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Vidal O, Drögemüller C, Obexer-Ruff G, Reber I, Jordana J, Martínez A, Bâlteanu VA, Delgado JV, Eghbalsaied S, Landi V, Goyache F, Traoré A, Pazzola M, Vacca GM, Badaoui B, Pilla F, D'Andrea M, Álvarez I, Capote J, Sharaf A, Pons À, Amills M. Differential distribution of Y-chromosome haplotypes in Swiss and Southern European goat breeds. Sci Rep 2017; 7:16161. [PMID: 29170508 PMCID: PMC5701018 DOI: 10.1038/s41598-017-15593-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 07/24/2017] [Accepted: 10/27/2017] [Indexed: 11/09/2022] Open
Abstract
The analysis of Y-chromosome variation has provided valuable clues about the paternal history of domestic animal populations. The main goal of the current work was to characterize Y-chromosome diversity in 31 goat populations from Central Eastern (Switzerland and Romania) and Southern Europe (Spain and Italy) as well as in reference populations from Africa and the Near East. Towards this end, we have genotyped seven single nucleotide polymorphisms (SNPs), mapping to the SRY, ZFY, AMELY and DDX3Y Y-linked loci, in 275 bucks from 31 populations. We have observed a low level of variability in the goat Y-chromosome, with just five haplotypes segregating in the whole set of populations. We have also found that Swiss bucks carry exclusively Y1 haplotypes (Y1A: 24%, Y1B1: 15%, Y1B2: 43% and Y1C: 18%), while in Italian and Spanish bucks Y2A is the most abundant haplotype (77%). Interestingly, in Carpathian goats from Romania the Y2A haplotype is also frequent (42%). The high Y-chromosome differentiation between Swiss and Italian/Spanish breeds might be due to the post-domestication spread of two different Near Eastern genetic stocks through the Danubian and Mediterranean corridors. Historical gene flow between Southern European and Northern African goats might have also contributed to generate such pattern of genetic differentiation.
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Affiliation(s)
- Oriol Vidal
- Departament de Biologia, Universitat de Girona, 17003, Girona, Spain.
| | - Cord Drögemüller
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | | | - Irene Reber
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Valentin Adrian Bâlteanu
- Institute of Life Sciences, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine, 400372, Cluj-Napoca, Romania
| | | | - Shahin Eghbalsaied
- Transgenesis Center of Excellence, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
| | - Vincenzo Landi
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Felix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, Gijón, 33394, Spain
| | - Amadou Traoré
- Institut de l'Environnement et Recherches Agricoles, 04 BP 8645, Ouagadougou, 04, Burkina Faso
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
| | | | - Bouabid Badaoui
- University Mohammed V, Agdal, Faculty of Sciences, 4 Av. Ibn Battota, Rabat, Morocco
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università Degli Studi Del Molise, Campobasso, Italy
| | - Mariasilvia D'Andrea
- Dipartimento Agricoltura, Ambiente e Alimenti, Università Degli Studi Del Molise, Campobasso, Italy
| | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, Gijón, 33394, Spain
| | - Juan Capote
- Instituto Canario de Investigaciones Agrarias, Canary Islands, Tenerife, La Laguna 38108, Spain
| | - Abdoallah Sharaf
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czechia.,Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Àgueda Pons
- Unitat de Races Autòctones, Servei de Millora Agrària, (SEMILLA-SAU), Son Ferriol, 07198, Spain
| | - Marcel Amills
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
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Burren A, Neuditschko M, Signer-Hasler H, Frischknecht M, Reber I, Menzi F, Drögemüller C, Flury C. Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds. Anim Genet 2016; 47:727-739. [PMID: 27436146 DOI: 10.1111/age.12476] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2016] [Indexed: 01/03/2023]
Abstract
We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (FROH ) with pedigree-based inbreeding coefficients (FPED ). The linear relationship between FROH and FPED was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). FROH appears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.
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Affiliation(s)
- A Burren
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland.
| | - M Neuditschko
- Swiss National Stud Farm, Agroscope Research Station, Les Longs-Prés, 1580, Avenches, Switzerland
| | - H Signer-Hasler
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland
| | - M Frischknecht
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland
| | - I Reber
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109, 3001, Bern, Switzerland
| | - F Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109, 3001, Bern, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109, 3001, Bern, Switzerland
| | - C Flury
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland
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Menzi F, Keller I, Reber I, Beck J, Brenig B, Schütz E, Leeb T, Drögemüller C. Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation. Sci Rep 2016; 6:28438. [PMID: 27329507 PMCID: PMC4916431 DOI: 10.1038/srep28438] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 03/07/2016] [Accepted: 06/06/2016] [Indexed: 02/08/2023] Open
Abstract
The South African Boer goat displays a characteristic white spotting phenotype, in which the pigment is limited to the head. Exploiting the existing phenotype variation within the breed, we mapped the locus causing this white spotting phenotype to chromosome 17 by genome wide association. Subsequent whole genome sequencing identified a 1 Mb copy number variant (CNV) harboring 5 genes including EDNRA. The analysis of 358 Boer goats revealed 3 alleles with one, two, and three copies of this CNV. The copy number is correlated with the degree of white spotting in goats. We propose a hypothesis that ectopic overexpression of a mutant EDNRA scavenges EDN3 required for EDNRB signaling and normal melanocyte development and thus likely lead to an absence of melanocytes in the non-pigmented body areas of Boer goats. Our findings demonstrate the value of domestic animals as reservoir of unique mutants and for identifying a precisely defined functional CNV.
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Affiliation(s)
- Fiona Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Irene Keller
- Department of Clinical Research and Swiss Institute of Bioinformatics, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Irene Reber
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Julia Beck
- Chronix Biomedical, Goetheallee 8, 37073 Göttingen, Germany
| | - Bertram Brenig
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
| | - Ekkehard Schütz
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
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Peters M, Reber I, Jagannathan V, Raddatz B, Wohlsein P, Drögemüller C. DNA-based diagnosis of rare diseases in veterinary medicine: a 4.4 kb deletion of ITGB4 is associated with epidermolysis bullosa in Charolais cattle. BMC Vet Res 2015; 11:48. [PMID: 25890340 PMCID: PMC4351973 DOI: 10.1186/s12917-015-0366-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 10/24/2014] [Accepted: 02/23/2015] [Indexed: 11/16/2022] Open
Abstract
Background Rare diseases in livestock animals are traditionally poorly diagnosed. Other than clinical description and pathological examination, the underlying causes have, for the most part, remained unknown. A single case of congenital skin fragility in cattle was observed, necropsy, histological and ultrastructural examinations were carried out and whole genome sequencing was utilized to identify the causative mutation. Results A single purebred female Charolais calf with severe skin lesions was delivered full-term and died spontaneously after birth. The clinical and pathological findings exactly matched the gross description given by previous reports on epitheliogenesis imperfecta and epidermolysis bullosa (EB) in cattle. Histological and ultrastructural changes were consistent with EB junctionalis (EBJ). Genetic analysis revealed a previously unpublished ITGB4 loss-of-function mutation; the affected calf was homozygous for a 4.4 kb deletion involving exons 17 to 22, and the dam carried a single copy of the deletion indicating recessive inheritance. The homozygous mutant genotype did not occur in healthy controls of various breeds but some heterozygous carriers were found among Charolais cattle belonging to the affected herd. The mutant allele was absent in a representative sample of unrelated sires of the German Charolais population. Conclusion This is the first time in which a recessively inherited ITGB4 associated EBJ has been reported in cattle. The identification of heterozygous carriers is of importance in avoiding the transmission of this defect in future. Current DNA sequencing methods offer a powerful tool for understanding the genetic background of rare diseases in domestic animals having a reference genome sequence available. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0366-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Peters
- Chemisches und Veterinäruntersuchungsamt Westfalen, Zur Taubeneiche 10-12, 59821, Arnsberg, Germany.
| | - Irene Reber
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
| | - Barbara Raddatz
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559, Hannover, Germany.
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559, Hannover, Germany.
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
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Reber I, Keller I, Becker D, Flury C, Welle M, Drögemüller C. Wattles in goats are associated with the FMN1/GREM1 region on chromosome 10. Anim Genet 2015; 46:316-20. [PMID: 25736034 PMCID: PMC5024000 DOI: 10.1111/age.12279] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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] [Accepted: 01/23/2015] [Indexed: 01/29/2023]
Abstract
The presence of congenital appendages (wattles) on the throat of goats is supposed to be under genetic control with a dominant mode of inheritance. Wattles contain a cartilaginous core covered with normal skin resembling early stages of extremities. To map the dominant caprine wattles (W) locus, we collected samples of 174 goats with wattles and 167 goats without wattles from nine different Swiss goat breeds. The samples were genotyped with the 53k goat SNP chip for a subsequent genome-wide association study. We obtained a single strong association signal on chromosome 10 in a region containing functional candidate genes for limb development and outgrowth. We sequenced the whole genomes of an informative family trio containing an offspring without wattles and its heterozygous parents with wattles. In the associated goat chromosome 10 region, a total of 1055 SNPs and short indels perfectly co-segregate with the W allele. None of the variants were perfectly associated with the phenotype after analyzing the genome sequences of eight additional goats. We speculate that the causative mutation is located in one of the numerous gaps in the current version of the goat reference sequence and/or represents a larger structural variant which influences the expression of the FMN1 and/or GREM1 genes. Also, we cannot rule out possible genetic or allelic heterogeneity. Our genetic findings support earlier assumptions that wattles are rudimentary developed extremities.
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Affiliation(s)
- I Reber
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland; DermFocus, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
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