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Jacinto JGP, Häfliger IM, Letko A, Weber J, Freick M, Gentile A, Drögemüller C, Agerholm JS. Multiple independent de novo mutations are associated with the development of schistosoma reflexum, a lethal syndrome in cattle. Vet J 2024; 304:106069. [PMID: 38281659 DOI: 10.1016/j.tvjl.2024.106069] [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: 08/11/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
Schistosoma reflexum (SR) is a lethal congenital syndrome characterized by U-shaped dorsal retroflexion of the spine and exposure of abdominal viscera. SR is usually associated with severe dystocia. The syndrome is thought to be inherited as a Mendelian trait. We collected a series of 23 SR-affected calves from four breeds (20 Holstein, one Red Danish, one Limousin, one Romagnola) and performed whole-genome sequencing (WGS). WGS was performed on 51 cattle, including 14 cases with parents (trio-based; Group 1) and nine single cases (solo-based; Group 2). Sequencing-based genome-wide association studies with 20 Holstein cases and 154 controls showed no association (above Bonferroni threshold; P-value<3 ×10-09). Assuming a monogenic recessive inheritance, no region of shared homozygosity was observed, suggesting heterogeneity. Alternatively, the presence of possible dominant acting de novo mutations were assessed. In Group 1, heterozygous private variants, absent in both parents, were found in seven cases. These involved the ACTL6A, FLNA, GLG1, IQSEC2, MAST3, MBTPS2, and MLLT1 genes. In addition, heterozygous private variants affecting the genes DYNC1LI1, PPP2R2B, SCAF8, SUGP1, and UBP1 were identified in five cases from Group 2. The detected frameshift and missense variants are predicted to cause haploinsufficiency. Each of these 12 affected genes belong to the class of haploinsufficient loss-of-function genes or are involved in embryonic and pre-weaning lethality or are known to be associated with severe malformation syndromes in humans and/or mice. This study presents for the first time a detailed genomic evaluation of bovine SR, suggesting that independent de novo mutations may explain the sporadic occurrence of SR in cattle.
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Affiliation(s)
- J G P Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano dell'Emilia (Bologna), Italy; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland
| | - I M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland
| | - A Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland
| | - J Weber
- Clinic for Ruminants, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland
| | - M Freick
- Faculty of Agriculture/Environment/Chemistry, HTW Dresden-University of Applied Sciences, 01326 Dresden, Germany
| | - A Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano dell'Emilia (Bologna), Italy
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland.
| | - J S Agerholm
- Department of Veterinary Clinical Sciences, University of Copenhagen, Højbakkegaard Allé 5A, 2630 Taastrup, Denmark
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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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Widmer S, Seefried FR, Häfliger IM, Signer-Hasler H, Flury C, Drögemüller C. WNT10B: A locus increasing risk of brachygnathia inferior in Brown Swiss cattle. J Dairy Sci 2023; 106:8969-8978. [PMID: 37641348 DOI: 10.3168/jds.2023-23315] [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: 01/31/2023] [Accepted: 05/15/2023] [Indexed: 08/31/2023]
Abstract
Shortening of the mandible (brachygnathia inferior) is a congenital, often inherited and variably expressed craniofacial anomaly in domestic animals including cattle. Brachygnathia inferior can lead to poorer animal health and welfare and reduced growth, which ultimately affects productivity. Within the course of the systematic conformation scoring, cases with a frequency of about 0.1% were observed in the Brown Swiss cattle population of Switzerland. In contrast, this anomaly is almost unknown in the Original Braunvieh population, representing the breed of origin. Because none of the individually examined 46 living offspring of our study cohort of 145 affected cows showed the trait, we can most likely exclude a monogenic-dominant mode of inheritance. We hypothesized that either a monogenic recessive or a complex mode of inheritance was underlying. Through a genome-wide association study of 145 cases and 509 controls with imputed 624k SNP data, we identified a 4.5 Mb genomic region on bovine chromosome 5 significantly associated with this anomaly. This locus was fine-mapped using whole-genome sequencing data. A run of homozygosity analysis revealed a critical interval of 430 kb. A breed specific frameshift duplication in WNT10B (rs525007739; c.910dupC; p.Arg304ProfsTer14) located in this genomic region was found to be associated with a 21.5-fold increased risk of brachygnathia inferior in homozygous carriers. Consequently, we present for the first time a genetic locus associated with this well-known anomaly in cattle, which allows DNA-based selection of Brown Swiss animals at decreased risk for mandibular shortening. In addition, this study represents the first large animal model of a WNT10B-related inherited developmental disorder in a mammalian species.
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Affiliation(s)
- Sarah Widmer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; Qualitas AG, 6300 Zug, Switzerland
| | | | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052 Zollikofen, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052 Zollikofen, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
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Jacinto JGP, Küchler LB, Peters LM, Van der Vekens E, Gurtner C, Seefried FR, Meylan M, Drögemüller C. MOCOS-associated renal syndrome in a Brown Swiss cattle. J Vet Intern Med 2023; 37:2603-2609. [PMID: 37675885 PMCID: PMC10658536 DOI: 10.1111/jvim.16856] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND A recessive form of MOCOS-associated xanthinuria type II is described in Tyrolean grey cattle. A similar case was identified in a 5-month-old Brown Swiss calf with hoof overgrowth, rough coat, urine sediment, and pneumonia. HYPOTHESIS/OBJECTIVES To characterize the disease phenotype, to evaluate its genetic etiology, and to determine the prevalence of the deleterious allele in the Brown Swiss population. ANIMALS An affected calf, its parents, and 65 441 Swiss dairy cattle. METHODS The affected animal was clinically examined and necropsied. Microarray genotyping was used to determine the genotypes and to assess the frequency of the MOCOS allele in a Brown Swiss control cohort. RESULTS Ultrasonography revealed hyperechoic renal pyramids with multifocal distal shadowing and echogenic sediment in the urinary bladder. Necropsy revealed suppurative bronchopneumonia and urolithiasis. Histology revealed numerous nephroliths with multifocal chronic lymphohistiocytic interstitial infiltrates, fibrosis, tubular degeneration, chronic multifocal glomerulonephritis with sclerosis, and bilateral hydronephrosis. Dysplastic changes were observed in the corium of the claw and the cornea. Genetic testing identified the homozygous presence of a known MOCOS frameshift variant in the case. Both parents were heterozygous and the prevalence of carriers in genotyped Brown Swiss cattle was 1.4% (342/24337). CONCLUSIONS AND CLINICAL IMPORTANCE The findings were consistent with the diagnosis of a recessive renal syndrome similar to xanthinuria type II described in Tyrolean grey cattle. The prevalence of the deleterious MOCOS allele is low in the Brown Swiss breed. However, mating of carriers should be avoided to prevent further losses.
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Affiliation(s)
- Joana G. P. Jacinto
- Department of Veterinary Medical SciencesUniversity of BolognaOzzanoItaly
- Institute of Genetics, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | | | - Laureen M. Peters
- Clinical Diagnostic Laboratory, Department of Clinical Veterinary Medicine, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | - Elke Van der Vekens
- Division of Clinical Radiology, Department of Clinical Veterinary Medicine, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | - Corinne Gurtner
- Institute of Veterinary Pathology, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | | | - Mireille Meylan
- Clinic for Ruminants, Department of Clinical Veterinary Medicine, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse FacultyUniversity of BernBernSwitzerland
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Schäfer J, May A, Wittenberg J, Hahn K, Graubner C, Gerber V, Drögemüller C, Unger L. [DDB2-associated incidence of squamous cell carcinoma in Haflingers: risk minimization by genotyping]. SCHWEIZ ARCH TIERH 2023; 165:707-715. [PMID: 37905572 DOI: doi.org/10.17236/sat00409] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
INTRODUCTION SCC (squamous cell carinomas) are among the most common eye neoplasms in horses. In recent studies Haflinger horses with a homozygous genotype for a missense variant in the DDB2 gene (damage specific DNA binding protein 2) had a significant increased risk of developing ocular SCC. The aims of this study were to determine the frequency of the SCC-associated risk allele in the DDB2 gene in Swiss and Austrian Haflinger populations and to validate the previously described phenotypic correlation. For this purpose, Haflingers presented at various horse clinics in Switzerland (n = 21, including 11 SCC cases), privately kept Haflingers (n = 52, including 1 SCC case), and Haflingers from a stud farm in the Austrian Tyrol (n = 53) were recruited. The individual DDB2 genotype of the animals was determined using a polymerase chain ceaction (PCR) test using hair follicle or whole blood samples. Of the 12 horses suffering from SCC, nine had ocular SCC and three had non-ocular SCC. Six of the nine Haflingers with ocular SCC and one of the three Haflingers with non-ocular SCC were homozygous for the DDB2 variant. Of the 113 clinically normal animals, 7/113 were homozygous (6 %) and 42/113 were heterozygous (37 %), which corresponds to an allele frequency of 24,8 % in the control cohort. The risk of ocular SCC occurring in Haflingers is significantly increased with the homozygous DDB2 genotype. However, not all animals with SCC carry this gene variant and not all DDB2 homozygous animals develop SCC, which can be explained by the multifactorial genesis of the disease. Due to the high frequency of the undesirable allele, we recommend taking the individual DDB2 genotype of breeding animals into account in order to avoid homozygous offspring with a greatly increased SCC risk by excluding high-risk matings.
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Affiliation(s)
- J Schäfer
- Swiss Institute of Equine Medicine (ISME), Departement für klinische Veterinärmedizin, Vetsuisse-Fakultät, Universität Bern
| | - A May
- Pferdeklinik der Ludwig-Maximilians-Universität München, Universität München
| | - J Wittenberg
- Pferdeklinik der Ludwig-Maximilians-Universität München, Universität München
| | - K Hahn
- Pferdeklinik der Ludwig-Maximilians-Universität München, Universität München
| | - C Graubner
- Swiss Institute of Equine Medicine (ISME), Departement für klinische Veterinärmedizin, Vetsuisse-Fakultät, Universität Bern
| | - V Gerber
- Swiss Institute of Equine Medicine (ISME), Departement für klinische Veterinärmedizin, Vetsuisse-Fakultät, Universität Bern
| | - C Drögemüller
- Institut für Genetik, Vetsuisse-Fakultät, Universität Bern
| | - L Unger
- Swiss Institute of Equine Medicine (ISME), Departement für klinische Veterinärmedizin, Vetsuisse-Fakultät, Universität Bern
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Jacinto JGP, Wohlsein P, Häfliger IM, Karl M, Pohlers M, Plobner L, Grünberg W, Drögemüller C. A missense variant in DGKG as a recessive functional variant for hepatic fibrinogen storage disease in Wagyu cattle. J Vet Intern Med 2023; 37:2631-2637. [PMID: 37681469 PMCID: PMC10658517 DOI: 10.1111/jvim.16865] [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: 03/16/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
Hepatic fibrinogen storage disease (HFSD) was diagnosed in a 5-month-old Wagyu calf with a history of recurrent respiratory disease. It was characterized by lethargy, dehydration, acidemia, and increased liver enzyme activities. Histologically, disseminated hepatocytes were swollen and showed a single, sharply demarcated, faintly eosinophilic cytoplasmic inclusion with a ground-glass appearance, with the nucleus in an eccentric position. Cytoplasmic inclusions did not stain with the periodic acid-Schiff (PAS) reaction. Using a rabbit polyclonal antibody against fibrinogen, the cytoplasmic vacuoles in the hepatocytes stained intensely. Electron microscopy disclosed hepatocytes with membrane-bound cytoplasmic inclusions filled with fine granular material interspersed with a few coarse-grained electron-dense granules. A trio whole-genome sequencing approach identified a deleterious homozygous missense variant in DGKG (p.Thr721Ile). The allele frequency in 209 genotyped Wagyu was 7.2%. This is a report of a DGKG-related recessive inherited disorder in cattle and adds DGKG to the list of candidate genes for HFSD in other species.
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Affiliation(s)
- Joana G. P. Jacinto
- Department of Veterinary Medical SciencesUniversity of BolognaBolognaSwitzerland
- Institute of Genetics, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | - Peter Wohlsein
- Department of PathologyUniversity of Veterinary Medicine HannoverHannoverGermany
| | - Irene M. Häfliger
- Institute of Genetics, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | | | | | | | - Walter Grünberg
- Clinic for Cattle, University of Veterinary Medicine HannoverHannoverGermany
- Clinic for Ruminants and Herd Health Management, Justus‐Liebig University GiessenGießenGermany
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse FacultyUniversity of BernBernSwitzerland
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Lindtke D, Seefried FR, Drögemüller C, Neuditschko M. Increased heterozygosity in low-pass sequencing data allows identification of blood chimeras in cattle. Anim Genet 2023; 54:613-618. [PMID: 37313694 DOI: 10.1111/age.13334] [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: 05/31/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/15/2023]
Abstract
In about 90% of multiple pregnancies in cattle, shared blood circulation between fetuses leads to genetic chimerism in peripheral blood and can reduce reproductive performance in heterosexual co-twins. However, the early detection of heterosexual chimeras requires specialized tests. Here, we used low-pass sequencing data with a median coverage of 0.64× generated from blood samples of 322 F1 crosses between beef and dairy cattle and identified 20 putative blood chimeras through increased levels of genome-wide heterozygosity. In contrast, for 77 samples with routine SNP microarray data generated from hair bulbs of the same F1s, we found no evidence of chimerism, simultaneously observing high levels of genotype discordance with sequencing data. Fifteen out of 18 reported twins showed signs of blood chimerism, in line with previous reports, whereas the presence of five alleged singletons with strong signs of chimerism suggests that the in-utero death rate of co-twins is at the upper limit of former estimates. Together, our results show that low-pass sequencing data allow reliable screening for blood chimeras. They further affirm that blood is not recommended as a source of DNA for the detection of germline variants.
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Schäfer J, Graubner C, Gerber V, Drögemüller C, Underberg J, Gurtner C, Unger L. [Ocular and non-ocular squamous cell carcinomas in the Haflinger: Eight cases at the Institut Suisse de Médecine Equine (2015-2022)]. SCHWEIZ ARCH TIERH 2023; 165:644-655. [PMID: 37822247 DOI: doi.org/10.17236/sat00406] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
INTRODUCTION This case series describes the clinical course of ocular and non-ocular squamous cell carinoma (SCC) in the Haflinger horse and is intended to raise awareness of the high recurrence rate and tendency to metastasize. Eight Haflingers with histologically confirmed SCC were included, five ocular and three non-ocular, who were presented at the Institut Suisse de Médecine Équine (ISME) Bern between July 2015 and January 2022. The ocular SCC cases were all presented because of an apparent mass, which in most cases was post-treatment recurrence. The occurrence of recurrences was observed between 3 weeks and 16 years after initial therapy. Four of five Haflingers with ocular SCC had an enucleation, three of which were clinically normal at the time of the completion of this study, one case was euthanized due to confirmed metastases and one due to lameness. The result of enucleations for therapy of ocular SCC was good if no metastases occurred. Of the three non-ocular SCC cases, only one case, a penile SCC, had an apparent mass. Therapy was initiated in this case, while the other two cases were euthanized shortly after diagnosis due to the poor prognosis of SCC in the appropriate locations (maxillary sinus, mandible). Metastases occurred three and two years after removal of the primary tumor in ocular SCC in the scapula, liver and lungs and in non-ocular SCC from the penis to the nostrils. Since a postmortem pathological examination was not carried out on all Haflingers, further metastases cannot be ruled out. Haflingers with SCC should be monitored by a veterinarian over the long term, as recurrences and/or metastases can still occur years later.
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Affiliation(s)
- J Schäfer
- Institut Suisse de Médecine Equine (ISME), Departement für klinische Veterinärmedizin, Vetsuisse-Fakultät, Universität Bern
| | - C Graubner
- Institut Suisse de Médecine Equine (ISME), Departement für klinische Veterinärmedizin, Vetsuisse-Fakultät, Universität Bern
| | - V Gerber
- Institut Suisse de Médecine Equine (ISME), Departement für klinische Veterinärmedizin, Vetsuisse-Fakultät, Universität Bern
| | - C Drögemüller
- Institut für Genetik, Vetsuisse-Fakultät, Universität Bern
| | - J Underberg
- Klinische Radiologie, Departement für klinische Veterinärmedizin, Vetsuisse-Fakultät, Universität Bern
| | - C Gurtner
- Institut für Tierpathologie, Vetsuisse-Fakultät, Universität Bern
| | - L Unger
- Institut Suisse de Médecine Equine (ISME), Departement für klinische Veterinärmedizin, Vetsuisse-Fakultät, Universität Bern
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Jacinto JGP, Bolcato M, Häfliger IM, Oevermann A, Gentile A, Drögemüller C. DYRK1B haploinsufficiency in a Holstein cattle with epilepsy. Anim Genet 2023; 54:623-627. [PMID: 37580898 DOI: 10.1111/age.13348] [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: 07/16/2023] [Revised: 07/16/2023] [Accepted: 07/22/2023] [Indexed: 08/16/2023]
Abstract
In this study, epilepsy with focal seizures progressing to generalized seizures was diagnosed in a 6-month-old Holstein heifer. The seizures were characterized by a brief pre-ictal phase with depression and vocalization. During the ictal phase eyelid spasms, tongue contractions, nodding and abundant salivation were observed, rapidly followed by a convulsive phase with bilateral tonic, clonic or tonic-clonic activity and loss of consciousness. Finally, during the postictal phase the heifer was obtunded and disorientated, unable to perceive obstacles and hypermetric, and pressed its head against objects. In the inter-seizure phase, the heifer was clinically normal. Neuropathology revealed axonal degeneration in the brainstem and diffuse astrocytic hypertrophic gliosis. Whole genome sequencing of the affected heifer identified a private heterozygous splice-site variant in DYRK1B (NM_001081515.1: c.-101-1G>A), most likely resulting in haploinsufficiency owing to loss-of-function. This represents a report of a DYRK1B-associated disease in cattle and adds DYRK1B to the candidate genes for epilepsy.
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Affiliation(s)
- Joana G P Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Marilena Bolcato
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Anna Oevermann
- Division of Neurological Sciences, DCR-VPH, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Arcangelo Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Letko A, Brülisauer F, Häfliger IM, Corr E, Scholes S, Drögemüller C. Loss-of-function variant in the ovine TMCO6 gene in North Country Cheviot sheep with motor neuron disease. Genomics 2023; 115:110689. [PMID: 37488055 DOI: 10.1016/j.ygeno.2023.110689] [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: 05/03/2023] [Revised: 06/27/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
In North Country Cheviot lambs with early-onset progressive ataxia and motor neuron degeneration, whole-genome sequencing identified a homozygous loss-of-function variant in the ovine transmembrane and coiled-coil domains (TMCO6) gene. The familial recessive form of motor neuron disease in sheep is due to a pathogenic 4 bp deletion leading to a 50% protein truncation that is assumed to result in the absence of a functional TMCO6. This uncharacterised protein is proposed to interact with ubiquilin 1 which is associated with Alzheimer's disease, whereas sporadic forms of amyotrophic lateral sclerosis are caused by variants in UBQLN2. Our findings provide a first spontaneous animal model for TMCO6, which could have implications in the studies of other comparative neurodegenerative diseases. In addition, these results will allow the design of a genetic test to prevent the occurrence of this fatal disease in the affected sheep population.
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Affiliation(s)
- Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland.
| | - Franz Brülisauer
- SRUC Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, United Kingdom.
| | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland.
| | - Eilidh Corr
- SRUC Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, United Kingdom.
| | - Sandra Scholes
- SRUC Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, United Kingdom
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland.
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12
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Brunetti B, Bacci B, Abbate JM, Tura G, Paciello O, Vaccaro E, Prisco F, Gandini G, Okonji S, Paola AD, Letko A, Drögemüller C, Jagannathan V, Turba ME, Ogundipe TG, Lorenzini L, Rosati M, Psalla D, Leeb T, Drögemüller M. SGCD Missense Variant in a Lagotto Romagnolo Dog with Autosomal Recessively Inherited Limb-Girdle Muscular Dystrophy. Genes (Basel) 2023; 14:1641. [PMID: 37628692 PMCID: PMC10454570 DOI: 10.3390/genes14081641] [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: 07/27/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
An 8-month-old female Lagotto Romagnolo dog was presented for a 1-month history of an initial severe reluctance to move, rapidly progressing to a marked stiff gait and progressive muscular weakness and evolving to tetraparesis, which persuaded the owner to request euthanasia. A primary muscle pathology was supported by necropsy and histopathological findings. Macroscopically, the muscles were moderately atrophic, except for the diaphragm and the neck muscles, which were markedly thickened. Histologically, all the skeletal muscles examined showed atrophy, hypertrophy, necrosis with calcification of the fibers, and mild fibrosis and inflammation. On immunohistochemistry, all three dystrophin domains and sarcoglycan proteins were absent. On Western blot analysis, no band was present for delta sarcoglycan. We sequenced the genome of the affected dog and compared the data to more than 900 control genomes of different dog breeds. Genetic analysis revealed a homozygous private protein-changing variant in the SGCD gene encoding delta- sarcoglycan in the affected dog. The variant was predicted to induce a SGCD:p.(Leu242Pro) change in the protein. In silico tools predicted the change to be deleterious. Other 770 Lagotto Romagnolo dogs were genotyped for the variant and all found to be homozygous wild type. Based on current knowledge of gene function in other mammalian species, including humans, hamsters, and dogs, we propose the SGCD missense variant as the causative variant of the observed form of muscular dystrophy in the index case. The absence of the variant allele in the Lagotto Romagnolo breeding population indicates a rare allele that has appeared recently.
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Affiliation(s)
- Barbara Brunetti
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Barbara Bacci
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | | | - Giorgia Tura
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Orlando Paciello
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (O.P.); (E.V.); (F.P.)
| | - Emanuela Vaccaro
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (O.P.); (E.V.); (F.P.)
| | - Francesco Prisco
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (O.P.); (E.V.); (F.P.)
| | - Gualtiero Gandini
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Samuel Okonji
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Andrea di Paola
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (C.D.); (V.J.); (T.L.); (M.D.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (C.D.); (V.J.); (T.L.); (M.D.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (C.D.); (V.J.); (T.L.); (M.D.)
| | | | - Tolulope Grace Ogundipe
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Luca Lorenzini
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Marco Rosati
- Section of Clinical & Comparative Neuropathology, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universitaet-Muenchen, 80539 Munich, Germany;
| | - Dimitra Psalla
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (C.D.); (V.J.); (T.L.); (M.D.)
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (C.D.); (V.J.); (T.L.); (M.D.)
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13
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Jacinto JGP, Schiavon E, Häfliger IM, Coin P, Seefried FR, Drögemüller C. MYH3
‐associated non‐syndromic palatoschisis (cleft palate, CP) in Limousine cattle. Anim Genet 2023. [PMID: 36967223 DOI: 10.1111/age.13317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023]
Affiliation(s)
- Joana G P Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Eliana Schiavon
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Irene M Häfliger
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Patrizio Coin
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
- Dipartimento Veterinario e Sicurezza Alimenti di Origine Animale Agenzie di Tutela della Salute, Brescia, Italy
| | | | - Cord Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
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14
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Jacinto JGP, Schiavon E, Häfliger IM, Coin P, Seefried FR, Drögemüller C. MYH3-associated non-syndromic palatoschisis (cleft palate, CP) in Limousine cattle. Anim Genet 2023. [PMID: 36944326 DOI: 10.1111/age.13316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/23/2023]
Affiliation(s)
- Joana G P Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Eliana Schiavon
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Irene M Häfliger
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Patrizio Coin
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
- Dipartimento Veterinario e Sicurezza Alimenti di Origine Animale Agenzie di Tutela della Salute, Brescia, Italy
| | | | - Cord Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
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15
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Scheemaeker S, Inglebert M, Daminet S, Dettwiler M, Letko A, Drögemüller C, Kessler M, Ducatelle R, Rottenberg S, Campos M. Organoids of patient-derived medullary thyroid carcinoma: The first milestone towards a new in vitro model in dogs. Vet Comp Oncol 2023; 21:111-122. [PMID: 36583463 DOI: 10.1111/vco.12872] [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: 08/12/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 12/31/2022]
Abstract
Organoid cultures could constitute a valuable in vitro model to explore new treatments for canine (c) medullary thyroid carcinoma (MTC). The study's objectives were to establish and characterize 3D organoid cultures of cMTC using histology and immunohistochemistry (IHC) and to evaluate the effect of antitumor drugs on organoids' viability. Five cMTC tissue samples were used to develop organoid cultures of which one organoid line, named cMTC N°2, could be passaged for an extended period. This cMTC N°2 organoid line was further compared to the primary tumour regarding morphology and IHC expression of thyroid transcription factor-1 (TTF-1), thyroglobulin, calcitonin, synaptophysin, vimentin, Ki-67, cyclooxygenase-2 (COX-2), P-glycoprotein and vascular endothelial growth factor (VEGF). Quality control of the cMTC N°2 organoid line was achieved by a single nucleotide polymorphism (SNP) array of the organoids, primary tumour and healthy blood cells of the same dog. The effect of carboplatin, meloxicam and toceranib phosphate (TOC) on cMTC N°2 organoids' viability was evaluated. The cMTC N°2 organoid line was cultured for 94 days and showed similar histological features with the primary tumour. Immunolabelling for TTF-1, thyroglobulin, calcitonin and VEGF was similar between the primary tumour and cMTC N°2 organoids. Compared to the primary tumour, organoids showed higher immunolabelling for vimentin and Ki-67, and lower immunolabelling for synaptophysin, COX-2 and P-glycoprotein. The SNP genotype was similar for each chromosome between healthy blood cells, primary tumour and cMTC N°2 organoids. Carboplatin, meloxicam and TOC had no effect on cMTC N°2 organoid cell viability within achievable in vivo concentration range. In conclusion, the cMTC N°2 organoid line is a promising first milestone towards an established in vitro organoid model to explore pathophysiology and new treatment modalities in cMTC.
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Affiliation(s)
- Stephanie Scheemaeker
- Department of Small Animals, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Marine Inglebert
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sylvie Daminet
- Department of Small Animals, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Martina Dettwiler
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Richard Ducatelle
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Sven Rottenberg
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Miguel Campos
- Department of Clinical Veterinary Science, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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16
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Signer-Hasler H, Casanova L, Barenco A, Maitre B, Bagnato A, Vevey M, Berger B, Simčič M, Boichon D, Capitan A, Medugorac I, Bennewitz J, Mészáros G, Sölkner J, Drögemüller C, Flury C. Genomic regions underlying positive selection in local, Alpine cattle breeds. Anim Genet 2023; 54:239-253. [PMID: 36737525 DOI: 10.1111/age.13295] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
We used genome-wide SNP data from 18 local cattle breeds from six countries of the Alpine region to characterize population structure and identify genomic regions underlying positive selection. The geographically close breeds Evolèner, Eringer, Valdostana Pezzata Nera, and Valdostana Castana were found to differ from all other Alpine breeds. In addition, three breeds, Simmental, and Original Braunvieh from Switzerland and Pinzgauer from Austria built three separate clusters. Of the 18 breeds studied, the intra-alpine Swiss breed Evolèner had the highest average inbreeding based on runs of homozygosity (FROH ) and the highest average genomic relationship within the breed. In contrast, Slovenian Cika cattle had the lowest average genomic inbreeding and the lowest average genomic relationship within the breed. We found selection signatures on chromosome 6 near known genes such as KIT and LCORL explaining variation in coat color and body size in cattle. The most prominent selection signatures were similar regardless of marker density and the breeds in the data set. In addition, using available high-density SNP data from 14 of the breeds we identified 47 genome regions as ROH islands. The proportion of homozygous animals was higher in all studied animals of local breeds than in Holstein and Brown Swiss cattle, the two most important commercial breeds in the Alpine region. We report ROH islands near genes related to thermoregulation, coat color, production, and stature. The results of this study serve as a basis for the search for causal variants underlying adaptation to the alpine environment and other specific characteristics selected during the evolution of local Alpine cattle breeds.
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Affiliation(s)
- Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | | | - Blaise Maitre
- Schweizerischer Eringerviehzuchtverband, Sion, Switzerland
| | | | | | | | - Mojca Simčič
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Aurélien Capitan
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried/Planegg, Germany
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences, Vienna, Wien, Austria
| | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Wien, Austria
| | - Cord Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland
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17
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Seidl R, Drögemüller C, Krütli P, Walther C. The role of trust and risk perception in current German nuclear waste management. Risk Anal 2022; 42:2704-2719. [PMID: 35092964 DOI: 10.1111/risa.13889] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
One of the lessons learned in various countries that have to deal with spent nuclear fuel is that finding a proper place and siting a repository for high-level nuclear waste (HLW) cannot be achieved without public consent. After decades of obstruction, Germany recently launched a new, participatory, site-selection process for the disposal of HLW in deep geological formations. Nonetheless, significant opposition is assumed. Therefore, citizens' trust in the procedure and the agents involved may be paramount. We conducted an online survey (N ≈ 5000) in March/April 2020 to test a theoretical model on trust, perceived risks and benefits, and acceptance. We differentiated acceptance as a dependent variable according to distinct phases: the procedure, a possible decision on a disposal location, and the repository facility itself. The results show that trust is mainly important for explaining acceptance of the ongoing procedure and less so for the acceptance of the decision or the repository facility itself. Moreover, our investigation of the sample using a cluster analysis reveals characteristic patterns of trust, risk perception, and acceptance by three clusters: a cluster focusing on risk perception, an ambivalent cluster, and an indifferent cluster. Trust is lowest in the risk-focused cluster and highest in the ambivalent cluster.
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Affiliation(s)
- Roman Seidl
- Institute of Radioecology and Radiation Protection, Leibniz University Hannover, Hannover, Germany
| | - Cord Drögemüller
- Institute of Radioecology and Radiation Protection, Leibniz University Hannover, Hannover, Germany
| | | | - Clemens Walther
- Institute of Radioecology and Radiation Protection, Leibniz University Hannover, Hannover, Germany
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18
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Akyürek EE, Busato F, Murgiano L, Bianchini E, Carotti M, Sandonà D, Drögemüller C, Gentile A, Sacchetto R. Differential Analysis of Gly211Val and Gly286Val Mutations Affecting Sarco(endo)plasmic Reticulum Ca 2+-ATPase (SERCA1) in Congenital Pseudomyotonia Romagnola Cattle. Int J Mol Sci 2022; 23:ijms232012364. [PMID: 36293223 PMCID: PMC9604440 DOI: 10.3390/ijms232012364] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/29/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Congenital pseudomyotonia in cattle (PMT) is a rare skeletal muscle disorder, clinically characterized by stiffness and by delayed muscle relaxation after exercise. Muscle relaxation impairment is due to defective content of the Sarco(endo)plasmic Reticulum Ca2+ ATPase isoform 1 (SERCA1) protein, caused by missense mutations in the ATP2A1 gene. PMT represents the only mammalian model of human Brody myopathy. In the Romagnola breed, two missense variants occurring in the same allele were described, leading to Gly211Val and Gly286Val (G211V/G286V) substitutions. In this study, we analyzed the consequences of G211V and G286V mutations. Results support that the reduced amount of SERCA1 is a consequence of the G211V mutation, the G286V mutation almost being benign and the ubiquitin–proteasome system (UPS) being involved. After blocking the proteasome using a proteasome inhibitor, we found that the G211V mutant accumulates in cells at levels comparable to those of WT SERCA1. Our conclusion is that G211/286V mutations presumably originate in a folding-defective SERCA1 protein, recognized and diverted to degradation by UPS, although still catalytically functional, and that the main role is played by G211V mutation. Rescue of mutated SERCA1 to the sarcoplasmic reticulum membrane can re-establish resting cytosolic Ca2+ concentration and prevent the appearance of pathological signs, paving the way for a possible therapeutic approach against Brody disease.
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Affiliation(s)
- Eylem Emek Akyürek
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, Legnaro, 35020 Padova, Italy
| | - Francesca Busato
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, Legnaro, 35020 Padova, Italy
- Veterinary Clinic San Marco, Viale dell’Industria 3, Veggiano, 35030 Padova, Italy
| | - Leonardo Murgiano
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, 3900 Delancey Street, Philadelphia, PA 19104, USA
| | - Elisa Bianchini
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
- Aptuit, Via A. Fleming 4, 37135 Verona, Italy
| | - Marcello Carotti
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
| | - Dorianna Sandonà
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland
| | - Arcangelo Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, Italy
| | - Roberta Sacchetto
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, Legnaro, 35020 Padova, Italy
- Correspondence: ; Tel.: +39-049-827-2653
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19
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Jacinto JGP, Muscatello LV, Häfliger IM, Benazzi C, Bolcato M, Gentile A, Drögemüller C. A Missense Variant in PLP2 in Holstein Cattle with X-Linked Congenital Mast Cell Tumor. Animals (Basel) 2022; 12:ani12182329. [PMID: 36139188 PMCID: PMC9494957 DOI: 10.3390/ani12182329] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/28/2022] [Accepted: 09/05/2022] [Indexed: 12/02/2022] Open
Abstract
Congenital tumors occur infrequently in cattle. The aim of this study was to detail the clinicopathological phenotype of a Holstein calf with a congenital mast cell tumor and to identify the genetic cause by a whole-genome sequencing (WGS) trio-approach. An 18-day-old male Holstein calf was clinically examed and revealed multifocal, alopecic, thick and wrinkled skin lesions over the entire body. At 6 months of age, the general condition of the calf was characterized by retarded growth, poor nutritional status, and ulceration of the skin lesions. Histopathological examination revealed a primary cutaneous, poorly differentiated embryonal mast cell tumor with metastases in the lymph nodes and liver. Genetic analysis revealed a private X-linked variant in the PLP2 gene (chrX:87216480C > T; c.50C > T), which was present only in the genomes of the case (hemizygous) and his mother (heterozygous). It was absent in the sire as well as in 5365 control genomes. The identified missense variant exchanges the encoded amino acid of PLP2 at position 17 (p.Thr17Ile), which is classified as deleterious and affects a protein that plays a role in tumor growth and metastasis. Therefore, we suggested that the detected PLPL2 variant could be a plausible cause for this congenital condition in the affected calf.
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Affiliation(s)
- Joana G. P. Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Luisa Vera Muscatello
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy
| | - Irene M. Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Cinzia Benazzi
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy
- Correspondence:
| | - Marilena Bolcato
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy
| | - Arcangelo Gentile
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
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20
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Capuzzello G, Jacinto JGP, Häfliger IM, Chapman GE, Martin SS, Viora L, Jonsson NN, Drögemüller C. A large deletion encompassing exon 2 of the ectodysplasin A (EDA) gene in a British blue crossbred calf with hypohidrotic ectodermal dysplasia. Acta Vet Scand 2022; 64:23. [PMID: 36068608 PMCID: PMC9446731 DOI: 10.1186/s13028-022-00641-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 05/04/2022] [Accepted: 08/26/2022] [Indexed: 12/02/2022] Open
Abstract
Background Hypohidrotic ectodermal dysplasia (HED) is a congenital syndrome of mammals affecting organs and tissues of ectodermal origin characterized by absence or hypoplasia of hair, teeth, and eccrine glands. The disorder has been reported in several species, including humans, mice, dogs and cattle, associated with variants in genes affecting the ectodysplasin pathway, including the X-linked ectodysplasin A (EDA) gene. Until now, nine pathogenic variants have been found in the bovine EDA gene. Here we report a novel variant in EDA in a crossbreed male Belgian Blue calf with HED, and provide an overview of the phenotypic and allelic heterogeneity of EDA-related forms of HED in cattle. Case presentation A 45-day-old male crossbreed British Blue calf was referred with congenital hypotrichosis, oligodontia and omphalitis. On histopathological examination of the nasal planum, nasolabial glands and ducts were not observed. The density of hair follicles was low, and they were small, with a predominance of telogen-phase hairs, and some serocellular crusts. The phenotype of the calf resembled that of HED. Whole-genome sequencing (WGS) was performed and revealed a 21,899 base-pair deletion encompassing the coding exon 2 of EDA, predicted to result in an altered transcript and aberrant protein. Conclusions The clinicopathological and genetic findings were consistent with a case of X-linked HED. A very similar EDA deletion has been previously reported in a family of Holstein cattle with HED. The newly identified hemizygous EDA loss-of-function variant is certainly pathogenic and therefore is the genetic cause for the observed phenotype. This case report provides an additional example of the potential of WGS-based precise diagnostics in livestock species such as cattle to increase the diagnostic yield in rare diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s13028-022-00641-2.
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Affiliation(s)
- Giovanni Capuzzello
- College of Medical, Veterinary & Life Sciences, University of Glasgow, 464 Bearsden Rd, Glasgow, G61 1QH, UK
| | - Joana Gonçalves Pontes Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50Ozzano dell'Emilia, 40064, Bologna, Italy.,Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
| | - Irene Monika Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
| | - Gail E Chapman
- College of Medical, Veterinary & Life Sciences, University of Glasgow, 464 Bearsden Rd, Glasgow, G61 1QH, UK
| | - Sara Soto Martin
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
| | - Lorenzo Viora
- College of Medical, Veterinary & Life Sciences, University of Glasgow, 464 Bearsden Rd, Glasgow, G61 1QH, UK
| | - Nicholas N Jonsson
- College of Medical, Veterinary & Life Sciences, University of Glasgow, 464 Bearsden Rd, Glasgow, G61 1QH, UK.
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
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21
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Consortium VG, Nijman IJ, Rosen BD, Bardou P, Faraut T, Cumer T, Daly KG, Zheng Z, Cai Y, Asadollahpour H, Kul BÇ, Zhang WY, Guangxin E, Ayin A, Baird H, Bakhtin M, Bâlteanu VA, Barfield D, Berger B, Blichfeldt T, Boink G, Bugiwati SRA, Cai Z, Carolan S, Clark E, Cubric-Curik V, Dagong MIA, Dorji T, Drew L, Guo J, Hallsson J, Horvat S, Kantanen J, Kawaguchi F, Kazymbet P, Khayatzadeh N, Kim N, Shah MK, Liao Y, Martínez A, Masangkay JS, Masaoka M, Mazza R, McEwan J, Milanesi M, Faruque MO, Nomura Y, Ouchene-Khelifi NA, Pereira F, Sahana G, Salavati M, Sasazaki S, Da Silva A, Simčič M, Sölkner J, Sutherland A, Tigchelaar J, Zhang H, Consortium E, Ajmone-Marsan P, Bradley DG, Colli L, Drögemüller C, Jiang Y, Lei C, Mannen H, Pompanon F, Tosser-Klopp G, Lenstra JA. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions. Mol Ecol 2022; 31:4364-4380. [PMID: 35751552 DOI: 10.1111/mec.16579] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/12/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022]
Abstract
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and 7 wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during the migrations into northern Europe, eastern and southern Asia and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographic range.
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Affiliation(s)
| | - Isaäc J Nijman
- Utrecht Univ., Netherlands.,Univ. Medical Center Utrecht, Utrecht Univ, The Netherlands
| | | | - Philippe Bardou
- GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Thomas Faraut
- GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Tristan Cumer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | | | - Zhuqing Zheng
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | - Yudong Cai
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | | | | | | | | | | | - Hayley Baird
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | - Valentin A Bâlteanu
- Inst. of Life SciencesUniv. Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | | | - Beate Berger
- Univ. Natural Resources and Life Sciences Vienna (BOKU)
| | - Thor Blichfeldt
- Norwegian Association of Sheep and Goat Breeders, Aas, Norway
| | - Geert Boink
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands
| | | | | | | | | | | | | | - Tashi Dorji
- International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | | | | | | | - Simon Horvat
- Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | | | | | - Namshin Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | | | - Yuying Liao
- Guangxi Key Laboratory of Livestock Genetic Improvement, Guangxi, China
| | | | | | | | - Raffaele Mazza
- Laboratorio Genetica e Servizi, Agrotis srl, Cremona, Italy
| | - John McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | | | | | | | - Filipe Pereira
- IDENTIFICA Genetic Testing Maia & Centre for Functional Ecology, Porto, Portugal
| | | | | | | | | | - Mojca Simčič
- Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | | | | | | | | | | | - Paolo Ajmone-Marsan
- Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy.,UCSC PRONUTRIGEN Nutrigenomics Res. Centre, Piacenza, Italy
| | | | - Licia Colli
- Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy.,UCSC BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy
| | | | - Yu Jiang
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | - Chuzhao Lei
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | | | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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22
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Widmer S, Seefried FR, von Rohr P, Häfliger IM, Spengeler M, Drögemüller C. Associated regions for multiple birth in Brown Swiss and Original Braunvieh cattle on chromosomes 15 and 11. Anim Genet 2022; 53:557-569. [PMID: 35748198 PMCID: PMC9539900 DOI: 10.1111/age.13229] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/19/2022] [Accepted: 06/04/2022] [Indexed: 11/30/2022]
Abstract
Twin and multiple births have negative effects on the performance and health of cows and calves. To decipher the genetic architecture of this trait in the two Swiss Brown Swiss cattle populations, we performed various association analyses based on de-regressed breeding values. Genome-wide association analyses were executed using ~600 K imputed SNPs for the maternal multiple birth trait in ~3500 Original Braunvieh and ~7800 Brown Swiss animals. Significantly associated QTL were observed on different chromosomes for both breeds. We have identified on chromosome 11 a QTL that explains ~6% of the total genetic variance of the maternal multiple birth trait in Original Braunvieh. For the Brown Swiss breed, we have discovered a QTL on chromosome 15 that accounts for ~4% of the total genetic variance. For Original Braunvieh, subsequent haplotype analysis revealed a 90-kb window on chromosome 11 at 88 Mb, where a likely regulatory region is located close to the ID2 gene. In Brown Swiss, a 130-kb window at 75 Mb on chromosome 15 was identified. Analysis of whole-genome sequence data using linkage-disequilibrium estimation revealed possible causal variants for the identified QTL. A presumably regulatory variant in the non-coding 5' region of the ID2 gene was strongly associated with the haplotype for Original Braunvieh. In Brown Swiss, an intron variant in PRDM11, one 3' UTR variant in SYT13 and three intergenic variants 5' upstream of SYT13 were identified as candidate variants for the trait multiple birth maternal. In this study, we report for the first time QTL for the trait of multiple births in Original Braunvieh and Brown Swiss cattle. Moreover, our findings are another step towards a better understanding of the complex genetic architecture of this polygenic trait.
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Affiliation(s)
- Sarah Widmer
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | | | | | - Irene M Häfliger
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | | | - Cord Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
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23
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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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24
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Jacinto JGP, Häfliger IM, Caivano D, Drögemüller C. A germline de novo variant in NUMB associated with a double-outlet right ventricle in Chianina cattle. Anim Genet 2022; 53:713-714. [PMID: 35748177 PMCID: PMC9545765 DOI: 10.1111/age.13236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Joana G P Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (Bologna), Italy.,Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Irene M Häfliger
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Domenico Caivano
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - Cord Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
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25
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Jacinto JGP, Sbarra F, Quaglia A, Gentile A, Drögemüller C. Short communication: Prevalence of deleterious variants causing recessive disorders in Italian Chianina, Marchigiana and Romagnola cattle. Animal 2022; 16:100569. [PMID: 35717834 DOI: 10.1016/j.animal.2022.100569] [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: 03/18/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 11/01/2022] Open
Abstract
In the last two decades, the molecular cause of six monogenic autosomal recessive disorders has been identified in native Italian beef cattle: two different ATP2A1 variants for the pseudomyotonia congenita, the first in Chianina and Romagnola (PMT1) and the second in Romagnola (PMT2); a KDM2B variant for the paunch calf syndrome (PCS) in Marchigiana and Romagnola; a NID1 variant for the congenital cataract (CC) in Romagnola; a LAMB1 variant for the hemifacial microsomia (HFM) in Romagnola; an ABCA12 variant for the ichthyosis fetalis (IF) in Chianina and a FA2H variant for the ichthyosis congenita (IC) in Chianina. The aim of this study was to evaluate the potential impact of these disorders in the affected Italian populations. For this purpose, 3331 Chianina, 2812 Marchigiana and 1680 Romagnola bulls born in the last 40 years were considered. The allelic frequency (AF) of the variant for PMT1 was 1.0% in Romagnola, 4.6% in Marchigiana and 5.9% in Chianina. The AF of the variant for PMT2 was 3.3% in Romagnola and 0% in the other two breeds. The AF of the variant for PCS was 11.7% in Romagnola, 2.0% in Marchigiana and 0% in Chianina. The AF of the variants for CC, HFM, IF and IC resulted below 3%, being the variants detected only in the breed populations in which they were previously reported. Considering a selected male population in the single breed, Chianina showed carrier prevalence of 11.9% for PMT1, 7.7% for IC and 6.4% for IF. Romagnola showed carrier prevalence of 23.4% for PCS, 6.7% for PMT2, 4.1% for HFM, 3.2% for CC and 2.0% for PMT1. Marchigiana showed carrier prevalence of 9.1% for PMT1 and 4.0% for PCS. With respect to the Romagnola cattle, the concerning presence of a total of five defect alleles in the population hampers a general approach based on the prevention of carriers from artificial insemination. However, identification of carriers may allow conscious mating to prevent the risk of homozygous descendants as well as the spread of heterozygous offspring. Therefore, systematic genotyping for all seven known harmful alleles is recommended to prevent risk mating between carriers, in particular to avoid the occurrence of affected offspring.
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Affiliation(s)
- J G P Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse109a, 3012 Bern, Switzerland
| | - F Sbarra
- National Association of Italian Beef-Cattle Breeders, Strada del Vio Viscioloso, 21, 06132 Perugia, Italy
| | - A Quaglia
- National Association of Italian Beef-Cattle Breeders, Strada del Vio Viscioloso, 21, 06132 Perugia, Italy
| | - A Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse109a, 3012 Bern, Switzerland.
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26
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Jacinto JGP, Häfliger IM, Christen M, Paris JM, Seefried FR, Drögemüller C. Is a heterozygous missense variant in SGSH the cause of a syndromic form of congenital amastia in an Original Braunvieh calf? Anim Genet 2022; 53:530-531. [PMID: 35535008 DOI: 10.1111/age.13207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Joana G P Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (Bologna), Italy.,Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Irene M Häfliger
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Matthias Christen
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Julia M Paris
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | | | - Cord Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
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27
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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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28
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Hauser M, Signer-Hasler H, Küttel L, Capitan A, Guldbrandtsen B, Hinrichs D, Flury C, Seefried FR, Drögemüller C. Identification of two new recessive MC1R alleles in red-coloured Evolèner cattle and other breeds. Anim Genet 2022; 53:427-435. [PMID: 35451516 PMCID: PMC9373916 DOI: 10.1111/age.13206] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 04/09/2022] [Indexed: 11/27/2022]
Abstract
Sequence variations in the melanocortin-1 receptor (MC1R) gene are associated with melanism in different animal species. Six functionally relevant alleles have been described in cattle to date. In a hypothesis-free approach we performed a genome-wide allelic association study with black, red and wild-coloured cattle of three Alpine cattle breeds (Eringer, Evolèner and Valdostana), revealing a single significant association signal close to the MC1R gene. We searched for candidate causative variants by sequencing the entire coding sequence and identified two novel protein-changing variants. We propose designating the mutant alleles at MC1R:c.424C>T as ev1 and at MC1R:c.263G>A as ev2 . Both affect conserved amino acid residues in functionally important transmembrane domains (p.Arg142Cys and p.Ser88Asn). Both alleles segregate predominantly in the Swiss Evolèner breed. They occur in other European cattle breeds such as Abondance and Rotes Höhenvieh as well. We observed almost perfect association between the MC1R genotypes and the coat colour phenotype in a cohort of 513 black, red and wild-coloured cattle. Animals carrying two copies of MC1R loss-of-function alleles or that were compound heterozygous for e, ev1 , or ev2 have a red to dark red (chestnut-like red) coat colour. These findings expand the spectrum of causal MC1R variants causing recessive red in cattle.
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Affiliation(s)
- Miriam Hauser
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences (HAFL), Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Luzia Küttel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Aurélien Capitan
- ALLICE, Paris, France.,INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Bernt Guldbrandtsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Dirk Hinrichs
- Department of Animal Breeding, Faculty of Organic Agricultural Sciences, University of Kassel, Witzenhausen, Germany
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences (HAFL), Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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29
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Jacinto JGP, Häfliger IM, Baes CF, de Oliveira HR, Drögemüller C. A de novo start-lost variant in ANKRD28 in a Holstein calf with dwarfism. Anim Genet 2022; 53:470-471. [PMID: 35451514 PMCID: PMC9373846 DOI: 10.1111/age.13204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Joana G P Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (Bologna), Italy.,Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Irene M Häfliger
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Christine F Baes
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland.,Department of Animal Biosciences, Centre for the Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Hinayah R de Oliveira
- Department of Animal Biosciences, Centre for the Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Cord Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
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30
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Häfliger IM, Spengeler M, Seefried FR, Drögemüller C. Four novel candidate causal variants for deficient homozygous haplotypes in Holstein cattle. Sci Rep 2022; 12:5435. [PMID: 35361830 PMCID: PMC8971413 DOI: 10.1038/s41598-022-09403-6] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/07/2022] [Indexed: 12/23/2022] Open
Abstract
Mendelian variants can determine both insemination success and neonatal survival and thus influence fertility and rearing success of cattle. We present 24 deficient homozygous haplotype regions in the Holstein population of Switzerland and provide an overview of the previously identified haplotypes in the global Holstein breed. This study encompasses massive genotyping, whole-genome sequencing (WGS) and phenotype association analyses. We performed haplotype screenings on almost 53 thousand genotyped animals including 114 k SNP data with two different approaches. We revealed significant haplotype associations to several survival, birth and fertility traits. Within haplotype regions, we mined WGS data of hundreds of bovine genomes for candidate causal variants, which were subsequently evaluated by using a custom genotyping array in several thousand breeding animals. With this approach, we confirmed the known deleterious SMC2:p.Phe1135Ser missense variant associated with Holstein haplotype (HH) 3. For two previously reported deficient homozygous haplotypes that show negative associations to female fertility traits, we propose candidate causative loss-of-function variants: the HH13-related KIR2DS1:p.Gln159* nonsense variant and the HH21-related NOTCH3:p.Cys44del deletion. In addition, we propose the RIOX1:p.Ala133_Glu142del deletion as well as the PCDH15:p.Leu867Val missense variant to explain the unexpected low number of homozygous haplotype carriers for HH25 and HH35, respectively. In conclusion, we demonstrate that with mining massive SNP data in combination with WGS data, we can map several haplotype regions and unravel novel recessive protein-changing variants segregating at frequencies of 1 to 5%. Our findings both confirm previously identified loci and expand the spectrum of undesired alleles impairing reproduction success in Holstein cattle, the world's most important dairy breed.
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Affiliation(s)
- Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
| | | | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
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Häfliger IM, Wolf-Hofstetter S, Casola C, Hetzel U, Seefried FR, Drögemüller C. A de novo variant in the bovine ADAMTSL4 gene in an Original Braunvieh calf with congenital cataract. Anim Genet 2022; 53:416-421. [PMID: 35233794 PMCID: PMC9311076 DOI: 10.1111/age.13178] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/26/2022]
Abstract
Inherited forms of cataract are a heterogeneous group of eye disorders known in livestock species. Clinicopathological analysis of a single case of impaired vision in a newborn Original Braunvieh calf revealed nuclear cataract. Whole‐genome sequencing of the parent‐offspring trio revealed a de novo mutation of ADAMTSL4 in this case. The heterozygous p.Arg776His missense variant affects a conserved residue of the ADAMTSL4 gene that encodes a secreted glycoprotein expressed in the lens throughout embryonic development. In humans, ADAMTSL4 genetic variants cause recessively inherited forms of subluxation of the lens. Given that ADAMTSL4 is a functional candidate gene for inherited disorders of the lens, we suggest that heterozygosity for the identified missense variant may have caused the congenital cataract in the affected calf. Cattle populations should be monitored for unexplained cataract cases, with subsequent DNA sequencing a hypothesized pathogenic effect of heterozygous ADAMTSL4 variants could be confirmed.
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Affiliation(s)
- Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Christina Casola
- Ophthalmology Section, Equine Department, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Udo Hetzel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Graber JK, Signer-Hasler H, Burren A, Drögemüller C. Evaluation of truncating variants in the LCORL gene in relation to body size of goats from Switzerland. Anim Genet 2022; 53:237-239. [PMID: 35118693 PMCID: PMC9305788 DOI: 10.1111/age.13177] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 02/05/2023]
Affiliation(s)
| | - Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Alexander Burren
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Signer-Hasler H, Henkel J, Bangerter E, Bulut Z, Drögemüller C, Leeb T, Flury C. Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection. Genet Sel Evol 2022; 54:6. [PMID: 35073837 PMCID: PMC8785455 DOI: 10.1186/s12711-022-00695-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 05/26/2021] [Accepted: 01/06/2022] [Indexed: 11/16/2022] Open
Abstract
Background The domestication of goat (Capra hircus) started 11,000 years ago in the fertile crescent. Breed formation in the nineteenth century, establishment of herd books, and selection for specific traits resulted in 10 modern goat breeds in Switzerland. We analyzed whole-genome sequencing (WGS) data from 217 modern goats and nine wild Bezoar goats (Capra aegagrus). After quality control, 27,728,288 biallelic single nucleotide variants (SNVs) were used for the identification of runs of homozygosity (ROH) and the detection of ROH islands. Results Across the 226 caprine genomes from 11 populations, we detected 344 ROH islands that harbor 1220 annotated genes. We compared the ROH islands between the modern breeds and the Bezoar goats. As a proof of principle, we confirmed a signature of selection, which contains the ASIP gene that controls several breed-specific coat color patterns. In two other ROH islands, we identified two missense variants, STC1:p.Lys139Arg and TSHR:p.Ala239Thr, which might represent causative functional variants for domestication signatures. Conclusions We have shown that the information from ROH islands using WGS data is suitable for the analysis of signatures of selection and allowed the detection of protein coding variants that may have conferred beneficial phenotypes during goat domestication. We hypothesize that the TSHR:p.Ala239Thr variant may have played a role in changing the seasonality of reproduction in modern domesticated goats. The exact functional significance of the STC1:p.Lys139Arg variant remains unclear and requires further investigation. Nonetheless, STC1 might represent a new domestication gene affecting relevant traits such as body size and/or milk yield in goats. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00695-w.
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Affiliation(s)
- Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052, Zollikofen, Switzerland.
| | - Jan Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Erika Bangerter
- Swiss Goat Breeding Association SZZV, Schützenstrasse 10, 3052, Zollikofen, Switzerland
| | - Zafer Bulut
- Department of Biochemistry, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052, Zollikofen, Switzerland
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Häfliger IM, Koch CT, Michel A, Rüfenacht S, Meylan M, Welle MM, Drögemüller C. DSP missense variant in a Scottish Highland calf with congenital ichthyosis, alopecia, acantholysis of the tongue and corneal defects. BMC Vet Res 2022; 18:20. [PMID: 34996433 PMCID: PMC8739657 DOI: 10.1186/s12917-021-03113-3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ichthyosis describes a localized or generalized hereditary cornification disorder caused by an impaired terminal keratinocyte differentiation resulting in excessive stratum corneum with the formation of more or less adherent scales. Ichthyosis affects humans and animals. Two rare bovine forms are reported, the severe harlequin ichthyosis and the less severe congenital ichthyosis, both characterized by a severe orthokeratotic lamellar hyperkeratosis. RESULTS A 2-weeks-old purebred Scottish Highland calf was referred because of a syndrome resembling congenital ichthyosis. The clinical phenotype included diffuse alopecia and a markedly lichenified skin covered with large and excessive scales. Additionally, conjunctivitis and ulceration of the cornea were noted. Post-mortem examination revealed deep fissures in the diffusely thickened tongue and histopathological findings in the skin confirmed the clinical diagnosis. Whole-genome sequencing of the affected calf and comparison of the data with control genomes was performed. A search for private variants in known candidate genes for skin phenotypes including genes related with erosive and hyperkeratotic lesions revealed a single homozygous protein-changing variant, DSP: c.6893 C>A, or p.Ala2298Asp. The variant is predicted to change a highly conserved residue in the C-terminal plakin domain of the desmoplakin protein, which represents a main intracellular component of desmosomes, important intercellular adhesion molecules in various tissues including epidermis. Sanger sequencing confirmed the variant was homozygous in the affected calf and heterozygous in both parents. Further genotyping of 257 Scottish Highland animals from Switzerland revealed an estimated allele frequency of 1.2%. The mutant allele was absent in more than 4800 controls from various other cattle breeds. CONCLUSIONS This study represents the first report of combined lesions compatible with congenital ichthyosis, alopecia, acantholysis of the tongue and corneal defects associated with a DSP missense variant as the most likely underlying cause. To the best of our knowledge, this study is also the first report of a DSP-related syndromic form of congenital ichthyosis in domestic animals. The results of our study enable genetic testing to avoid the unintentional occurrence of further affected cattle. The findings were added to the Online Mendelian Inheritance in Animals (OMIA) database (OMIA 002243-9913).
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Affiliation(s)
- Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Caroline T Koch
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Astrid Michel
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Silvia Rüfenacht
- Division of Clinical Dermatology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Dermavet, Tierklinik Aarau-West, Oberentfelden, Switzerland
| | - Mireille Meylan
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Monika M Welle
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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Ben Braiek M, Moreno-Romieux C, Allain C, Bardou P, Bordes A, Debat F, Drögemüller C, Plisson-Petit F, Portes D, Sarry J, Tadi N, Woloszyn F, Fabre S. A Nonsense Variant in CCDC65 Gene Causes Respiratory Failure Associated with Increased Lamb Mortality in French Lacaune Dairy Sheep. Genes (Basel) 2021; 13:genes13010045. [PMID: 35052387 PMCID: PMC8774411 DOI: 10.3390/genes13010045] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/04/2022] Open
Abstract
We recently demonstrated that the Lacaune deficient homozygous haplotype 6 (LDHH6) potentially hosts a recessive perinatal lethal mutation in Lacaune dairy sheep mapped on OAR3. In the present study, we have analyzed the whole-genome sequences of two Lacaune ram heterozygous carriers of LDHH6. After variant calling and filtering against the variants of 86 non-carrier rams, we have identified a single nucleotide variant (SNV) in the two LDHH6 carriers whose variant allele induced a premature stop codon (p.Glu111*) in the Coiled-Coil Domain Containing 65 (CCDC65) gene. CCDC65 is involved in the assembly of the nexin-dynein regulatory complex for the formation of microtubules in ciliated cells. In order to identify the phenotype in homozygous sheep, we generated at-risk matings (n = 17) between rams and ewes heterozygous for the candidate variant in CCDC65. A total of 16 lambs were born alive with five genotyped as homozygous carriers. The homozygous lambs suffered from respiratory problems, and four of them died within the first month of life. At necropsy, we observed a broad hepatization of lung lobes possibly induced by infectious pneumonia. The management of this lethal recessive allele (frequency of 0.06) through reasoned mating in the Lacaune sheep selection schemes could reduce lamb mortality by 2%.
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Affiliation(s)
- Maxime Ben Braiek
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Carole Moreno-Romieux
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Charlotte Allain
- UE Domaine de La Fage, Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), 12250 Saint-Jean et Saint-Paul, France; (C.A.); (D.P.)
| | - Philippe Bardou
- Sigenae, Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), 31326 Castanet-Tolosan, France;
| | - Arnaud Bordes
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Frédéric Debat
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Florence Plisson-Petit
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - David Portes
- UE Domaine de La Fage, Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), 12250 Saint-Jean et Saint-Paul, France; (C.A.); (D.P.)
| | - Julien Sarry
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Némuel Tadi
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Florent Woloszyn
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Stéphane Fabre
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
- Correspondence:
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Häfliger IM, Seefried FR, Spengeler M, Drögemüller C. Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success. Genet Sel Evol 2021; 53:95. [PMID: 34915862 PMCID: PMC8675516 DOI: 10.1186/s12711-021-00686-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/11/2021] [Accepted: 11/26/2021] [Indexed: 11/30/2022] Open
Abstract
Background This study was carried out on the two Braunvieh populations reared in Switzerland, the dairy Brown Swiss (BS) and the dual-purpose Original Braunvieh (OB). We performed a genome-wide analysis of array data of trios (sire, dam, and offspring) from the routine genomic selection to identify candidate regions showing missing homozygosity and phenotypic associations with five fertility, ten birth, and nine growth-related traits. In addition, genome-wide single SNP regression studies based on 114,890 single nucleotide polymorphisms (SNPs) for each of the two populations were performed. Furthermore, whole-genome sequencing data of 430 cattle including 70 putative haplotype carriers were mined to identify potential candidate variants that were validated by genotyping the current population using a custom array. Results Using a trio-based approach, we identified 38 haplotype regions for BS and five for OB that segregated at low to moderate frequencies. For the BS population, we confirmed two known haplotypes, BH1 and BH2. Twenty-four variants that potentially explained the missing homozygosity and associated traits were detected, in addition to the previously reported TUBD1:p.His210Arg variant associated with BH2. For example, for BS we identified a stop-gain variant (p.Arg57*) in the MRPL55 gene in the haplotype region on chromosome 7. This region is associated with the ‘interval between first and last insemination’ trait in our data, and the MRPL55 gene is known to be associated with early pregnancy loss in mice. In addition, we discuss candidate missense variants in the CPT1C, MARS2, and ACSL5 genes for haplotypes mapped in BS. In OB, we highlight a haplotype region on chromosome 19, which is potentially caused by a frameshift variant (p.Lys828fs) in the LIG3 gene, which is reported to be associated with early embryonic lethality in mice. Furthermore, we propose another potential causal missense variant in the TUBGCP5 gene for a haplotype mapped in OB. Conclusions We describe, for the first time, several haplotype regions that segregate at low to moderate frequencies and provide evidence of causality by trait associations in the two populations of Swiss Braunvieh. We propose a list of six protein-changing variants as potentially causing missing homozygosity. These variants need to be functionally validated and incorporated in the breeding program. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00686-3.
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Affiliation(s)
- Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
| | | | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
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Häfliger IM, Seefried FR, Drögemüller C. Reverse Genetic Screen for Deleterious Recessive Variants in the Local Simmental Cattle Population of Switzerland. Animals (Basel) 2021; 11:3535. [PMID: 34944310 PMCID: PMC8698008 DOI: 10.3390/ani11123535] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/05/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
We herein report the result of a large-scale reverse genetic screen in the Swiss Simmental population, a local dual-purpose cattle breed. We aimed to detect possible recessively inherited variants affecting protein-coding genes, as such deleterious variants can impair fertility and rearing success significantly. We used 115,000 phased SNP data of almost 10 thousand cattle with pedigree data. This revealed evidence for 11 genomic regions of 1.17 Mb on average, with haplotypes (SH1 to SH11) showing a significant depletion in homozygosity and an allele frequency between 3.2 and 10.6%. For the proposed haplotypes, it was unfortunately not possible to evaluate associations with fertility traits as no corresponding data were available. For each haplotype region, possible candidate genes were listed based on their known function in development and disease. Subsequent mining of single-nucleotide variants and short indels in the genomes of 23 sequenced haplotype carriers allowed us to identify three perfectly linked candidate causative protein-changing variants: a SH5-related DIS3:p.Ile678fs loss-of-function variant, a SH8-related CYP2B6:p.Ile313Asn missense variant, and a SH9-related NUBPL:p.Ser143Tyr missense variant. None of these variants occurred in homozygous state in any of more than 5200 sequenced cattle of various breeds. Selection against these alleles in order to reduce reproductive failure and animal loss is recommended.
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Affiliation(s)
- Irene M. Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
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Jacinto JGP, Häfliger IM, Bernardini M, Mandara MT, Bianchi E, Bolcato M, Romagnoli N, Gentile A, Drögemüller C. A homozygous missense variant in laminin subunit beta 1 as candidate causal mutation of hemifacial microsomia in Romagnola cattle. J Vet Intern Med 2021; 36:292-299. [PMID: 34796979 PMCID: PMC8783352 DOI: 10.1111/jvim.16316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/11/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 11/29/2022] Open
Abstract
Hemifacial microsomia (HFM) was diagnosed in a 9‐day‐old Romagnola calf. The condition was characterized by microtia of the left ear, anotia of the right ear, asymmetry of the face, and deafness. Magnetic resonance imaging revealed agenesis of the right pinna and both tympanic bullae, asymmetry of the temporal bones and temporomandibular joints, and right pontine meningocele. Brainstem auditory evoked responses confirmed the impaired auditory capacity. At gross post mortem examination, there was agenesis and hypoplasia of the right and the left external ear, respectively. No histological abnormalities were detected in the inner ears. A trio whole‐genome sequencing approach was carried out and identified a private homozygous missense variant in LAMB1 affecting a conserved residue (p.Arg668Cys). Genotyping of 221 Romagnola bulls revealed a carrier prevalence <2%. This represents a report of a LAMB1‐related autosomal recessive inherited disorder in domestic animals and adds LAMB1 to the candidate genes for HFM.
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Affiliation(s)
- Joana G P Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano, Italy.,Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Marco Bernardini
- Anicura Portoni Rossi Veterinary Hospital, Zola Predosa, Bologna, Italy.,Department of Animal Medicine, Productions and Health, University of Padua, Padua, Italy
| | - Maria Teresa Mandara
- Department of Veterinary Medicine, Neuropathology Laboratory, University of Perugia, Perugia, Italy
| | - Ezio Bianchi
- Department of Veterinary Medical Sciences, University of Parma, Parma, Italy
| | - Marilena Bolcato
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano, Italy
| | - Noemi Romagnoli
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano, Italy
| | - Arcangelo Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano, Italy
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Jacinto JGP, Häfliger IM, Veiga IMB, Letko A, Gentile A, Drögemüller C. A frameshift insertion in FA2H causes a recessively inherited form of ichthyosis congenita in Chianina cattle. Mol Genet Genomics 2021; 296:1313-1322. [PMID: 34599683 PMCID: PMC8550120 DOI: 10.1007/s00438-021-01824-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/23/2021] [Indexed: 01/14/2023]
Abstract
The aim of this study was to characterize the phenotype and to identify the genetic etiology of a syndromic form of ichthyosis congenita (IC) observed in Italian Chianina cattle and to estimate the prevalence of the deleterious allele in the population. Sporadic occurrence of different forms of ichthyosis including IC have been previously reported in cattle. However, so far, no causative genetic variant has been found for bovine IC. Nine affected cattle presenting congenital xerosis, hyperkeratosis and scaling of the skin as well as urolithiasis and cystitis associated with retarded growth were examined. Skin histopathology revealed a severe, diffuse orthokeratotic hyperkeratosis with mild to moderate epidermal hyperplasia. The pedigree records indicated a monogenic recessive trait. Homozygosity mapping and whole-genome sequencing allowed the identification of a homozygous frameshift 1 bp insertion in the FA2H gene (c.9dupC; p.Ala4ArgfsTer142) located in a 1.92 Mb shared identical-by-descent region on chromosome 18 present in all cases, while the parents were heterozygous as expected for obligate carriers. These findings enable the selection against this sub-lethal allele showing an estimated frequency of ~ 7.5% in Chianina top sires. A sporadic incidence of mild clinical signs in the skin of heterozygous carriers was observed. So far, pathogenic variants affecting the encoded fatty acid 2-hydroxylase catalyzing the synthesis of 2-hydroxysphingolipids have been associated with myelin disorders. In conclusion, this study represents the first report of an FA2H-related autosomal recessive inherited skin disorder in a mammalian species and adds FA2H to the list of candidate genes for ichthyosis in humans and animals. Furthermore, this study provides a DNA-based diagnostic test that enables selection against the identified pathogenic variant in the Chianina cattle population. However, functional studies are needed to better understand the expression of FA2H in IC-affected Chianina cattle.
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Affiliation(s)
- Joana G. P. Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, 40064 Bologna, Italy
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Irene M. Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Inês M. B. Veiga
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Arcangelo Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, 40064 Bologna, Italy
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
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40
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Henkel J, Dubacher A, Bangerter E, Herren U, Ammann P, Drögemüller C, Flury C, Leeb T. Introgression of ASIP and TYRP1 Alleles Explains Coat Color Variation in Valais Goats. J Hered 2021; 112:452-457. [PMID: 34050662 DOI: 10.1093/jhered/esab024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/18/2020] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
The Valais Blackneck goat is a Swiss goat breed with a characteristic coat color phenotype. Before the revision of the breed standard in 1938, 4 different color varieties of Valais goats were known. Besides Blackneck animals resembling the modern breed standard, the brown and white Copperneck goat, the white Capra Sempione, and the greyish Grüenochte comprised the historic Valais goats. The brown pigmentation of Copperneck goats had previously been traced back to an introgression of a mutant TYRP1 allele from Toggenburg goats. In the present study, we identified additional introgression events of distinct ASIP alleles causing the remaining 2 rare coat color patterns within the Valais Blackneck goat breed. We identified the introgression of the AWt allele from Appenzell or Saanen goats in white Capra Sempione goats. Similarly, introgression of the Apc allele from Peacock goats resulted in the greyish Grüenochte phenotype. These results demonstrate past hybridization events between breeds that are separated today. A perfect genotype-phenotype association in 393 Valais goats supported the causality of the genotyped variants for the different coat color phenotypes. Our study gives insights into the introgression of functionally relevant copy number variant (CNV) alleles controlling pigmentation between goat breeds with strikingly different coat color patterns.
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Affiliation(s)
- Jan Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,DermFocus, University of Bern, 3001 Bern, Switzerland
| | - Alexandra Dubacher
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Erika Bangerter
- Swiss Goat Breeding Association, 3052 Zollikofen, Switzerland
| | - Ursula Herren
- Swiss Goat Breeding Association, 3052 Zollikofen, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,DermFocus, University of Bern, 3001 Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052 Zollikofen, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,DermFocus, University of Bern, 3001 Bern, Switzerland
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41
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Allais-Bonnet A, Hintermann A, Deloche MC, Cornette R, Bardou P, Naval-Sanchez M, Pinton A, Haruda A, Grohs C, Zakany J, Bigi D, Medugorac I, Putelat O, Greyvenstein O, Hadfield T, Jemaa SB, Bunevski G, Menzi F, Hirter N, Paris JM, Hedges J, Palhiere I, Rupp R, Lenstra JA, Gidney L, Lesur J, Schafberg R, Stache M, Wandhammer MD, Arbogast RM, Guintard C, Blin A, Boukadiri A, Rivière J, Esquerré D, Donnadieu C, Danchin-Burge C, Reich CM, Riley DG, Marle-Koster EV, Cockett N, Hayes BJ, Drögemüller C, Kijas J, Pailhoux E, Tosser-Klopp G, Duboule D, Capitan A. Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae. Mol Biol Evol 2021; 38:2260-2272. [PMID: 33528505 PMCID: PMC8136503 DOI: 10.1093/molbev/msab021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In the course of evolution, pecorans (i.e., higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as “headgear,” which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae.
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Affiliation(s)
- Aurélie Allais-Bonnet
- ALLICE, Paris, France.,Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Aurélie Hintermann
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Marie-Christine Deloche
- ALLICE, Paris, France.,Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Raphaël Cornette
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France.,INRAE, Sigenae, Castanet-Tolosan, France
| | | | - Alain Pinton
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Ashleigh Haruda
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Cécile Grohs
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Jozsef Zakany
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Daniele Bigi
- Dipartimento di Scienza e Tecnologie Agro-Alimentari, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Olivier Putelat
- Archéologie Alsace, Sélestat, France.,UMR 7044, ARCHIMEDE, MISHA, Strasbourg, France
| | - Ockert Greyvenstein
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - Tracy Hadfield
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Slim Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, Ariana, Tunisia
| | - Gjoko Bunevski
- Livestock Department, Faculty of Agricultural Sciences and Food Institute of Animal Biotechnology, University Ss. Cyril and Methodius, Skopje, North Macedonia
| | - Fiona Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nathalie Hirter
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Julia M Paris
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - John Hedges
- Manx Loaghtan Sheep Breeders' Group, Bassingbourn, Cambridgeshire, United Kingdom
| | - Isabelle Palhiere
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Louisa Gidney
- Rent a Peasant, Tow Law, Bishop Auckland, Durham County, United Kingdom
| | - Joséphine Lesur
- Unité Archéozoologie, Archéobotanique, Sociétés Pratiques et Environnements (AASPE), CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Renate Schafberg
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Michael Stache
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | | | | | - Claude Guintard
- Unité d'Anatomie Comparée, Ecole Nationale Vétérinaire de l'Agroalimentaire et de l'Alimentation, Nantes Atlantique-ONIRIS, Nantes, France.,Groupe d'Études Remodelage Osseux et bioMatériaux (GEROM), Université d'Angers, Unité INSERM 922, LHEA/IRIS-IBS, CHU d'Angers, Angers, France
| | - Amandine Blin
- Muséum National d'Histoire Naturelle, CNRS, UMS 2700 2AD, Paris, France
| | - Abdelhak Boukadiri
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Julie Rivière
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,INRAE, Micalis Institute, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Diane Esquerré
- INRAE, US, 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | | | - Coralie M Reich
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - David G Riley
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | | | - Noelle Cockett
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Benjamin J Hayes
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Animal Science, University of Queensland, St. Lucia, QLD, Australia
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - James Kijas
- CSIRO Agriculture & Food, St. Lucia, QLD, Australia
| | - Eric Pailhoux
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | | | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Swiss Cancer Research Institute, EPFL, Lausanne, Switzerland.,Collège de France, Paris, France
| | - Aurélien Capitan
- ALLICE, Paris, France.,Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
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42
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Bögeholz A, Falker-Gieske C, Guélat M, Gurtner C, Hunziker S, Oevermann A, Thaller G, Drögemüller C, Tetens J. GWAS Hits for Bilateral Convergent Strabismus with Exophthalmos in Holstein Cattle Using Imputed Sequence Level Genotypes. Genes (Basel) 2021; 12:genes12071039. [PMID: 34356055 PMCID: PMC8303712 DOI: 10.3390/genes12071039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/22/2022] Open
Abstract
Bilateral convergent strabismus with exophthalmos (BCSE) is a malformation of the eyes and is recognized as a mild but progressive disorder that affects cattle in the first two years of life. This most likely inherited disorder is rarely described in cattle resembling autosomal dominantly inherited forms of human progressive external ophthalmoplegia (PEO). In German Braunvieh cattle, two linked genome regions were found that could be responsible for the development and/or progression of BCSE. The goal of this study was to phenotypically characterize BCSE in Holstein cattle from Germany and Switzerland as well as to identify associated genome regions by GWAS. The clinicopathological phenotype of 52 BCSE-affected Holstein cattle was in accordance with the phenotype described in German Braunvieh cattle, but in addition, signs of degeneration and cellular infiltration in the eye muscles were found. By using imputed sequence level genotype data, three genome-wide significant GWAS hits were revealed on different chromosomes that were not detected by initial GWAS based on high density SNP array data highlighting the usefulness of this approach for mapping studies. The associated genome regions include the ABCC4 gene as well as markers adjacent to the NCOR2 and DNAJC3 genes all illustrating possible functional candidate genes. Our results challenge a monogenic mode of inheritance and indicate a more complex inheritance of BCSE in Holstein cattle. Furthermore, in comparison to previous results from German Braunvieh cattle, it illustrates an obvious genetic heterogeneity causing BSCE in cattle. Subsequent whole genome sequencing (WGS)-based analyses might elucidate pathogenic variants in the future.
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Affiliation(s)
- Anke Bögeholz
- Department of Animal Sciences, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany; (A.B.); (C.F.-G.)
| | - Clemens Falker-Gieske
- Department of Animal Sciences, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany; (A.B.); (C.F.-G.)
| | - Monika Guélat
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstr. 109a, 3012 Bern, Switzerland;
| | - Corinne Gurtner
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstr. 124, 3012 Bern, Switzerland;
| | - Sibylle Hunziker
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstr. 109a, 3012 Bern, Switzerland; (S.H.); (C.D.)
| | - Anna Oevermann
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bremgartenstr. 109a, 3012 Bern, Switzerland;
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Hermann-Rodewald-Str. 6, 24118 Kiel, Germany;
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstr. 109a, 3012 Bern, Switzerland; (S.H.); (C.D.)
| | - Jens Tetens
- Department of Animal Sciences, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany; (A.B.); (C.F.-G.)
- Center for Integrated Breeding Research, Georg-August-University Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
- Correspondence:
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43
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Widmer S, Seefried FR, von Rohr P, Häfliger IM, Spengeler M, Drögemüller C. A major QTL at the LHCGR/FSHR locus for multiple birth in Holstein cattle. Genet Sel Evol 2021; 53:57. [PMID: 34217202 PMCID: PMC8255007 DOI: 10.1186/s12711-021-00650-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 02/02/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Twin and multiple births are rare in cattle and have a negative impact on the performance and health of cows and calves. Therefore, selection against multiple birth would be desirable in dairy cattle breeds such as Holstein. We applied different methods to decipher the genetic architecture of this trait using de-regressed breeding values for maternal multiple birth of ~ 2500 Holstein individuals to perform genome-wide association analyses using ~ 600 K imputed single nucleotide polymorphisms (SNPs). RESULTS In the population studied, we found no significant genetic trend over time of the estimated breeding values for multiple birth, which indicates that this trait has not been selected for in the past. In addition to several suggestive non-significant quantitative trait loci (QTL) on different chromosomes, we identified a major QTL on chromosome 11 for maternal multiple birth that explains ~ 16% of the total genetic variance. Using a haplotype-based approach, this QTL was fine-mapped to a 70-kb window on chromosome 11 between 31.00 and 31.07 Mb that harbors two functional candidate genes (LHCGR and FSHR). Analysis of whole-genome sequence data by linkage-disequilibrium estimation revealed a regulatory variant in the 5'-region of LHCGR as a possible candidate causal variant for the identified major QTL. Furthermore, the identified haplotype showed significant effects on stillbirth and days to first service. CONCLUSIONS QTL detection and subsequent identification of causal variants in livestock species remain challenging in spite of the availability of large-scale genotype and phenotype data. Here, we report for the first time a major QTL for multiple birth in Holstein cattle and provide evidence for a linked variant in the non-coding region of a functional candidate gene. This discovery, which is a first step towards the understanding of the genetic architecture of this polygenic trait, opens the path for future selection against this undesirable trait, and thus contributes to increased animal health and welfare.
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Affiliation(s)
- Sarah Widmer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | | | | | - Irene M. Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
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44
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Bertani V, Prioni S, Di Lecce R, Gazza F, Ragionieri L, Merialdi G, Bonilauri P, Jagannathan V, Grassi S, Cabitta L, Paoli A, Morrone A, Sonnino S, Drögemüller C, Cantoni AM. A pathogenic HEXA missense variant in wild boars with Tay-Sachs disease. Mol Genet Metab 2021; 133:297-306. [PMID: 34119419 DOI: 10.1016/j.ymgme.2021.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 12/27/2022]
Abstract
Gangliosidoses are inherited lysosomal storage disorders caused by reduced or absent activity of either a lysosomal enzyme involved in ganglioside catabolism, or an activator protein required for the proper activity of a ganglioside hydrolase, which results in the intra-lysosomal accumulation of undegraded metabolites. We hereby describe morphological, ultrastructural, biochemical and genetic features of GM2 gangliosidosis in three captive bred wild boar littermates. The piglets were kept in a partially-free range farm and presented progressive neurological signs, starting at 6 months of age. Animals were euthanized at approximately one year of age due to their poor conditions. Neuropathogens were excluded as a possible cause of the signs. Gross examination showed a reduction of cerebral and cerebellar consistency. Central (CNS) and peripheral (PNS) nervous system neurons were enlarged and foamy, with severe and diffuse cytoplasmic vacuolization. Transmission electron microscopy (TEM) of CNS neurons demonstrated numerous lysosomes, filled by parallel or concentric layers of membranous electron-dense material, defined as membranous cytoplasmic bodies (MCB). Biochemical composition of gangliosides analysis from CNS revealed accumulation of GM2 ganglioside; furthermore, Hex A enzyme activity was less than 1% compared to control animals. These data confirmed the diagnosis of GM2 gangliosidosis. Genetic analysis identified, at a homozygous level, the presence of a missense nucleotide variant c.1495C > T (p Arg499Cys) in the hexosaminidase subunit alpha gene (HEXA), located within the GH20 hexosaminidase superfamily domain of the encoded protein. This specific HEXA variant is known to be pathogenic and associated with Tay-Sachs disease in humans, but has never been identified in other animal species. This is the first report of a HEXA gene associated Tay-Sachs disease in wild boars and provides a comprehensive description of a novel spontaneous animal model for this lysosomal storage disease.
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Affiliation(s)
- Valeria Bertani
- Department of Veterinary Science, University of Parma, Via Taglio, 8, 43100 Parma, Italy.
| | - Simona Prioni
- Department of Medical Biotechnology and Translational Medicine, University of Milano, Via Fratelli Cervi 93, 20129 Segrate, Italy
| | - Rosanna Di Lecce
- Department of Veterinary Science, University of Parma, Via Taglio, 8, 43100 Parma, Italy
| | - Ferdinando Gazza
- Department of Veterinary Science, University of Parma, Via Taglio, 8, 43100 Parma, Italy
| | - Luisa Ragionieri
- Department of Veterinary Science, University of Parma, Via Taglio, 8, 43100 Parma, Italy
| | - Giuseppe Merialdi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via Pietro Fiorini, 5, 40127, Bologna, Italy
| | - Paolo Bonilauri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via Pietro Fiorini, 5, 40127, Bologna, Italy
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Sara Grassi
- Department of Medical Biotechnology and Translational Medicine, University of Milano, Via Fratelli Cervi 93, 20129 Segrate, Italy
| | - Livia Cabitta
- Department of Medical Biotechnology and Translational Medicine, University of Milano, Via Fratelli Cervi 93, 20129 Segrate, Italy
| | - Antonella Paoli
- Molecular and Cell Biology Laboratory, Paediatric Neurology Unit and Laboratories, Neuroscience Department, A. Meyer Children's Hospital, Florence, Italy
| | - Amelia Morrone
- Molecular and Cell Biology Laboratory, Paediatric Neurology Unit and Laboratories, Neuroscience Department, A. Meyer Children's Hospital, Florence, Italy; Department of Neurosciences, Psychology, Pharmacology and Child Health, University of Florence, Italy
| | - Sandro Sonnino
- Department of Medical Biotechnology and Translational Medicine, University of Milano, Via Fratelli Cervi 93, 20129 Segrate, Italy
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Anna Maria Cantoni
- Department of Veterinary Science, University of Parma, Via Taglio, 8, 43100 Parma, Italy
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45
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Jacinto JGP, Häfliger IM, Gentile A, Drögemüller C. A Heterozygous Missense Variant in MAP2K2 in a Stillborn Romagnola Calf with Skeletal-Cardio-Enteric Dysplasia. Animals (Basel) 2021; 11:ani11071931. [PMID: 34209498 PMCID: PMC8300254 DOI: 10.3390/ani11071931] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Skeletal dysplasias encompass a clinical-, pathological- and genetically heterogeneous group of disorders characterized by abnormal cartilage and/or bone formation, growth, and remodeling. They may belong to the so-called RASopathies, congenital conditions caused by heterozygous variants in genes that encode components of the Ras/mitogen-activated protein kinase (MAPK) cell signaling pathway. Herein, an affected calf of the Italian Romagnola breed was reported showing a skeletal-cardio-enteric dysplasia. We identified a most likely disease-causing mutation in the MAP2K2 gene by whole-genome sequencing (WGS). The MAP2K2 gene is known to be related with dominant inherited cardio-facio-cutaneous syndrome in humans, but it was so far unknown to cause a similar disease in domestic animals. We assume that the identified missense variant that was predicted to impair the function of the protein, occurred either within the germline of the dam or post-zygotically in the embryo. Rare lethal diseases such as the skeletal-cardio-enteric dysplasia in livestock are usually not characterized to the molecular level, mainly because of the lack of funds and diagnostic opportunities. Precise WGS-based diagnostics enables the understanding of rare diseases and supports the value of monitoring cattle breeding populations for fatal genetic defects. Abstract RASopathies are a group of developmental disorders caused by dominant mutations in genes that encode components of the Ras/mitogen-activated protein kinase (MAPK) cell signaling pathway. The goal of this study was to characterize the pathological phenotype of a Romagnola stillborn calf with skeletal-cardio-enteric dysplasia and to identify a genetic cause by whole-genome sequencing (WGS). The calf showed reduced fetal growth, a short-spine, a long and narrow face, cardiac defects and heterotopy of the spiral colon. Genetic analysis revealed a private heterozygous missense variant in MAP2K2:p.Arg179Trp, located in the protein kinase domain in the calf, and not found in more than 4500 control genomes including its sire. The identified variant affecting a conserved residue was predicted to be deleterious and most likely occurred de novo. This represents the first example of a dominant acting, and most likely pathogenic, variant in MAP2K2 in domestic animals, thereby providing the first MAP2K2-related large animal model, especially in respect to the enteric malformation. In addition, this study demonstrates the utility of WGS-based precise diagnostics for understanding sporadic congenital syndromic anomalies in cattle and the general utility of continuous surveillance for rare hereditary defects in cattle.
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Affiliation(s)
- Joana G. P. Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, 40064 Bologna, Italy; (J.G.P.J.); (A.G.)
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Irene M. Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Arcangelo Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, 40064 Bologna, Italy; (J.G.P.J.); (A.G.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
- Correspondence:
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46
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Letko A, Bützberger C, Hirter N, Paris JM, Abril C, Drögemüller C. Genetic evaluation of small ruminant lentivirus susceptibility in Valais blacknose sheep. Anim Genet 2021; 52:781-782. [PMID: 34166534 PMCID: PMC8518827 DOI: 10.1111/age.13108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - Charis Bützberger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - Nathalie Hirter
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - Julia M Paris
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - Carlos Abril
- Institute of Virology and Immunology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, Bern, 3001, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
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de Preux M, Gurtner C, Klebic I, Waschk MA, Drögemüller C, Brünisholz HP. Skeletal metastasis from a squamous cell carcinoma of the nictitating membrane in a Haflinger horse. EQUINE VET EDUC 2021. [DOI: 10.1111/eve.13180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. de Preux
- Swiss Institute for Equine Medicine Vetsuisse Faculty University of Bern, and Agroscope Bern Switzerland
| | - C. Gurtner
- Institute of Animal Pathology Vetsuisse Faculty University of Bern BernSwitzerland
| | - I. Klebic
- Institute of Animal Pathology Vetsuisse Faculty University of Bern BernSwitzerland
| | - M. A. Waschk
- Division of Clinical Radiology Vetsuisse Faculty University of Bern BernSwitzerland
| | - C. Drögemüller
- Institute of Genetics Vetsuisse Faculty University of Bern BernSwitzerland
| | - H. P. Brünisholz
- Swiss Institute for Equine Medicine Vetsuisse Faculty University of Bern, and Agroscope Bern Switzerland
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Butty AM, Chud TCS, Cardoso DF, Lopes LSF, Miglior F, Schenkel FS, Cánovas A, Häfliger IM, Drögemüller C, Stothard P, Malchiodi F, Baes CF. Genome-wide association study between copy number variants and hoof health traits in Holstein dairy cattle. J Dairy Sci 2021; 104:8050-8061. [PMID: 33896633 DOI: 10.3168/jds.2020-19879] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 11/07/2020] [Accepted: 01/31/2021] [Indexed: 01/06/2023]
Abstract
Genome-wide association studies based on SNP have been completed for multiple traits in dairy cattle; however, copy number variants (CNV) could add genomic information that has yet to be harnessed. The objectives of this study were to identify CNV in genotyped Holstein animals and assess their association with hoof health traits using deregressed estimated breeding values as pseudophenotypes. A total of 23,256 CNV comprising 1,645 genomic regions were identified in 5,845 animals. Fourteen genomic regions harboring structural variations, including 9 deletions and 5 duplications, were associated with at least 1 of the studied hoof health traits. This group of traits included digital dermatitis, interdigital dermatitis, heel horn erosion, sole ulcer, white line lesion, sole hemorrhage, and interdigital hyperplasia; no regions were associated with toe ulcer. Twenty candidate genes overlapped with the regions associated with these traits including SCART1, NRXN2, KIF26A, GPHN, and OR7A17. In this study, an effect on infectious hoof lesions could be attributed to the PRAME (Preferentially Expressed Antigen in Melanoma) gene. Almost all genes detected in association with noninfectious hoof lesions could be linked to known metabolic disorders. The knowledge obtained considering information of associated CNV to the traits of interest in this study could improve the accuracy of estimated breeding values. This may further increase the genetic gain for these traits in the Canadian Holstein population, thus reducing the involuntary animal losses due to lameness.
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Affiliation(s)
- Adrien M Butty
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Tatiane C S Chud
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Diercles F Cardoso
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Lucas S F Lopes
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Filippo Miglior
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Flavio S Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Angela Cánovas
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Irene M Häfliger
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern 3012, Switzerland
| | - Cord Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern 3012, Switzerland
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton T6G 2R3, Canada
| | - Francesca Malchiodi
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada; The Semex Alliance, Guelph, Ontario N1H 6J2, Canada
| | - Christine F Baes
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern 3012, Switzerland.
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Gallina L, Koch MC, Gentile A, Treglia I, Bombardi C, Mandrioli L, Bolcato M, Scagliarini A, Drögemüller C, Seuberlich T, Ciulli S. Bovine viral diarrhoea virus 1b infection associated with congenital tremor and hypomyelination in Holstein calves. Vet Microbiol 2021; 256:109047. [PMID: 33866081 DOI: 10.1016/j.vetmic.2021.109047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 11/20/2020] [Accepted: 03/19/2021] [Indexed: 02/02/2023]
Abstract
Hypomyelination is a rare consequence of in utero bovine viral diarrhoea virus (BVDV) infection. We describe a BVDV outbreak in a naïve Holstein dairy herd in northern Italy, with an unusually high prevalence of calves with neurological signs, generalised tremors and ataxia. Histological analysis showed that hypomyelination was the predominant lesion and that the most typical BVDV neuropathological findings (e.g. cerebellar hypoplasia) were absent. Virological and molecular analyses showed that non-cytopathic BVDV genotype 1b was associated with the calves' neurological signs and excluded other viruses responsible for congenital infection or neurological disorders. Whole-genome sequencing of BVDVs from the brain of a calf with neurological signs and the whole blood of a persistently infected herd-mate with no such sign showed >99.7 % sequence identity. Analysis of the quasispecies distribution revealed the greatest variation rates in regions coding for the structural proteins E1 and E2. Variation was slightly greater in the brain- than in the blood-derived sequence and occurred at different sites, suggesting the occurrence of distinct evolutionary processes in the two persistently infected calves. Molecular characterisation of BVDV genomes from five other calves with neurological signs from the same farm confirmed that the E1 and E2 regions were the most variable. Several factors, including genetic variability and host factors, appear to have contributed to the observed unique BVDV disease phenotype, characterised by hypomyelination and neurological signs.
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Affiliation(s)
- Laura Gallina
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Michel C Koch
- Division of Neurological Sciences, NeuroCenter, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland
| | - Arcangelo Gentile
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Ida Treglia
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Cristiano Bombardi
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Luciana Mandrioli
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Marilena Bolcato
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Alessandra Scagliarini
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Cord Drögemüller
- Institute of Genetics, University of Bern, Bremgartenstrasse 109, 3012, Bern, Switzerland
| | - Torsten Seuberlich
- Division of Neurological Sciences, NeuroCenter, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland
| | - Sara Ciulli
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy.
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Eager KLM, Cauchi M, Willet CE, Häfliger IM, Drögemüller C, O'Rourke BA, Tammen I. The previously reported LRP4 c.4940C>T variant is not associated with syndactyly in cattle. Anim Genet 2021; 52:380-381. [PMID: 33751600 DOI: 10.1111/age.13061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Katie L M Eager
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, 2568, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, 2570, Australia
| | - Monique Cauchi
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, 2570, Australia
| | - Cali E Willet
- Sydney Informatics Hub, Core Research Facilities, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Berne, Bremgartenstrasse 109a, Berne, 3001, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Berne, Bremgartenstrasse 109a, Berne, 3001, Switzerland
| | - Brendon A O'Rourke
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, 2568, Australia
| | - Imke Tammen
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, 2570, Australia
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