaya
- Department of Archaeology, Dicle University, Diyarbakir, Türkiye
| | - Jacqui Mullville
- School of History, Archaeology and Religion, Cardiff University, Cardiff CF10 3EU, UK
| | | | - Ingrid Mainland
- The University of the Highlands and Islands Orkney, Kirkwall, UK
| | - Nick Card
- The University of the Highlands and Islands Orkney, Kirkwall, UK
| | | | - Niall Sharples
- School of History, Archaeology and Religion, Cardiff University, Cardiff CF10 3EU, UK
| | - David Griffiths
- University of Oxford, OUDCE, Rewley House, Oxford OX1 2JA, UK
| | - David Allen
- Hampshire Cultural Trust, Chilcomb House, Winchester, SO23 8RB, UK
| | - Benjamin Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jordan T. Abell
- Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | - Güneş Duru
- Department of Archaeology, Mimar Sinan Fine Arts University, 34381 Şişli/İstanbul, Türkiye
| | - Susan M. Mentzer
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Department of Geosciences, Tübingen University, 72074 Tübingen, Germany
| | - Natalie D. Munro
- Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA
| | - Melis Uzdurum
- Department of Archaeology, Ondokuz Mayıs University, 55270 Atakum/Samsun, Türkiye
| | - Sevil Gülçur
- Prehistory Department, Faculty of Letters, Istanbul University, 34134 Istanbul, Türkiye
| | | | - Elena Gladyr
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region, Russia
| | - Mary C. Stiner
- School of Anthropology, University of Arizona, Tucson, AZ 85721, USA
| | - Nadja Pöllath
- Bavarian Natural History Collections, State Collection of Palaeoanatomy Munich, 80333 Munich, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
| | - Mihriban Özbaşaran
- Prehistory Department, Faculty of Letters, Istanbul University, 34134 Istanbul, Türkiye
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Joachim Burger
- Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Laurent Frantz
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Joris Peters
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- Bavarian Natural History Collections, State Collection of Palaeoanatomy Munich, 80333 Munich, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
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Davaasuren N, Molaee V, Erdene-Ochir TO, Nyamdavaa G, Ganzorig S, Mazzei M, Sakoda Y, Lühken G, Tumenjargal S. Phylogenetic analysis of small ruminant lentiviruses in Mongolian sheep supports an ancient east-west split for the genotype A. Vet Res Commun 2024:10.1007/s11259-024-10361-9. [PMID: 38530579 DOI: 10.1007/s11259-024-10361-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/22/2024] [Indexed: 03/28/2024]
Abstract
The ovine maedi-visna virus (MVV) and caprine arthritis-encephalitis virus (CAEV) are small ruminant lentiviruses (SRLVs) with striking genetic and structural similarities. The presence of SRLV in Mongolian sheep and goats was serologically demonstrated more than a decade ago; however, the viral genotype remains unknown. In total, 329 blood samples were collected from two sheep breeds (i.e., Khalkha and Sumber) in Tov, Govisumber, Arkhangay, Dornogovi, Zavkhan, and Sukhbaatar provinces, Mongolia. Serological and phylogenetic analyses were performed regardless of any apparent clinical signs, although most of the animals appeared healthy. All sheep in three of the six provinces were seronegative, whereas the seroprevalence in the Tov, Govisumber, and Zavkhan provinces averaged 7.9%. Genomic DNA from seropositive animals was tested using hemi-nested polymerase chain reaction, and sub-genomic SRLV sequences were determined from nine samples. Mongolian SRLV sequences clustered within the divergent subtype A22, which was previously found only in Fertile Crescent regions, including Lebanon, Jordan, and Iran, where the first sheep-domestication (Ovis aries) occurred. According to the phylogenetic analysis, genotype A has two ancestors from the ancient Fertile Crescent: (1) Turkish strains and (2) Iranian, Jordanian, and Lebanese strains. The first ancestor spread westward, whereas the second spread eastward, ultimately reaching Mongolia.
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Affiliation(s)
- Nergui Davaasuren
- Department of Infectious Diseases and Microbiology, School of Veterinary Medicine, Mongolian University of Life Sciences, Zaisan, Ulaanbaatar, 17024, Mongolia
| | - Vahid Molaee
- Institute of Animal Breeding and Genetics, Justus Liebig University of Giessen, Ludwigstrasse 21, 35390, Giessen, Germany
| | - Tseren-Ochir Erdene-Ochir
- Department of Infectious Diseases and Microbiology, School of Veterinary Medicine, Mongolian University of Life Sciences, Zaisan, Ulaanbaatar, 17024, Mongolia
| | - Guugandaa Nyamdavaa
- Department of Infectious Diseases and Microbiology, School of Veterinary Medicine, Mongolian University of Life Sciences, Zaisan, Ulaanbaatar, 17024, Mongolia
| | - Sumiya Ganzorig
- Department of Biology, National University of Mongolia, Ulaanbaatar, 14021, Mongolia
| | - Maurizio Mazzei
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 20159, Pisa, Italy
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, 060-0818, Japan
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University of Giessen, Ludwigstrasse 21, 35390, Giessen, Germany
| | - Sharav Tumenjargal
- Department of Infectious Diseases and Microbiology, School of Veterinary Medicine, Mongolian University of Life Sciences, Zaisan, Ulaanbaatar, 17024, Mongolia.
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Tan K, Adeniyi OO, Letko A, RuddGarces G, Manz E, Wagner H, Zanolari P, Drögemüller C, Lühken G. Identification of genomic regions associated with differences in fleece type in Huacaya and Suri alpacas (Vicugna pacos). Anim Genet 2024; 55:163-167. [PMID: 37985006 DOI: 10.1111/age.13377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023]
Abstract
The difference in fleece type is the distinguishing trait between the two types of alpacas (Vicugna pacos), Huacaya and Suri. The Suri fleece type has been found to be inherited dominantly over the Huacaya type, resulting in offspring with the Suri phenotype. The aim of our study was to map genomic regions associated with the two different fleece types. In this study, 91 alpacas (54 Huacayas and 37 Suris) from Germany and Switzerland were genotyped using the 76k alpaca SNP array. Only 59k chromosome-localised markers map to the alpaca reference assembly VicPac3.1, and after quality control 49 866 SNPs, were retained for population structure assessment and to conduct a genome-wide association study. Both principal component and neighbour-joining tree analysis showed that the two fleece-type cohorts overlapped rather than forming two distinct clusters. Genome-wide significantly associated markers were observed in the scaffold region of chromosome 16 (NW_021964192.1), which contains a cluster of keratin genes. A haplotype predominantly found in Suri alpacas has been identified which supports dominant inheritance. Variant filtering of nine whole-genome sequenced alpacas from both fleece types in the critical interval of 0.4 Mb did not reveal perfect segregation of either fleece type for specific variants. To our knowledge, this is the first study to use the recently developed species-specific SNP array to identify genomic regions associated with differences in fleece type in alpacas. There are still some limitations, such as the preliminary status of the reference assembly and the incomplete annotation of the alpaca genome.
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Affiliation(s)
- K Tan
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
| | - O O Adeniyi
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
| | - A Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G RuddGarces
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
| | - E Manz
- Generatio GmbH, Heidelberg, Germany
| | - H Wagner
- Animal Clinic for Reproduction and Neonatology, Justus Liebig University Giessen, Giessen, Germany
| | - P Zanolari
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
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Rudd Garces G, Letko A, Häfliger IM, Müller J, Herden C, Nesseler A, Wagner H, Schmidt MJ, Drögemüller C, Lühken G. MFSD2A frameshift variant in Kerry Hill sheep with microcephaly. Anim Genet 2024; 55:152-157. [PMID: 37921236 DOI: 10.1111/age.13374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Microcephaly is a rare neurodevelopmental disorder characterized by reduced skull circumference and brain volume that occurs sporadically in farm animals. We investigated an early-onset neurodegenerative disorder observed in seven lambs of purebred Kerry Hill sheep. Clinical signs included inability to stand or severe ataxia, convulsions, and early death. Diagnostic imaging and brain necropsy confirmed microcephaly. The pedigree of the lambs suggested monogenic autosomal recessive inheritance. We sequenced the genome of one affected lamb, and comparison with 115 control genomes revealed a single private protein-changing variant. This frameshift variant, MFSD2A: c.285dupA, p.(Asp96fs*9), represents a 1-bp duplication predicted to truncate 80% of the open reading frame. MFSD2A is a transmembrane protein that is essential for maintaining blood-brain barrier homeostasis and plays a key role in regulating brain lipogenesis. Human MFSD2A pathogenic variants are associated with a neurodevelopmental disorder with progressive microcephaly, spasticity, and brain imaging abnormalities (NEDMISBA, OMIM 616486). Here we present evidence for the occurrence of a recessively inherited form of microcephaly in sheep due to a loss-of-function variant in MFSD2A (OMIA 002371-9940). To the best of our knowledge, this is the first report of a spontaneous MFSD2A variant in domestic animals.
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Affiliation(s)
- Gabriela Rudd Garces
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jana Müller
- Institute for Veterinary Pathology, Justus Liebig University Giessen, Giessen, Germany
| | - Christiane Herden
- Institute for Veterinary Pathology, Justus Liebig University Giessen, Giessen, Germany
- Center for Mind, Brain and Behavior, Justus Liebig University Giessen, Giessen, Germany
| | | | - Henrik Wagner
- Veterinary Clinic for Reproduction and Neonatology, Justus Liebig University, Giessen, Germany
| | - Martin J Schmidt
- Clinic for Small Animals, Neurosurgery, Neuroradiology and Clinical Neurology, Justus Liebig University Giessen, Giessen, Germany
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
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Simon R, Kiener S, Thom N, Schäfer L, Müller J, Schlohsarczyk EK, Gärtner U, Herden C, Leeb T, Lühken G. Identification of an ADAMTS2 frameshift variant in a cat family with Ehlers-Danlos syndrome. G3 (Bethesda) 2023; 13:jkad152. [PMID: 37462293 PMCID: PMC10468306 DOI: 10.1093/g3journal/jkad152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/01/2023] [Indexed: 09/01/2023]
Abstract
We investigated 4 European domestic shorthair kittens with skin lesions consistent with the dermatosparaxis type of the Ehlers-Danlos syndrome, a connective tissue disorder. The kittens were sired by the same tomcat but were born by 3 different mothers. The kittens had easily torn skin resulting in nonhealing skin wounds. Both clinically and histologically, the skin showed thin epidermis in addition to inflammatory changes. Changes in collagen fibers were visible in electron micrographs. The complete genome of an affected kitten was sequenced. A one base pair duplication leading to a frameshift in the candidate gene ADAMTS2 was identified, p.(Ser235fs*3). All 4 affected cats carried the frameshift duplication in a homozygous state. Genotypes at this variant showed perfect cosegregation with the autosomal recessive Ehlers-Danlos syndrome phenotype in the available family. The mutant allele did not occur in 48 unrelated control cats. ADAMTS2 loss-of-function variants cause autosomal recessive forms of Ehlers-Danlos syndrome in humans, mice, dogs, cattle, and sheep. The available evidence from our investigation together with the functional knowledge on ADAMTS2 in other species allows to classify the identified ADAMTS2 variant as pathogenic and most likely causative variant for the observed Ehlers-Danlos syndrome.
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Affiliation(s)
- Rebecca Simon
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen 35390, Germany
| | - Sarah Kiener
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
- Dermfocus, University of Bern, Bern 3001, Switzerland
| | - Nina Thom
- Small Animal Clinic, Justus Liebig University, Giessen 35392, Germany
| | - Laura Schäfer
- Small Animal Clinic, Justus Liebig University, Giessen 35392, Germany
| | - Janina Müller
- Institute of Veterinary Pathology, Justus Liebig University, Giessen 35392, Germany
| | - Elfi K Schlohsarczyk
- Institute of Veterinary Pathology, Justus Liebig University, Giessen 35392, Germany
| | - Ulrich Gärtner
- Institute of Anatomy and Cell Biology, Justus Liebig University, Giessen 35385, Germany
| | - Christiane Herden
- Institute of Veterinary Pathology, Justus Liebig University, Giessen 35392, Germany
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
- Dermfocus, University of Bern, Bern 3001, Switzerland
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen 35390, Germany
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Adeniyi OO, Medugorac I, Grochowska E, Düring RA, Lühken G. Single-Locus and Multi-Locus Genome-Wide Association Studies Identify Genes Associated with Liver Cu Concentration in Merinoland Sheep. Genes (Basel) 2023; 14:genes14051053. [PMID: 37239413 DOI: 10.3390/genes14051053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Economic losses due to copper intoxication or deficiency is a problem encountered by sheep farmers. The aim of this study was to investigate the ovine genome for genomic regions and candidate genes responsible for variability in liver copper concentration. Liver samples were collected from slaughtered lambs of the Merinoland breed from two farms, and used for measurement of copper concentration and genome-wide association study (GWAS). A total of 45,511 SNPs and 130 samples were finally used for analysis, in which single-locus and several multi-locus GWAS (SL-GWAS; ML-GWAS) methods were employed. Gene enrichment analysis was performed for identified candidate genes to detect gene ontology (GO) terms significantly associated with hepatic copper levels. The SL-GWAS and a minimum of two ML-GWAS identified two and thirteen significant SNPs, respectively. Within genomic regions surrounding identified SNPs, we observed nine promising candidate genes such as DYNC1I2, VPS35, SLC38A9 and CHMP1A. GO terms such as lysosomal membrane, mitochondrial inner membrane and sodium:proton antiporter activity were significantly enriched. Genes involved in these identified GO terms mediate multivesicular body (MVB) fusion with lysosome for degradation and control mitochondrial membrane permeability. This reveals the polygenic status of this trait and candidate genes for further studies on breeding for copper tolerance in sheep.
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Affiliation(s)
- Olusegun O Adeniyi
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Ludwigstrasse 21, 35390 Giessen, Germany
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Ludwig Maximilian University Munich, Lena-Christ-Str. 48, 82152 Martinsried, Germany
| | - Ewa Grochowska
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka 28 St., 85-084 Bydgoszcz, Poland
| | - Rolf-Alexander Düring
- Institute of Soil Science and Soil Conservation, Interdisciplinary Research Center for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Ludwigstrasse 21, 35390 Giessen, Germany
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Ceccobelli S, Landi V, Senczuk G, Mastrangelo S, Sardina MT, Ben-Jemaa S, Persichilli C, Karsli T, Bâlteanu VA, Raschia MA, Poli MA, Ciappesoni G, Muchadeyi FC, Dzomba EF, Kunene NW, Lühken G, Deniskova TE, Dotsev AV, Zinovieva NA, Zsolnai A, Anton I, Kusza S, Carolino N, Santos-Silva F, Kawęcka A, Świątek M, Niżnikowski R, Špehar M, Anaya G, Granero A, Perloiro T, Cardoso P, Grande S, de Los Santos BL, Danchin-Burge C, Pasquini M, Martínez Martínez A, Delgado Bermejo JV, Lasagna E, Ciani E, Sarti FM, Pilla F. A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds. Genet Sel Evol 2023; 55:24. [PMID: 37013467 PMCID: PMC10069132 DOI: 10.1186/s12711-023-00797-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. RESULTS The results indicate that a large part of the Merino's genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. CONCLUSIONS To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes.
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Affiliation(s)
- Simone Ceccobelli
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy.
| | - Vincenzo Landi
- Department of Veterinary Medicine, University of Bari ''Aldo Moro", 70010, Valenzano, Italy
| | - Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Maria Teresa Sardina
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Slim Ben-Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, 2049, Ariana, Tunisia
| | - Christian Persichilli
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, Eskisehir Osmangazi University, 26040, Eskisehir, Turkey
| | - Valentin-Adrian Bâlteanu
- Laboratory of Genomics, Biodiversity, Animal Breeding and Molecular Pathology, Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, 400372, Cluj-Napoca, Romania
| | - María Agustina Raschia
- Instituto de Genética "Ewald A. Favret", Instituto Nacional de Tecnología Agropecuaria, CICVyA-CNIA, B1686, Hurlingham, Buenos Aires, Argentina
| | - Mario Andrés Poli
- Instituto de Genética "Ewald A. Favret", Instituto Nacional de Tecnología Agropecuaria, CICVyA-CNIA, B1686, Hurlingham, Buenos Aires, Argentina
| | - Gabriel Ciappesoni
- Instituto Nacional de Investigación Agropecuaria, 90200, Canelones, Uruguay
| | | | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, 3209, Scottsville, Pietermaritzburg, South Africa
| | | | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University, 35390, Giessen, Germany
| | | | | | | | - Attila Zsolnai
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, 2053, Herceghalom, Hungary
| | - István Anton
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, 2053, Herceghalom, Hungary
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032, Debrecen, Hungary
| | - Nuno Carolino
- Instituto Nacional de Investigação Agrária e Veterinária, 2005-048, Vale de Santarém, Portugal
| | - Fátima Santos-Silva
- Instituto Nacional de Investigação Agrária e Veterinária, 2005-048, Vale de Santarém, Portugal
| | - Aldona Kawęcka
- Department of Sheep and Goat Breeding, National Research Institute of Animal Production, 32-083, Kraków, Poland
| | - Marcin Świątek
- Department of Animal Breeding, Institute of Animal Sciences, Warsaw University of Life Sciences-SGGW, 02-786, Warsaw, Poland
| | - Roman Niżnikowski
- Department of Animal Breeding, Institute of Animal Sciences, Warsaw University of Life Sciences-SGGW, 02-786, Warsaw, Poland
| | - Marija Špehar
- Croatian Agency for Agriculture and Food, 10000, Zagreb, Croatia
| | - Gabriel Anaya
- MERAGEM Group, Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
| | - Antonio Granero
- Asociación Nacional de Criadores de Ganado Merino (ACME), 28028, Madrid, Spain
| | - Tiago Perloiro
- Associação Nacional de Criadores de Ovinos da Raça Merina (ANCORME), 7005-665, Évora, Portugal
| | - Pedro Cardoso
- Associação de Produtores Agropecuários (OVIBEIRA), 6000-244, Castelo Branco, Portugal
| | - Silverio Grande
- Associazione Nazionale della Pastorizia (ASSONAPA), 00187, Rome, Italy
| | | | | | - Marina Pasquini
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy
| | | | | | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Elena Ciani
- Department of Bioscience, Biotechnology and Biopharmaceutics, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
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8
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Pakpahan S, Widayanti R, Artama WT, Budisatria IGS, Lühken G. Genetic variability of the prion protein gene in Indonesian goat breeds. Trop Anim Health Prod 2023; 55:87. [PMID: 36806784 PMCID: PMC9938069 DOI: 10.1007/s11250-023-03486-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 01/23/2023] [Indexed: 02/19/2023]
Abstract
Scrapie is a naturally occurring transmissible spongiform encephalopathy in sheep and goats. Resistance or susceptibility of small ruminants to classical scrapie is influenced by polymorphisms in the prion protein gene (PRNP). PRNP variability in Indonesian indigenous goat breeds has not been investigated so far and therefore was the goal of this study. Sanger sequencing of the PRNP gene coding region in 72 goats of the seven Indonesian breeds Kacang, Gembrong, Samosir, Kejobong, Benggala, Jawarandu, and Peranakan Etawah revealed three amino acid substitutions, namely W102G, H143R, and S240P. Some silent mutations were also found at codons 42 (a/g), 138 (c/t), and 179 (g/t). The PRNP alleles K222 and D/S146 known to have significant protective effects on resistance to classical scrapie in goats were not detected. The allele R143, which may have a moderate protective effect, had a frequency of 12% among the analyzed Indonesian goat breeds. While R143 was missing in Kacang and Benggala, its frequency was highest in the breed Gembrong (32%). No scrapie cases have been reported in Indonesia until now. However, in the case that selection for protective PRNP variants would become a breeding goal, the analyzed breeds will not be very useful resources. Other goat breeds which are present in the country should be investigated regarding resistance to scrapie, too.
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Affiliation(s)
- Suhendra Pakpahan
- Research Center for Applied Zoology, Research Organization for Life Sciences, National Research and Innovation Agency (BRIN), Jl. Jakarta-Bogor Km.46, Cibinong, 16911 West Java Indonesia
| | - Rini Widayanti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, 55281 Indonesia
| | - Wayan Tunas Artama
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, 55281 Indonesia
| | - I. Gede Suparta Budisatria
- Department of Animal Production, Faculty of Animal Science, Gadjah Mada University, Yogyakarta, 55281 Indonesia
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus-Liebig University, 35390, Giessen, Germany.
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9
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Lagler DK, Hannemann E, Eck K, Klawatsch J, Seichter D, Russ I, Mendel C, Lühken G, Krebs S, Blum H, Upadhyay M, Medugorac I. Fine-mapping and identification of candidate causal genes for tail length in the Merinolandschaf breed. Commun Biol 2022; 5:918. [PMID: 36068271 PMCID: PMC9448734 DOI: 10.1038/s42003-022-03854-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/16/2022] [Indexed: 12/14/2022] Open
Abstract
Docking the tails of lambs in long-tailed sheep breeds is a common practice worldwide. But this practice is associated with pain. Breeding for a shorter tail could offer an alternative. Therefore, this study aimed to analyze the natural tail length variation in the Merinolandschaf and to identify causal alleles for the short tail phenotype segregating within long-tailed breeds. We used SNP-based association analysis and haplotype-based mapping in 362 genotyped (Illumina OvineSNP50) and phenotyped Merinolandschaf lambs. Genome-wide significant regions were capture sequenced in 48 lambs and comparatively analyzed in various long and short-tailed sheep breeds and wild sheep subspecies. Here we show a SNP located in the first exon of HOXB13 and a SINE element located in the promotor of HOXB13 as promising candidates. These results enable more precise breeding towards shorter tails, improve animal welfare by amplification of ancestral alleles and contribute to a better understanding of differential embryonic development. Using SNP-association analysis and genetic mapping, a SNP and an insertion in and close to HOXB13 associated with short tail length is identified in Merino sheep, which may be a target for safely selecting shorter tails and improving sheep welfare.
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Affiliation(s)
- Dominik Karl Lagler
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany.,Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Elisabeth Hannemann
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany
| | - Kim Eck
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany.,Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Jürgen Klawatsch
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany.,Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Doris Seichter
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Ingolf Russ
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Christian Mendel
- Institute for Animal Breeding, Bavarian State Research Center for Agriculture, Prof.-Dürrwaechter-Platz 1, 85586, Poing, Germany
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, JLU Gießen, Ludwigstr. 21, 35390, Gießen, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University Munich, 80539, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University Munich, 80539, Munich, Germany
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany.
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10
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Tan K, Roy M, Manz E, Wagner H, Zanolari P, Drögemüller C, Lühken G. The KIT:c.376G>A variant in German and Swiss alpacas (Vicugna pacos) with different coat colors. Anim Genet 2022; 53:718-720. [PMID: 35748185 DOI: 10.1111/age.13231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Kirsty Tan
- Institute for Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
| | - Mia Roy
- Institute for Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
| | | | - Henrik Wagner
- Clinic for Obstetrics, Gynaecology and Andrology of Large and Small Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Patrik Zanolari
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gesine Lühken
- Institute for Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
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11
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Simon R, Drögemüller C, Lühken G. The Complex and Diverse Genetic Architecture of the Absence of Horns (Polledness) in Domestic Ruminants, including Goats and Sheep. Genes (Basel) 2022; 13:genes13050832. [PMID: 35627216 PMCID: PMC9140736 DOI: 10.3390/genes13050832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 12/04/2022] Open
Abstract
Horns are the most obvious common feature of Bovidae. The naturally occurring absence of horns in these species, also known as polledness, is of surprisingly heterogeneous nature, although they are Mendelian traits. This review compares in detail the molecular differences among the causes of inherited polledness in the domestic ruminant species of cattle, yak, sheep, and goat based on the causal gene variants that have been discovered in recent years. The genetic causes for the lack of horns in small ruminants seem not only to be more complex, e.g., in sheep, breed-specific characteristics are still unexplained, but in goats, there is also the associated disorder of intersexuality—polled intersex syndrome (PIS). In connection with animal welfare and the associated discussion about a legal ban on the dehorning of all farm animals, naturally hornless animals and the causal genetic variants are of increasing research interest in the age of genome editing. However, the low acceptance of genetic engineering in livestock, especially in European societies, limits its use in food-producing animals. Therefore, genotype-based targeted selection of naturally occurring variants is still a widely used method for spreading this desired trait within and across populations, at least in cattle and sheep.
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Affiliation(s)
- Rebecca Simon
- Institute for Animal Breeding and Genetics, Justus Liebig University Giessen, 35390 Giessen, Germany; (R.S.); (G.L.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
- Correspondence:
| | - Gesine Lühken
- Institute for Animal Breeding and Genetics, Justus Liebig University Giessen, 35390 Giessen, Germany; (R.S.); (G.L.)
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12
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Bathke J, Lühken G. OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow. BMC Bioinformatics 2021; 22:402. [PMID: 34388963 PMCID: PMC8361789 DOI: 10.1186/s12859-021-04317-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/04/2021] [Indexed: 12/30/2022] Open
Abstract
Background The advent of next generation sequencing has opened new avenues for basic and applied research. One application is the discovery of sequence variants causative of a phenotypic trait or a disease pathology. The computational task of detecting and annotating sequence differences of a target dataset between a reference genome is known as "variant calling". Typically, this task is computationally involved, often combining a complex chain of linked software tools. A major player in this field is the Genome Analysis Toolkit (GATK). The "GATK Best Practices" is a commonly referred recipe for variant calling. However, current computational recommendations on variant calling predominantly focus on human sequencing data and ignore ever-changing demands of high-throughput sequencing developments. Furthermore, frequent updates to such recommendations are counterintuitive to the goal of offering a standard workflow and hamper reproducibility over time. Results A workflow for automated detection of single nucleotide polymorphisms and insertion-deletions offers a wide range of applications in sequence annotation of model and non-model organisms. The introduced workflow builds on the GATK Best Practices, while enabling reproducibility over time and offering an open, generalized computational architecture. The workflow achieves parallelized data evaluation and maximizes performance of individual computational tasks. Optimized Java garbage collection and heap size settings for the GATK applications SortSam, MarkDuplicates, HaplotypeCaller, and GatherVcfs effectively cut the overall analysis time in half. Conclusions The demand for variant calling, efficient computational processing, and standardized workflows is growing. The Open source Variant calling workFlow (OVarFlow) offers automation and reproducibility for a computationally optimized variant calling task. By reducing usage of computational resources, the workflow removes prior existing entry barriers to the variant calling field and enables standardized variant calling.
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Affiliation(s)
- Jochen Bathke
- Institute of Animal Breeding and Genetics, Justus Liebig University Gießen, Ludwigstraße 21, 35390, Gießen, Germany.
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University Gießen, Ludwigstraße 21, 35390, Gießen, Germany
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13
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Grochowska E, Lisiak D, Akram MZ, Adeniyi OO, Lühken G, Borys B. Association of a polymorphism in exon 3 of the IGF1R gene with growth, body size, slaughter and meat quality traits in Colored Polish Merino sheep. Meat Sci 2020; 172:108314. [PMID: 32987303 DOI: 10.1016/j.meatsci.2020.108314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/01/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023]
Abstract
This study aimed to genotype the polymorphism (c.654G > A) in the exon 3 of the insulin-like growth factor 1 receptor gene (IGF1R) and to analyze its association with growth, body size, slaughter and meat quality traits in Colored Polish Merino sheep. In total, 67 traits were analyzed. The IGF1R polymorphism was genotyped using the polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) method. The MIXED procedure of the SAS software was used to assess the genotypic effects of the polymorphism (c.654G > A) on production traits of interest. The IGF1R c.654G > A genotypes were found to have a significant effect on the average daily gain between the 56th and 78th day of life, cold carcass, leg part, leg cut, fore shank, and kidney weights, as well as eye of loin depth, intramuscular fat content, and water-holding capacity of meat. The results suggest that the studied polymorphism may provide useful information for marker-assisted selection for increased meat performance in Colored Polish Merino sheep.
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Affiliation(s)
- E Grochowska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, Mazowiecka 28 St, 85-084 Bydgoszcz, Poland.
| | - D Lisiak
- Department of Meat and Fat Technology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology, Rakowiecka 36 St., 02-532 Warsaw, Poland
| | - M Z Akram
- Department of Animal Production and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
| | - O O Adeniyi
- Institute of Animal Breeding and Genetics, Justus-Liebig University, Ludwigstrasse 21, 35390 Giessen, Germany
| | - G Lühken
- Institute of Animal Breeding and Genetics, Justus-Liebig University, Ludwigstrasse 21, 35390 Giessen, Germany
| | - B Borys
- National Research Institute of Animal Production, Experimental Station Kołuda Wielka, Parkowa 1 St., 88-160 Janikowo, Poland
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14
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Jost SM, Knoll A, Lühken G, Drögemüller C, Zanolari P. Prevalence of coat colour traits and congenital disorders of South American camelids in Austria, Germany and Switzerland. Acta Vet Scand 2020; 62:56. [PMID: 32948208 PMCID: PMC7501662 DOI: 10.1186/s13028-020-00554-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/14/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The increasing popularity of alpacas and llamas outside of South America is undeniable. The associated limited genetic diversity raises questions about health and other genetically determined traits like coat colour. Therefore, a survey studying the prevalence of congenital disorders and coat colours and patterns in South American camelids was performed in Austria, Germany and Switzerland. Moreover, the motivation for keeping these animals, the herd size and breeds was assessed. RESULTS A total of 146 questionnaires were returned corresponding to 16 farms from Austria, 69 farms from Germany, and 61 farms from Switzerland. In total, the returned surveys reported data on 2770 animals including ~ 85% alpacas and ~ 15% llamas. The most common alpaca breed was Huacaya (87.7%), the most common llama breed was Wooly (15.6%). Breeding (69.4%), wool production (63.3%) and keeping them as pets (53.7%) were the most common motivations to keep these animals, although this varied among countries. The three coat colour groups, solid white (24.8%), brown and black (64.8%) and grey (10.4%), occurred at different frequencies. About 7% of the South American camelids with solid white coat showed blue-pigmented eyes, corresponding to the known blue-eyed white phenotype, of which more than every second animal was apparently deaf. Uniform solid coloured animals occurred predominantly (81.4%), whereas pinto (8.8%), speckled (6.4%) and spotted (3.4%), also known as appaloosa, were comparably less prevalent. In total 161 observations of congenital disorders occurring during a 5-year-period were reported. The most prevalent disorders were in the group of musculoskeletal disorders such as spiral toe growth (16.4%), hyperextension of the fetlock joint (12.3%), angular limb deformities (11.0%) and axial rotation of the limbs (8.2%). CONCLUSIONS This survey revealed first insights into the occurrence of different traits and disorders in the current South American camelid population of Austria, Germany, and Switzerland. The identification of the most common musculoskeletal disorders might encourage the breeders to eliminate affected animals from their breeding program to decrease the incidence although traits such as spiral toe growth might also represent phenocopies.
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15
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Häfliger IM, Sickinger M, Holsteg M, Raeder LM, Henrich M, Marquardt S, Drögemüller C, Lühken G. An IL17RA frameshift variant in a Holstein cattle family with psoriasis-like skin alterations and immunodeficiency. BMC Genet 2020; 21:55. [PMID: 32448141 PMCID: PMC7247147 DOI: 10.1186/s12863-020-00860-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/14/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Skin lesions and dermatoses in cattle are often associated with infections due to bacteria, fungi or environmental risk factors. Dermatoses with genetic etiology have been described in cattle. Among these rare disorders, there are primary congenital dermatoses that are associated with inherited nutritional deficiencies, such as bovine hereditary zinc deficiency or zinc deficiency-like syndrome. This study presents three cases of Holstein cattle with congenital skin lesions observed on a single farm that resemble zinc deficiency-like syndrome. Close clinical and pathological examinations took place in two cases. Pedigree analysis indicated autosomal recessive inheritance and whole-genome sequencing of both affected calves was performed. RESULTS The two calves showed retarded growth and suffered from severe ulcerative dermatitis with hyperkeratosis, alopecia furunculosis and subcutaneous abscess formation. Blood analysis showed correspondent leukocytosis with neutrophilia whereas minerals, macro- and micronutrients were within the reference ranges. Variant calling and filtering against the 1000 Bull Genomes variant catalogue resulted in the detection of a single homozygous protein-changing variant exclusively present in both sequenced genomes. This single-nucleotide deletion in exon 3 of IL17RA on bovine chromosome 5 was predicted to have a deleterious impact on the encoded protein due to a frameshift leading to a truncated gene product. Genotyping of the affected cattle family confirmed recessive inheritance. CONCLUSIONS A loss-of-function mutation of the IL17RA transmembrane protein could be identified as most likely pathogenic variant for the psoriasis-like skin alterations observed in the two affected Holstein calves. In man, rare recessive diseases associated with IL17RA include immunodeficiency 51 and chronic mucocutaneous candidiasis. This supports the observed immunodeficiency of the presented cases. This study reports the first naturally occurring IL17RA-associated animal model.
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Affiliation(s)
- Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Marlene Sickinger
- Clinic for Obstetrics, Gynecology and Andrology of Large and Small Animals with Ambulatory Service, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Mark Holsteg
- Bovine Health Service, Chamber of Agriculture of North Rhine-Westphalia, 59505, Bad Sassendorf, Germany
| | - Leif M Raeder
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Manfred Henrich
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Siegfried Marquardt
- Veterinary Sharing Practice, Dr. Siegfried Marquardt and Peter Walter, 47574, Goch, Germany
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Faculty of Agricultural Sciences, Nutritional Sciences and Environmental Management, Justus-Liebig University Giessen, 35390, Giessen, Germany
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16
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Simon R, Lischer HEL, Pieńkowska-Schelling A, Keller I, Häfliger IM, Letko A, Schelling C, Lühken G, Drögemüller C. New genomic features of the polled intersex syndrome variant in goats unraveled by long-read whole-genome sequencing. Anim Genet 2020; 51:439-448. [PMID: 32060960 DOI: 10.1111/age.12918] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 01/19/2023]
Abstract
In domestic goats, the polled intersex syndrome (PIS) refers to XX female-to-male sex reversal associated with the absence of horn growth (polled). The causal variant was previously reported as a 11.7 kb deletion at approximately 129 Mb on chromosome 1 that affects the transcription of both FOXL2 and several long non-coding RNAs. In the meantime the presence of different versions of the PIS deletion was postulated and trials to establish genetic testing with the existing molecular genetic information failed. Therefore, we revisited this variant by long-read whole-genome sequencing of two genetically female (XX) goats, a PIS-affected and a horned control. This revealed the presence of a more complex structural variant consisting of a deletion with a total length of 10 159 bp and an inversely inserted approximately 480 kb-sized duplicated segment of a region located approximately 21 Mb further downstream on chromosome 1 containing two genes, KCNJ15 and ERG. Publicly available short-read whole-genome sequencing data, Sanger sequencing of the breakpoints and FISH using BAC clones corresponding to both involved genome regions confirmed this structural variant. A diagnostic PCR was developed for simultaneous genotyping of carriers for this variant and determination of their genetic sex. We showed that the variant allele was present in all 334 genotyped polled goats of diverse breeds and that all analyzed 15 PIS-affected XX goats were homozygous. Our findings enable for the first time a precise genetic diagnosis for polledness and PIS in goats and add a further genomic feature to the complexity of the PIS phenomenon.
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Affiliation(s)
- R Simon
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, 35390, Germany
| | - H E L Lischer
- Interfaculty Bioinformatics Unit, University of Bern, Bern, 3001, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - A Pieńkowska-Schelling
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland.,Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zürich, Zürich, 8057, Switzerland
| | - I Keller
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.,Department for BioMedical Research, University of Bern, Bern, 3001, Switzerland
| | - I M Häfliger
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - A Letko
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - C Schelling
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zürich, Zürich, 8057, Switzerland
| | - G Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, 35390, Germany
| | - C Drögemüller
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
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Molaee V, Bazzucchi M, De Mia GM, Otarod V, Abdollahi D, Rosati S, Lühken G. Phylogenetic analysis of small ruminant lentiviruses in Germany and Iran suggests their expansion with domestic sheep. Sci Rep 2020; 10:2243. [PMID: 32042070 PMCID: PMC7010740 DOI: 10.1038/s41598-020-58990-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/21/2020] [Indexed: 11/09/2022] Open
Abstract
Small ruminant lentiviruses (SRLVs) are found in sheep in Germany and Iran. SRLVs have been classified into four genotypes: A-C and E. Genotype A has been subdivided into 20 subtypes. Previous studies suggested that, first, the ancestors of genotype A are those SRLVs found in Turkey, second, the evolution of SRLVs is related to the domestication process, and, third, SRLV infection was first observed in sheep in Iceland and the source of that infection was a flock imported from Germany. This study generated, for the first time, partial SRLV sequence data from German and Iranian sheep, enhancing our knowledge of the genetic and evolutionary relationships of SRLVs, and their associations with the domestication process. Based on 54 SRLV sequences from German and Iranian sheep, our results reveal: (1) SRLV subtypes A4, A5, A11, A16 and A21 (new) are found in German sheep and A22 (new) in Iranian sheep. (2) Genotype A has potentially an additional ancestor (A22), found in Iran, Lebanon and Jordan. (3) Subtype A22 is likely an old version of SRLVs. (4) The transmission routes of some SRLVs are compatible with domestication pathways. (5) This study found no evidence of Icelandic subtype A1 in German sheep.
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Affiliation(s)
- Vahid Molaee
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen (JLU), Ludwigstraße 21, 35390, Gießen, Germany.
| | - Moira Bazzucchi
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche Togo Rosati (IZSUM), Via G. Salvemini 1, 06126, Perugia, Italy
| | - Gian Mario De Mia
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche Togo Rosati (IZSUM), Via G. Salvemini 1, 06126, Perugia, Italy
| | - Vahid Otarod
- Quarantine and Biosafety Directorate General, Iran Veterinary Organization (IVO), Vali Asr Avenue, Seyed Jamaledin Asad Abadi Street, 6349, Tehran, Iran
| | - Darab Abdollahi
- Bureau of Animal Health and Disease Management, Iran Veterinary Organization (IVO), Vali Asr Avenue, Seyed Jamaledin Asad Abadi Street, 6349, Tehran, Iran
| | - Sergio Rosati
- Department of Veterinary Science, University of Turin (UNITO), Largo Paolo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen (JLU), Ludwigstraße 21, 35390, Gießen, Germany
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Molaee V, Eltanany M, Lühken G. First survey on association of TMEM154 and CCR5 variants with serological maedi-visna status of sheep in German flocks. Vet Res 2018; 49:36. [PMID: 29673399 PMCID: PMC5909245 DOI: 10.1186/s13567-018-0533-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/03/2018] [Indexed: 12/03/2022] Open
Abstract
Maedi-visna, a disease caused by small ruminant lentiviruses (SRLVs), is present in sheep from many countries, also including Germany. An amino acid substitution (E/K) at position 35 of the transmembrane protein 154 (TMEM154) as well as a deletion in the chemokine (C-C motif) receptor type 5 gene (CCR5) were reported to be associated with the serological MV status and/or the SRLV provirus concentration in North American sheep populations. The aim of this study was to test if those two gene variants might be useful markers for MV susceptibility in Germany. For this purpose, more than 500 sheep from 17 serologically MV positive German sheep flocks with different breed backgrounds were genotyped applying PCR-based methods. Both, crosstab and non-parametric analyses showed significant associations of the amino acid substitution at position 35 of TMEM154 with the serological MV status (cut-off-based classification) and the median MV ELISA S/P value in all samples and in two of the four analyzed breed subsets. The deletion in the CCR5 promoter did not show a consistent association with serological MV status or median ELISA S/P value. It can be concluded that the amino acid substitution at position 35 of TMEM154 is a promising marker for breeding towards a lower number of serologically MV positive sheep in German flocks, at least in flocks of the Texel breed, while this remains questionable for the deletion in the CCR5 promoter. The findings of this study still need to be verified in additional sheep breeds.
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Affiliation(s)
- Vahid Molaee
- Department of Animal Breeding and Genetics, Justus Liebig University of Giessen, Ludwigstrasse 21, 35390, Giessen, Germany
| | - Marwa Eltanany
- Department of Animal Breeding and Genetics, Justus Liebig University of Giessen, Ludwigstrasse 21, 35390, Giessen, Germany
| | - Gesine Lühken
- Department of Animal Breeding and Genetics, Justus Liebig University of Giessen, Ludwigstrasse 21, 35390, Giessen, Germany.
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Ali A, Ibrahim M, Mohammed M, Elobied A, Lühken G. Growth differentiation factor 9 gene variants in Sudanese desert sheep ecotypes. S AFR J ANIM SCI 2016. [DOI: 10.4314/sajas.v46i4.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Lühken G, Krebs S, Rothammer S, Küpper J, Mioč B, Russ I, Medugorac I. The 1.78-kb insertion in the 3'-untranslated region of RXFP2 does not segregate with horn status in sheep breeds with variable horn status. Genet Sel Evol 2016; 48:78. [PMID: 27760516 PMCID: PMC5072343 DOI: 10.1186/s12711-016-0256-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 10/12/2016] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The mode of inheritance of horn status in sheep is far more complex than a superficial analysis might suggest. Observations, which were mostly based on crossbreeding experiments, indicated that the allele that results in horns is dominant in males and recessive in females, and some authors even speculated about the involvement of more than two alleles. However, all recent genome-wide association analyses point towards a very strong effect of a single autosomal locus on ovine chromosome 10, which was narrowed down to a putatively causal insertion polymorphism in the 3'-untranslated region of the relaxin/insulin-like family peptide receptor 2 gene (RXFP2). The main objective of this study was to test this insertion polymorphism as the causal mutation in diverse sheep breeds, including breeds with a variable and/or sex-dependent horn status. RESULTS After re-sequencing a region of about 246 kb that covered the RFXP2 gene and its flanking regions for 24 sheep from six completely horned and six completely polled breeds, we identified the same insertion polymorphism that was previously published as segregating with horn status in these breeds. Multiplex PCR genotyping of 489 sheep from 34 breeds and some crosses between sheep breeds showed a nearly perfect segregation of the insertion polymorphism with horn status in sheep breeds of Central and Western European origin. In these breeds and their crossings, heterozygous males were horned and heterozygous females were polled. However, this segregation pattern was not, or at least not completely, reproducible in breeds with sex-dependent and/or variable horn status, especially in sheep that originated from even more southern European regions and from Africa. In such breeds, we observed almost all possible combinations of genotype, sex and horn status phenotype. CONCLUSIONS The 1.78-kb insertion polymorphism in the 3'-untranslated region of RXFP2 and SNPs in the 3'-UTR, exon 14 and intron 11 of this gene that we analyzed in this study cannot be considered as the only cause of polledness in sheep and are not useful as a universal marker to define the genetic horn status in sheep.
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Affiliation(s)
- Gesine Lühken
- Department of Animal Breeding and Genetics, Justus Liebig University of Gießen, Ludwigstrasse 21a, 35390, Giessen, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center Munich, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Sophie Rothammer
- Chair of Animal Genetics and Husbandry, LMU Munich, Veterinaerstrasse 13, 80539, Munich, Germany
| | - Julia Küpper
- Department of Animal Breeding and Genetics, Justus Liebig University of Gießen, Ludwigstrasse 21a, 35390, Giessen, Germany
| | - Boro Mioč
- Department of Animal Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - Ingolf Russ
- Tierzuchtforschung e.V. München, Senator-Gerauer-Strasse 23, 85586, Poing, Germany
| | - Ivica Medugorac
- Chair of Animal Genetics and Husbandry, LMU Munich, Veterinaerstrasse 13, 80539, Munich, Germany.
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Lühken G, Krebs S, Rothammer S, Küpper JD, Mioč B, Russ I, Medugorac I. P5021 Indel polymorphism in 3‘-UTR of RXFP2 does not segregate with horns status in sheep breeds with a variable and/or sex-limited horns status. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4125a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Fleck K, Erhardt G, Lühken G. From single nucleotide substitutions up to chromosomal deletions: genetic pause of leucism-associated disorders in animals. Berl Munch Tierarztl Wochenschr 2016; 129:269-281. [PMID: 27529988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Leucism is characterized by a complete or partial white skin and hair in combination with pigmented irides, which can be vivid blue or heterochromatic. This is due to a complete or partial lack of melanocytes. The underlying pathogenesis is a disturbed emigration or differentiation of neural crest-derived cells. Therefore, leucistic phenotypes can be associated with defects, which mainly impair sensory organs and nerves. In humans, a well-known example is the Waardenburg syndrome. Leucism-associated disorders were also described in mouse, rat, hamster, rabbit, mink, cat, dog, pig, sheep, llama, alpaca, cattle and horse. In some of these species already identified causal mutations affect the genes EDN3, EDNRB, KIT, MITF, PAX3, SILV and SOX10. Defect alleles represent different types of genetic variation, ranging from single nucleotide substitutions up to larger chromosomal deletions. Some of the defect alleles produce desired coat color patterns. In some but not all cases, available genetic tests enable breeders to avoid production of animals affected by a leucism-associated disorder.
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Pauciullo A, Fleck K, Lühken G, Di Berardino D, Erhardt G. Dual-Color High-Resolution Fiber-FISH Analysis on Lethal White Syndrome Carriers in Sheep. Cytogenet Genome Res 2013; 140:46-54. [DOI: 10.1159/000350786] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2013] [Indexed: 11/19/2022] Open
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Lühken G, Fleck K, Pauciullo A, Huisinga M, Erhardt G. Familiar hypopigmentation syndrome in sheep associated with homozygous deletion of the entire endothelin type-B receptor gene. PLoS One 2012; 7:e53020. [PMID: 23300849 PMCID: PMC3534075 DOI: 10.1371/journal.pone.0053020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 11/22/2012] [Indexed: 11/24/2022] Open
Abstract
In humans, rodents and horses, pigmentary anomalies in combination with other disorders, notably intestinal aganglionosis, are associated with variants of the endothelin type-B receptor gene (EDNRB). In an inbred Cameroon sheep flock, five white lambs with light blue eyes were sired from the same ram and died within a few hours up to a few days after birth, some of them with signs of intestinal obstruction. The aim of this study was to investigate if the observed hypopigmentation and a possible lethal condition were associated with a molecular change at the ovine EDNRB locus, and to check if such a genetic alteration also occurs in other Cameroon sheep flocks. Sequence analysis revealed a deletion of about 110 kb on sheep chromosome 10, comprising the entire EDNRB gene, on both chromosomes in the two available hypopigmented lambs and on a single chromosome in the two dams and three other unaffected relatives. This micro-chromosomal deletion was also confirmed by quantitative real-time PCR and by fluorescence in situ hybridization. Genotyping of a total of 127 Cameroon sheep in 7 other flocks by duplex PCR did not identify additional carriers of the deletion. Although both hypopigmented lambs available for post-mortem examination had a considerably dilated cecum and remaining meconium, histopathological examination of intestinal samples showed morphologically normal ganglion cells in appropriate number and distribution. This is to our knowledge the first description of an ENDRB gene deletion and associated clinical signs in a mammalian species different from humans and rodents. In humans and rats it is postulated that the variable presence and severity of intestinal aganglionosis and other features in individuals with EDNRB deletion is due to a variable genetic background and multiple gene interactions. Therefore the here analyzed sheep are a valuable animal model to test these hypotheses in another species.
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Affiliation(s)
- Gesine Lühken
- Department of Animal Breeding and Genetics, Justus-Liebig University of Giessen, Giessen, Germany.
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Abstract
This review gives an overview on ovine and caprine defects/disorders, disease predispositions, production traits and coat colours for which causal gene variants are known. Most phenotypes are inherited autosomal-recessive or dominant and in the majority are caused by single nucleotide substitutions or deletions. Causative sequence variants mainly were identified by sequencing candidate genes in the past, and recently also by whole genome analysis using the ovine 50k SNP chip. While PCR-fragment length polymorphism analyses were developed for the majority of causative sequence variants, other low- to medium-throughput PCR-based methods as PCR-single strand conformation analysis and allele-specific PCR were also established frequently. For processing large sample numbers, high-throughput methods as MALDI-ToF MS or real-time PCR are available for some gene variants. Further progress in development of ovine and caprine genome sequences and SNP chips will be beneficial for the discovery of additional causative variants in these two species.
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Affiliation(s)
- Gesine Lühken
- Department of Animal Breeding and Genetics, Justus-Liebig University of Giessen, Ludwigstrasse 21B, 35390 Giessen, Germany.
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Lühken G, Gauly M, Kaufmann F, Erhardt G. Association study in naturally infected helminth layers shows evidence for influence of interferon-gamma gene variants on Ascaridia galli worm burden. Vet Res 2011; 42:84. [PMID: 21749701 PMCID: PMC3150263 DOI: 10.1186/1297-9716-42-84] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 07/12/2011] [Indexed: 11/13/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) in the genes for interleukin-4, -13 and interferon-gamma, and 21 additional SNPs which previously had been significantly associated with immune traits in the chicken, were genotyped in white and brown layer hens and analyzed for their association with helminth burden following natural infections. A nucleotide substitution located upstream of the promoter of the interferon-gamma gene was significantly associated with the log transformed number of Ascaridia galli in the brown layer line (genotype CC: 6.4 ± 1.0 worms; genotype CT: 11.7 ± 2.2 worms). Therefore, IFNG seems to be a promising candidate gene for further studies on helminth resistance in the chicken.
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Affiliation(s)
- Gesine Lühken
- Department of Animal Breeding and Genetics, Justus-Liebig University of Giessen, Ludwigstrasse 21B, 35390 Giessen, Germany.
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Caspari DK, Balkema-Buschman A, Brandt HR, Groschup MH, Erhardt G, Lühken G. Polymorphisms in genes <i>CTSB, CTSD, CAPN2, KLK1</i> and <i>TGFB1</i> not associated with susceptibility to atypical or classical ovine scrapie. Arch Anim Breed 2010. [DOI: 10.5194/aab-53-457-2010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. In the present study polymorphisms in the genes cathepsin B (CTSB), cathepsin D (CTSD), calpain, large polypeptide L2 (CAPN2), kallikrein 1 (KLK1) and transforming growth factor β1 (TGFB1) were investigated for association with scrapie susceptibility in sheep. Therefore single nucleotide polymorphisms in the respective genes were identified and examined for a potential impact on the gene function with different computer programs. Samples of 72 atypical and 104 classical scrapie cases as well as of 443 clinically healthy flock mates were genotyped by PCR-based screening methods. Neither allele frequencies nor genotype frequencies showed significant differences between scrapie positive sheep and control animals in any of the investigated genes.
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Lühken G, Glenske K, Brandt H, Erhardt G. Genetic variation in monoamine oxidase A and analysis of association with behaviour traits in beef cattle. J Anim Breed Genet 2010; 127:411-8. [DOI: 10.1111/j.1439-0388.2010.00855.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Caroli A, Rizzi R, Lühken G, Erhardt G. Short communication: Milk protein genetic variation and casein haplotype structure in the Original Pinzgauer cattle. J Dairy Sci 2010; 93:1260-5. [DOI: 10.3168/jds.2009-2521] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 11/09/2009] [Indexed: 11/19/2022]
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Goldammer T, Di Meo GP, Lühken G, Drögemüller C, Wu CH, Kijas J, Dalrymple BP, Nicholas FW, Maddox JF, Iannuzzi L, Cockett NE. Molecular cytogenetics and gene mapping in sheep (Ovis aries, 2n = 54). Cytogenet Genome Res 2009; 126:63-76. [PMID: 20016157 DOI: 10.1159/000245907] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2009] [Indexed: 11/19/2022] Open
Abstract
The development of a completely annotated sheep genome sequence is a key need for understanding the phylogenetic relationships and genetic diversity among the many different sheep breeds worldwide and for identifying genes controlling economically and physiologically important traits. The ovine genome sequence assembly will be crucial for developing optimized breeding programs based on highly productive, healthy sheep phenotypes that are adapted to modern breeding and production conditions. Scientists and breeders around the globe have been contributing to this goal by generating genomic and cDNA libraries, performing genome-wide and trait-associated analyses of polymorphism, expression analysis, genome sequencing, and by developing virtual and physical comparative maps. The International Sheep Genomics Consortium (ISGC), an informal network of sheep genomics researchers, is playing a major role in coordinating many of these activities. In addition to serving as an essential tool for monitoring chromosome abnormalities in specific sheep populations, ovine molecular cytogenetics provides physical anchors which link and order genome regions, such as sequence contigs, genes and polymorphic DNA markers to ovine chromosomes. Likewise, molecular cytogenetics can contribute to the process of defining evolutionary breakpoints between related species. The selective expansion of the sheep cytogenetic map, using loci to connect maps and identify chromosome bands, can substantially contribute to improving the quality of the annotated sheep genome sequence and will also accelerate its assembly. Furthermore, identifying major morphological chromosome anomalies and micro-rearrangements, such as gene duplications or deletions, that might occur between different sheep breeds and other Ovis species will also be important to understand the diversity of sheep chromosome structure and its implications for cross-breeding. To date, 566 loci have been assigned to specific chromosome regions in sheep and the new cytogenetic map is presented as part of this review. This review will also summarize the current cytogenomic status of the sheep genome, describe current activities in the sheep cytogenomics research sector, and will discuss the cytogenomics data in context with other major sheep genomics projects.
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Affiliation(s)
- T Goldammer
- Forschungsbereich Molekularbiologie, Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere (FBN), Dummerstorf, Germany. tomgoldammer @ fbn-dummerstorf.de
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Lühken G, Wagner HW, Seichter D, Hecht W, Erhardt G. Genetic characterization of a sheep-dwarf goat hybrid. Cytogenet Genome Res 2009; 125:158-61. [PMID: 19729920 DOI: 10.1159/000227841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2009] [Indexed: 11/19/2022] Open
Abstract
Twelve weeks after repeated spontaneous mating between a Bentheimer Landschaf ram and a West African dwarf doe was observed, the doe aborted a dead fetus. The aim of this study was to verify the parentage and the species of the supposed parents and the hybrid status of the fetus, using cytogenetic and molecular genetic methods. For this purpose, karyotypes were prepared using fresh blood samples from the ram and the doe, and genomic DNA was extracted from blood of the suspected parents and tissue of the aborted fetus. Fragments of the nuclear DNA-encoded interleukin-2 gene and the mitochondrial DNA-encoded 16S ribosomal RNA were sequenced and 19 microsatellites were genotyped in all 3 animals. The karyotypes and DNA sequences of the ram and the doe corresponded to domestic sheep and goat, respectively. The interleukin-2 sequence of the fetus was heterozygous at all positions where sheep and goat have different nucleotides. None of the 19 microsatellites excluded the ram and the dwarf doe as parents of the fetus. Taken together, we can conclude that the ram and the dwarf doe were from the species Ovis aries and Capra hircus, respectively, and that they were most likely the parents of the aborted fetus, which itself proved to be a hybrid of these 2 species.
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Affiliation(s)
- G Lühken
- Department of Animal Breeding and Genetics, Justus-Liebig University, Giessen, Germany.
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Wolff K, Lühken G, Litzke LF. Polydaktylia - In remembrance to Eurohippus messelensis – a case report. PFERDEHEILKUNDE 2009. [DOI: 10.21836/pem20090608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Lipsky S, Brandt H, Lühken G, Erhardt G. Analysis of prion protein genotypes in relation to reproduction traits in local and cosmopolitan German sheep breeds. Anim Reprod Sci 2008; 103:69-77. [PMID: 17204379 DOI: 10.1016/j.anireprosci.2006.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 11/29/2006] [Accepted: 12/04/2006] [Indexed: 11/27/2022]
Abstract
Due to the genetic determination of susceptibility to scrapie and other forms of transmissible spongiform encephalopathy (TSE) in sheep breeding to the less susceptible prion protein (PrP) genotype ARR/ARR was advanced within EU. In 4961 ewes of nine German sheep breeds (Coburg Fox sheep, Gray Horned Heath sheep, Merinoland sheep, Rhoen sheep, German Blackheaded Mutton sheep, Shropshire, Suffolk, Texel and White East Friesian Milk sheep) representing local and cosmopolitan breeds the reproductive traits number of lambs born, dead (including abortion at the end of pregnancy, stillbirth and death during the first 56 days post natum), weaned and rearing rate at each lambing were recorded and in 1641 of these ewes the PrP genotype was determined. A linear model was used to evaluate associations between PrP genotype and reproduction traits including the effects of PrP genotype (four classes: ewes with two, one and no copy of the ARR allele and with unknown PrP genotype), breed, interaction of PrP genotype and breed, number of lambing, lambing season and stock. Significant associations were only observed between the PrP genotype and the number of dead lambs at each lambing in Shropshire and Merinoland sheep and the rearing rate at each lambing in Shropshire. These significant associations were mainly caused by differences between animals with unknown PrP genotype and animals of the other PrP classes. In conclusion, breeding for TSE resistant sheep will not lead to a reduction in economically important reproduction traits.
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Affiliation(s)
- S Lipsky
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Ludwigstrasse 21 b, 35390 Giessen, Germany
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Groschup MH, Lacroux C, Buschmann A, Lühken G, Mathey J, Eiden M, Lugan S, Hoffmann C, Espinosa JC, Baron T, Torres JM, Erhardt G, Andreoletti O. Classic scrapie in sheep with the ARR/ARR prion genotype in Germany and France. Emerg Infect Dis 2007; 13:1201-7. [PMID: 17953092 PMCID: PMC2828083 DOI: 10.3201/eid1308.070077] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report 2 natural scrapie cases in sheep carrying the ARR/ARR prion genotype, which is believed to confer resistance against classic scrapie and bovine spongiform encephalopathy. In the past, natural scrapie and bovine spongiform encephalopathy (BSE) infections have essentially not been diagnosed in sheep homozygous for the A136R154R171 haplotype of the prion protein. This genotype was therefore assumed to confer resistance to BSE and classic scrapie under natural exposure conditions. Hence, to exclude prions from the human food chain, massive breeding efforts have been undertaken in the European Union to amplify this gene. We report the identification of 2 natural scrapie cases in ARR/ARR sheep that have biochemical and transmission characteristics similar to cases of classic scrapie, although the abnormally folded prion protein (PrPSc) was associated with a lower proteinase-K resistance. PrPSc was clearly distinct from BSE prions passaged in sheep and from atypical scrapie prions. These findings strongly support the idea that scrapie prions are a mosaic of agents, which harbor different biologic properties, rather than a unique entity.
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Affiliation(s)
- Martin H Groschup
- Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Insel Riems, Germany.
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Ibeagha-Awemu EM, Prinzenberg EM, Jann OC, Lühken G, Ibeagha AE, Zhao X, Erhardt G. Molecular characterization of bovine CSN1S2*B and extensive distribution of zebu-specific milk protein alleles in European cattle. J Dairy Sci 2007; 90:3522-9. [PMID: 17582136 DOI: 10.3168/jds.2006-679] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The B allele of the bovine alpha (S2)-casein gene (CSN1S2) was characterized at the molecular level and the distribution of zebu-specific milk protein alleles was determined in 26 cattle breeds originating from 3 continents. The CSN1S2*B allele is characterized by a C --> T transition affecting nucleotide 17 of exon 3, which leads to a change in the eighth amino acid of the mature protein, from Ser to Phe (i.e., TCC --> TTC). DNA-based methods were developed to identify carriers of CSN1S2*B and the other alleles (CSN1S2*A, C, and D) at the same locus. CSN1S2*B and other zebu-specific milk protein alleles and casein haplotypes are widely distributed in European cattle breeds, particularly those of southeastern origin. Alleles CSN1S2*B and CSN3*H are important in searching for zebu imprints in European cattle breeds. Diversity estimates at the milk protein loci were highest in the zebus followed by southeastern European taurines. Anatolian Black had the highest number of zebu alleles among European taurines. Common, group, and intergroup haplotypes occurred in the breeds and demonstrated relationships that concurred with developmental histories, genetic makeup, and, in particular, exposed the extent of zebu influence on southeastern European cattle.
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Affiliation(s)
- E M Ibeagha-Awemu
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, Ludwigstrasse 21b, D-35390 Giessen, Germany
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Lühken G, Zieleniewicz D, Brandt HR, Buschmann A, Groschup MH, Erhardt G. Microsatellites MCMA53 and MCMA16 on OAR15 are associated with susceptibility to atypical scrapie. Anim Genet 2007; 38:88-9. [PMID: 17257201 DOI: 10.1111/j.1365-2052.2006.01552.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- G Lühken
- Department of Animal Breeding and Genetics, Justus-Liebig University of Giessen, 35390 Giessen, Germany.
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Lühken G, Buschmann A, Brandt H, Eiden M, Groschup MH, Erhardt G. Epidemiological and genetical differences between classical and atypical scrapie cases. Vet Res 2006; 38:65-80. [PMID: 17156738 DOI: 10.1051/vetres:2006046] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 09/13/2006] [Indexed: 11/15/2022] Open
Abstract
The aim of this study was to analyze the epidemiology and prion protein (PrP) genetics in scrapie-affected sheep flocks in Germany. For this purpose, 224 German scrapie cases in sheep diagnosed between January 2002 and February 2006 were classified as classical or atypical scrapie and the amino acids at codons 136, 141, 154 and 171 were determined. Likewise, representative numbers of flock mates were genotyped. Significant epidemiological differences were observed between classical and atypical scrapie cases in regard to the numbers of scrapie-affected sheep within a flock, the sizes of flocks with only a single scrapie-positive sheep or more than one scrapie-positive sheep and the age distribution of the scrapie-positive sheep. Sheep with the ARQ/ARQ genotype had by far the highest risk for acquiring classical scrapie, but the risk for atypical scrapie was the highest for sheep carrying phenylalanine (F) at position 141 (AF(141)RQ) and/or the AHQ haplotype. However, atypical scrapie also occurred with a notable frequency in sheep with the PrP haplotypes ARR and/or ARQ in combination with Leucine at position 141 (AL(141)RQ). Furthermore, six atypical scrapie-positive sheep carried the PrP genotype ARR/ARR. The high proportion of sheep flocks affected by atypical scrapie underscores the importance of this scrapie type.
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Affiliation(s)
- Gesine Lühken
- Department of Animal Breeding and Genetics, Justus-Liebig University of Giessen, 35390 Giessen, Germany.
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Lühken G, Brandt HR, Buschmann A, Groschup MH, Erhardt G. Microsatellite CTSBJ12 is located distal to the ovine prion protein gene on OAR13 and is not associated with scrapie susceptibility. Anim Genet 2006; 37:426-7. [PMID: 16879367 DOI: 10.1111/j.1365-2052.2006.01465.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- G Lühken
- Department of Animal Breeding and Genetics, Justus-Liebig University of Giessen, 35390 Giessen, Germany.
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Lühken G, Stamm I, Menge C, Erhardt G. Functional analysis of a single nucleotide polymorphism in a potential binding site for GATA transcription factors in the ovine interleukin 2 gene. Vet Immunol Immunopathol 2005; 107:51-6. [PMID: 15869801 DOI: 10.1016/j.vetimm.2005.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2004] [Revised: 02/22/2005] [Accepted: 03/21/2005] [Indexed: 10/25/2022]
Abstract
The transcription factor GATA-3 is one regulator of Th1/Th2 differentiation. In sheep, we recently discovered a putative GATA-binding site (WGATAR) in the second intron of the Th1-cytokine gene interleukin 2 (IL2), showing a single nucleotide polymorphism (G/C). As genetic variations in cytokine genes are thought to regulate cytokine production, we studied the significance of this polymorphism for IL2 transcription. Sheep with different IL2 genotypes were identified by single-strand conformation polymorphism (SSCP)-analysis and IL2 transcription levels in peripheral blood mononuclear cells (PBMC) isolated from these animals were compared. For this purpose, transcription of IL2 mRNA was quantified by real-time polymerase chain reaction in unstimulated PBMC and in PBMC incubated for 4h in the presence of concanavalin A (ConA) or phorbol 12-myristate 13-acetate plus ionomycin (PMA/I). Compared to unstimulated cells, stimulation with ConA and PMA/I increased the IL2 mRNA transcription in average by 300- and 20-fold, respectively. Nevertheless, no significant differences in IL2 transcription between the genotypes could be detected. These findings were confirmed by band shift studies using different oligonucleotides containing variations of the potential binding motif, which showed no differences in the gel mobility after incubation with nuclear extract containing GATA-3. The obtained results argue against an impact of this polymorphism on the IL2 transcription and the genetic disease resistance in sheep.
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Affiliation(s)
- Gesine Lühken
- Department of Animal Breeding and Genetics, Justus-Liebig-University, Ludwigstrasse 21B, 35390 Giessen, Germany.
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Gretzschel A, Buschmann A, Eiden M, Ziegler U, Lühken G, Erhardt G, Groschup MH. Strain typing of German transmissible spongiform encephalopathies field cases in small ruminants by biochemical methods. ACTA ACUST UNITED AC 2005; 52:55-63. [PMID: 15752263 DOI: 10.1111/j.1439-0450.2005.00827.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Following the implementation of a large scale transmissible spongiform encephalopathies (TSE) surveillance programme of small ruminants, evidence for a natural transmission of bovine spongiform encephalopathy (BSE) to a French goat has been found. During the years 2002-2004, a massive TSE rapid testing programme on >250,000 small ruminants was carried out in Germany. In this national survey, 186 scrapie-affected sheep were found which originated from 78 flocks. The majority of these cases were of the classical TSE type (115 sheep belonging to 14 outbreaks). However, 71 cases coming from 64 flocks were of the novel atypical scrapie type. According to the regulation EU 999/2001, all TSE cases in small ruminants have to be examined by strain typing methods to explore any possibility of the existence of BSE cases in the field sheep population. Here we report on a biochemical typing strategy (termed FLI-test), which includes the determination of molecular masses, antibody binding affinities and glycosylation pattern of the TSE induced abnormal prion protein. Based on this typing approach none of the analysed German classical TSE outbreaks (total number of analysed sheep: 36) displayed biochemical features indicative for a BSE infection. However, in two cases distinct but BSE-unrelated PrP(Sc) types were found, which alludes to the existence of different scrapie strains in the German sheep population.
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Affiliation(s)
- A Gretzschel
- Friedrich-Loeffler-Institut (FLI), Institute for Novel and Emerging Diseases, Insel Riems, Germany
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Buschmann A, Lühken G, Schultz J, Erhardt G, Groschup MH. Neuronal accumulation of abnormal prion protein in sheep carrying a scrapie-resistant genotype (PrPARR/ARR). J Gen Virol 2004; 85:2727-2733. [PMID: 15302966 DOI: 10.1099/vir.0.79997-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The susceptibility of sheep to scrapie infection is influenced by prion gene alleles, which are modulated by polymorphic variations corresponding to amino acid positions 136, 154 and 173 of the prion protein (PrP). As no unquestioned report of a diseased sheep carrying homozygous alleles encoding alanine, arginine and arginine (PrPARR) at these sites has been published to date, sheep of this genotype are believed to be scrapie resistant. After the introduction of large-scale rapid testing for scrapie, a number of so-called ‘atypical’ scrapie cases have been found in Germany and elsewhere. Among those cases were two supposedly scrapie-resistant sheep. Brain samples from these animals tested positive for abnormal PrP (PrPSc) in one of four rapid tests available. Moreover, scrapie-associated fibril (SAF)-immunoblotting and immunohistochemistry, which are the generally accepted diagnostic techniques for scrapie, revealed prominent PrPSc deposition in the cerebellum. SAF immunoblotting also revealed PrPSc deposition in the obex, frontal cortex and brainstem. Transmission experiments to investigate the infectivity of scrapie propagated from these sheep have been initiated.
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Affiliation(s)
- Anne Buschmann
- Federal Research Centre for Virus Diseases of Animals, Institute for Novel and Emerging Infectious Diseases, Boddenblick 5a, 17493 Greifswald - Insel Riems, Germany
| | - Gesine Lühken
- Department of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Ludwigstraße 21B, 35390 Gießen, Germany
| | - Julia Schultz
- Federal Research Centre for Virus Diseases of Animals, Institute for Novel and Emerging Infectious Diseases, Boddenblick 5a, 17493 Greifswald - Insel Riems, Germany
| | - G Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Ludwigstraße 21B, 35390 Gießen, Germany
| | - Martin H Groschup
- Federal Research Centre for Virus Diseases of Animals, Institute for Novel and Emerging Infectious Diseases, Boddenblick 5a, 17493 Greifswald - Insel Riems, Germany
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Buschmann A, Biacabe AG, Ziegler U, Bencsik A, Madec JY, Erhardt G, Lühken G, Baron T, Groschup MH. Atypical scrapie cases in Germany and France are identified by discrepant reaction patterns in BSE rapid tests. J Virol Methods 2004; 117:27-36. [PMID: 15019257 DOI: 10.1016/j.jviromet.2003.11.017] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2003] [Revised: 11/13/2003] [Accepted: 11/18/2003] [Indexed: 10/26/2022]
Abstract
The intensified surveillance of scrapie in small ruminants in the European Union (EU) has resulted in a substantial increase of the number of diagnosed cases. Four rapid tests which have passed the EU evaluation for BSE testing of cattle are also recommended currently and used for the testing of small ruminants by the EU authorities. These tests include an indirect ELISA (cELISA), a colorimetric sandwich ELISA (sELISA I), a chemiluminescent sandwich ELISA (sELISA II), and a Western blot (WB). To this point, the majority of samples have been screened by using either sELISA I (predominantly in Germany) or WB (predominantly in France). In this study, it is shown that a number of the German and French scrapie cases show inconsistent results using rapid and confirmatory test methods. Forty-eight German sheep, 209 French sheep and 19 French goat transmissible spongiform encephalopathy (TSE) cases were tested. All cases were recognised by the sELISA I and either one of the confirmatory methods (scrapie-associated fibrils (SAF)-immunoblot or immunohistochemistry). Surprisingly, three rapid tests failed to detect a significant number of scrapie cases (29 in France and 24 in Germany). The possible reasons for these inconsistent reaction patterns of scrapie cases are discussed. Similar discrepancies have not been observed during rapid testing of cattle for BSE, the disease for which all diagnostic methods applied have been evaluated.
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Affiliation(s)
- A Buschmann
- Federal Research Centre for Virus Diseases of Animals, Institute for Novel and Emerging Infectious Diseases, Boddenblick 5a, 17493 Greifswald-Insel Riems, Germany
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Lühken G, Buschmann A, Groschup MH, Erhardt G. Prion protein allele A136 H154Q171 is associated with high susceptibility to scrapie in purebred and crossbred German Merinoland sheep. Arch Virol 2004; 149:1571-80. [PMID: 15290381 DOI: 10.1007/s00705-004-0303-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2003] [Accepted: 01/21/2004] [Indexed: 11/26/2022]
Abstract
Prion protein (PrP) genotypes were determined in eight sheep that have been tested positive for atypical scrapie from purebred or crossbred Merinoland sheep flocks in Germany and compared with the PrP genotypes of their flock mates. Two restriction fragment length polymorphism (RFLP) analyses were developed to determine all PRNP haplotypes occurring by variations at codons 136, 154 and 171. At least one copy of the A(136) H(154) Q(171) (AHQ) allele was found in all scrapie-positive sheep while the frequency of AHQ varied from over 23% to less than 3% in the whole flocks. There was a significant association between PrP genotype and a positive scrapie diagnosis over all flocks, suggesting a high scrapie susceptibility of PrP genotypes including the AHQ allele, at least in sheep of Merinoland type. These results argue that sheep with the AHQ allele are not generally less susceptible to scrapie and support the hypothesis that the influence of this allele on scrapie susceptibility may vary from flock to flock depending on genetic and/or epidemiological factors. This has to be considered when strategies for the eradication of scrapie in sheep are based on PrP genotypes.
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Affiliation(s)
- G Lühken
- Department of Animal Breeding and Genetics, Justus-Liebig University, Giessen, Germany.
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Affiliation(s)
- G Lühken
- Department of Animal Breeding and Genetics, Justus Liebig University Giessen, Ludwigstrasse, Giessen, Germany.
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Lühken G, Hiendleder S, Prinzenberg EM, Erhardt G. Rapid communication: a single-strand conformation polymorphism in the ovine interleukin-2 (IL-2) gene. J Anim Sci 2000; 78:2754-5. [PMID: 11048943 DOI: 10.2527/2000.78102754x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- G Lühken
- Department of Animal Breeding and Genetics, Justus-Liebig-University, Giessen, Germany.
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