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Wright EA, Reddock MB, Roberts EK, Legesse YW, Perry G, Bradley RD. Genetic characterization of the prion protein gene in camels ( Camelus) with comments on the evolutionary history of prion disease in Cetartiodactyla. PeerJ 2024; 12:e17552. [PMID: 38948234 PMCID: PMC11214740 DOI: 10.7717/peerj.17552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/20/2024] [Indexed: 07/02/2024] Open
Abstract
Transmissible spongiform encephalopathies (TSEs) are a fatal neurogenerative disease that include Creutzfeldt-Jakob disease in humans, scrapie in sheep and goats, bovine spongiform encephalopathy (BSE), and several others as well as the recently described camel prion disease (CPD). CPD originally was documented in 3.1% of camels examined during an antemortem slaughterhouse inspection in the Ouargla region of Algeria. Of three individuals confirmed for CPD, two were sequenced for the exon 3 of the prion protein gene (PRNP) and were identical to sequences previously reported for Camelus dromedarius. Given that other TSEs, such as BSE, are known to be capable of cross-species transmission and that there is household consumption of meat and milk from Camelus, regulations to ensure camel and human health should be a One Health priority in exporting countries. Although the interspecies transmissibility of CPD currently is unknown, genotypic characterization of Camelus PRNP may be used for predictability of predisposition and potential susceptibility to CPD. Herein, eight breeds of dromedary camels from a previous genetic (mitochondrial DNA and microsatellites) and morphological study were genotyped for PRNP and compared to genotypes from CPD-positive Algerian camels. Sequence data from PRNP indicated that Ethiopian camels possessed 100% sequence identity to CPD-positive camels from Algeria. In addition, the camel PRNP genotype is unique compared to other members of the Orders Cetartiodactyla and Perissodactyla and provides an in-depth phylogenetic analysis of families within Cetartiodactyla and Perissodactyla that was used to infer the evolutionary history of the PRNP gene.
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Affiliation(s)
- Emily A. Wright
- Natural Science Research Laboratory, Museum of Texas Tech University, Lubbock, TX, United States of America
| | - Madison B. Reddock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States of America
| | - Emma K. Roberts
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States of America
- Climate Center, Texas Tech University, Lubbock, TX, United States of America
| | - Yoseph W. Legesse
- School of Animal and Range Sciences, Haramaya University, Dire Dawa, Ethiopia
- Institute of Pastoral and Agropastoral Development Studies, Jigjiga University, Jigjiga, Ethiopia
| | - Gad Perry
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX, United States of America
| | - Robert D. Bradley
- Natural Science Research Laboratory, Museum of Texas Tech University, Lubbock, TX, United States of America
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States of America
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Evaluation of Resistance and Susceptibility to Prion Diseases in Pelibuey Sheep from Mexico. MACEDONIAN VETERINARY REVIEW 2022. [DOI: 10.2478/macvetrev-2022-0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Abstract
Transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative diseases with a chronic and fatal course, which are caused by a misfolded form of the cellular prion protein that is encoded by the host. The purpose of this work was to evaluate the resistance and genetic susceptibility to prion diseases in Pelibuey sheep from Mexico. The sequences of 99 Pelibuey sheep from the central and southwestern regions of Mexico were analyzed to determine the polymorphisms related to resistance and genetic susceptibility to scrapie, the Hardy-Weinberg equilibrium test and the D-Tajima test was used to identify the effect of evolutionary forces on the PRNP gene. Twelve non-synonymous polymorphisms Q101R, M112T, A116P, G127A, A136V, M137T, L141F, H143R, R154H, Q171R, Q171H, N176K were detected, in addition two synonymous substitutions 231R (agg/cgg) and 237L (ctc/ctg) were found. As a result of the sequence analysis, the ARR allele was not under the Hardy-Weinberg equilibrium, indicating that there is an evolutionary force at work, and the D-Tajima suggest the existence of purifying genetic selection. In conclusion, Pelibuey sheep exhibit genotypes for the PRNP gene that make them resistant to developing classic scrapie; at least 98% of the population is a carrier of an allele related to scrapie resistance; while for atypical scrapie there is a very high probability that an outbreak occurred in the herds, since the ARQ allele in combination with the L substitution at codon 141 confers susceptibility to carrier sheep.
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Perrin-Stowe TI, Ishida Y, Reed DM, Terrill EE, Ryder OA, Novakofski JE, Mateus-Pinilla NE, Pukazhenthi BS, Roca AL. Extrapolating the susceptibility of Eld’s deer (Rucervus eldii thamin) to chronic wasting disease from prion protein gene (PRNP) polymorphisms. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.1007100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chronic wasting disease (CWD) is a prion disease of North American cervids. The transmission of CWD to endangered cervid species is of concern for captive breeding programs. Trans-species transmission could occur via direct contact with infected wild deer, or via prion contaminated fomites. Variation in the prion protein gene, PRNP, is associated with differences in CWD susceptibility among cervids. We therefore sequenced PRNP in 36 endangered Eld’s deer (Rucervus eldii thamin), detecting five synonymous and two non-synonymous SNPs. Three haplotypes were inferred, suggesting that genetic management in captive breeding programs has been effective at maintaining PRNP diversity. The haplotypes encoded two PrP protein variants. The more common Eld’s deer PrP variant encodes methionine at codon 208 and glutamine at codon 226. Because this protein variant is identical to a common PrP variant in white-tailed deer and mule deer and is especially common in white-tailed deer positive for CWD, we recommend reducing the frequency of this variant in the breeding stock, while implementing strict management practices to avoid exposure to wild North American cervids. The frequency of the other PrP variant, which differs from variants present in these North American cervids, was low. It has the potential to reduce susceptibility to CWD and thus could be increased in frequency. While PRNP haplotype frequencies should be shifted, genetic diversity should be maintained. Ultimately protein diversity may be protective should CWD infect the species, and trans-species polymorphisms are suggestive of past balancing selection and a potential fitness advantage for PRNP diversity.
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Tewari D, Fasnacht M, Ritzman M, Livengood J, Bower J, Lehmkuhl A, Nichols T, Hamberg A, Brightbill K, Henderson D. Detection of chronic wasting disease in feces and recto-anal mucosal associated lymphoid tissues with RT-QuIC in a naturally infected farmed white-tailed deer herd. Front Vet Sci 2022; 9:959555. [PMID: 36176702 PMCID: PMC9513346 DOI: 10.3389/fvets.2022.959555] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/18/2022] [Indexed: 11/15/2022] Open
Abstract
Chronic wasting disease (CWD) is an infectious prion disease affecting the cervids, including white-tailed deer (WTD) (Odocoileus virginianus). CWD is typically diagnosed postmortem in farmed cervids by immunohistochemistry (IHC). Amplification-based detection methods are newer generation tests currently being evaluated to improve the detection of prion disease. In addition to improving sensitivity, antemortem detection by amplification assays is a focus for improving disease control and management. In this study, we evaluate the use of real-time quaking-induced conversion (RT-QuIC) to detect CWD in fecal and recto-anal mucosal-associated lymphoid tissue (RAMALT) samples from naturally infected farmed WTD herds at postmortem. We successfully detected the presence of CWD prions in WTD RAMALT with a specificity of 100% and a sensitivity of 85.7% (n = 71) and in feces with a specificity of 100% and a sensitivity of 60% (n = 69), utilizing RT-QuIC on samples collected postmortem. Seeding activity detected in RAMALT (15.3 ± 4.2%, n = 18) was much stronger than in feces (44.4 ± 4.2%, n = 15), as measured by cycle threshold (Ct) and rise in relative fluorescence in samples collected from the same WTD. Prion detection in the RAMALT (94.7%) and feces (70.5%) was highest when both obex and retropharyngeal lymph nodes (RPLNs) were positive for CWD via IHC. In the study group, we were also able to test prion protein gene variants and associated disease susceptibility. A majority of tested WTD were the CWD genotype (96 GG) and also harbored the highest percentage of positive animals (43.7%). The second highest population of WTD was the genotype 96 GS and had a CWD positivity rate of 37.5%. Each of these groups showed no difference in RAMALT or fecal detection of CWD.
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Affiliation(s)
- Deepanker Tewari
- Pennsylvania Veterinary Laboratory, Harrisburg, PA, United States
- *Correspondence: Deepanker Tewari
| | - Melinda Fasnacht
- Pennsylvania Veterinary Laboratory, Harrisburg, PA, United States
| | - Margaret Ritzman
- Pennsylvania Veterinary Laboratory, Harrisburg, PA, United States
| | - Julia Livengood
- Pennsylvania Veterinary Laboratory, Harrisburg, PA, United States
| | - Jessica Bower
- Pennsylvania Veterinary Laboratory, Harrisburg, PA, United States
| | - Aaron Lehmkuhl
- United States Department of Agriculture, APHIS, Veterinary Services, National Veterinary Services Laboratories, Ames, IA, United States
| | - Tracy Nichols
- Veterinary Services Cervid Health Program, United States Department of Agriculture, Animal and Plant Health Inspection Service, Fort Collins, CO, United States
| | - Alex Hamberg
- Bureau of Animal Health, Pennsylvania Department of Agriculture, Harrisburg, PA, United States
| | - Kevin Brightbill
- Bureau of Animal Health, Pennsylvania Department of Agriculture, Harrisburg, PA, United States
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Sezgin E, Teferedegn EY, Ün C, Yaman Y. Excessive replacement changes drive evolution of global sheep prion protein (PRNP) sequences. Heredity (Edinb) 2022; 128:377-385. [PMID: 35273383 PMCID: PMC9076837 DOI: 10.1038/s41437-022-00520-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
Sheep prion protein (PRNP) is the major host genetic factor responsible for susceptibility to scrapie. We aimed to understand the evolutionary history of sheep PRNP, and primarily focused on breeds from Turkey and Ethiopia, representing genome-wise ancient sheep populations. Population molecular genetic analyses are extended to European, South Asian, and East Asian populations, and for the first time to scrapie associated haplotypes. 1178 PRNP coding region nucleotide sequences were analyzed. High levels of nucleotide diversity driven by extensive low-frequency replacement changes are observed in all populations. Interspecific analyses were conducted using mouflon and domestic goat as outgroup species. Despite an abundance of silent and replacement changes, lack of silent or replacement fixations was observed. All scrapie-associated haplotype analyses from all populations also showed extensive low-frequency replacement changes. Neutrality tests did not indicate positive (directional), balancing or strong negative selection or population contraction for any of the haplotypes in any population. A simple negative selection history driven by prion disease susceptibility is not supported by the population and haplotype based analyses. Molecular function, biological process enrichment, and protein-protein interaction analyses suggested functioning of PRNP protein in multiple pathways, and possible other functional constraint selections. In conclusion, a complex selection history favoring excessive replacement changes together with weak purifying selection possibly driven by frequency-dependent selection is driving PRNP sequence evolution. Our results is not unique only to the Turkish and Ethiopian samples, but can be generalized to global sheep populations.
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Affiliation(s)
- Efe Sezgin
- Department of Food Engineering, Izmir Institute of Technology, Urla, Izmir, Turkey.
| | - Eden Yitna Teferedegn
- Department of Biology, Molecular Biology Division, Ege University, Izmir, Turkey
- Armauer Hansen research institute, Biotechnology and Bioinformatic Directorate, Addis Ababa, Ethiopia
| | - Cemal Ün
- Department of Biology, Molecular Biology Division, Ege University, Izmir, Turkey
| | - Yalçın Yaman
- Department of Breeding and Genetics, Bandırma Sheep Breeding Research Institute, Bandırma, Balıkesir, Turkey
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Evolution of Transmissible Spongiform Encephalopathies and the Prion Protein Gene (PRNP) in Mammals. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09557-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
Mammalian prion diseases are a group of neurodegenerative conditions caused by infection of the central nervous system with proteinaceous agents called prions, including sporadic, variant, and iatrogenic Creutzfeldt-Jakob disease; kuru; inherited prion disease; sheep scrapie; bovine spongiform encephalopathy; and chronic wasting disease. Prions are composed of misfolded and multimeric forms of the normal cellular prion protein (PrP). Prion diseases require host expression of the prion protein gene (PRNP) and a range of other cellular functions to support their propagation and toxicity. Inherited forms of prion disease are caused by mutation of PRNP, whereas acquired and sporadically occurring mammalian prion diseases are controlled by powerful genetic risk and modifying factors. Whereas some PrP amino acid variants cause the disease, others confer protection, dramatically altered incubation times, or changes in the clinical phenotype. Multiple mechanisms, including interference with homotypic protein interactions and the selection of the permissible prion strains in a host, play a role. Several non-PRNP factors have now been uncovered that provide insights into pathways of disease susceptibility or neurotoxicity.
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Affiliation(s)
- Simon Mead
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom;
| | - Sarah Lloyd
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom;
| | - John Collinge
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom;
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Wright AE, Fumagalli M, Cooney CR, Bloch NI, Vieira FG, Buechel SD, Kolm N, Mank JE. Male-biased gene expression resolves sexual conflict through the evolution of sex-specific genetic architecture. Evol Lett 2018; 2:52-61. [PMID: 30283664 PMCID: PMC6089503 DOI: 10.1002/evl3.39] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/04/2018] [Accepted: 01/09/2018] [Indexed: 12/20/2022] Open
Abstract
Many genes are subject to contradictory selection pressures in males and females, and balancing selection resulting from sexual conflict has the potential to substantially increase standing genetic diversity in populations and thereby act as an important force in adaptation. However, the underlying causes of sexual conflict, and the potential for resolution, remains hotly debated. Using transcriptome‐resequencing data from male and female guppies, we use a novel approach, combining patterns of genetic diversity and intersexual divergence in allele frequency, to distinguish the different scenarios that give rise to sexual conflict, and how this conflict may be resolved through regulatory evolution. We show that reproductive fitness is the main source of sexual conflict, and this is resolved via the evolution of male‐biased expression. Furthermore, resolution of sexual conflict produces significant differences in genetic architecture between males and females, which in turn lead to specific alleles influencing sex‐specific viability. Together, our findings suggest an important role for sexual conflict in shaping broad patterns of genome diversity, and show that regulatory evolution is a rapid and efficient route to the resolution of conflict.
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Affiliation(s)
- Alison E Wright
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus Imperial College London London United Kingdom
| | - Christopher R Cooney
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Natasha I Bloch
- Department of Genetics, Evolution and Environment University College London London United Kingdom
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | | | - Niclas Kolm
- Department of Zoology Stockholm University Stockholm Sweden
| | - Judith E Mank
- Department of Genetics, Evolution and Environment University College London London United Kingdom.,Department of Organismal Biology Uppsala University Uppsala Sweden
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10
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Stewart P, Campbell L, Skogtvedt S, Griffin KA, Arnemo JM, Tryland M, Girling S, Miller MW, Tranulis MA, Goldmann W. Genetic predictions of prion disease susceptibility in carnivore species based on variability of the prion gene coding region. PLoS One 2012; 7:e50623. [PMID: 23236380 PMCID: PMC3517517 DOI: 10.1371/journal.pone.0050623] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 10/23/2012] [Indexed: 11/19/2022] Open
Abstract
Mammalian species vary widely in their apparent susceptibility to prion diseases. For example, several felid species developed prion disease (feline spongiform encephalopathy or FSE) during the bovine spongiform encephalopathy (BSE) epidemic in the United Kingdom, whereas no canine BSE cases were detected. Whether either of these or other groups of carnivore species can contract other prion diseases (e.g. chronic wasting disease or CWD) remains an open question. Variation in the host-encoded prion protein (PrPC) largely explains observed disease susceptibility patterns within ruminant species, and may explain interspecies differences in susceptibility as well. We sequenced and compared the open reading frame of the PRNP gene encoding PrPC protein from 609 animal samples comprising 29 species from 22 genera of the Order Carnivora; amongst these samples were 15 FSE cases. Our analysis revealed that FSE cases did not encode an identifiable disease-associated PrP polymorphism. However, all canid PrPs contained aspartic acid or glutamic acid at codon 163 which we propose provides a genetic basis for observed susceptibility differences between canids and felids. Among other carnivores studied, wolverine (Gulo gulo) and pine marten (Martes martes) were the only non-canid species to also express PrP-Asp163, which may impact on their prion diseases susceptibility. Populations of black bear (Ursus americanus) and mountain lion (Puma concolor) from Colorado showed little genetic variation in the PrP protein and no variants likely to be highly resistant to prions in general, suggesting that strain differences between BSE and CWD prions also may contribute to the limited apparent host range of the latter.
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Affiliation(s)
- Paula Stewart
- Neurobiology Division, The Roslin Institute & R(D)SVS, University of Edinburgh, Roslin, United Kingdom
| | - Lauren Campbell
- Neurobiology Division, The Roslin Institute & R(D)SVS, University of Edinburgh, Roslin, United Kingdom
| | - Susan Skogtvedt
- Norwegian School of Veterinary Science, Dept. Basic Sciences & Aquatic Medicine, Oslo, Norway
| | - Karen A. Griffin
- Wildlife Research Center, Colorado Division of Parks and Wildlife, Fort Collins, Colorado, United States of America
| | - Jon M. Arnemo
- Department of Forestry & Wildlife Management, Faculty of Applied Ecology and Agricultural Sciences, Hedmark University College, Campus Evenstad, Elverum, Norway & Department of Wildlife, Fish and Environmental Studies, Faculty of Forest Sciences, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Morten Tryland
- Norwegian School of Veterinary Science, Section of Arctic Veterinary Medicine, Tromsø, Norway
- GenØk - Centre for Biosafety, Tromsø, Norway
| | - Simon Girling
- Royal Zoological Society of Scotland, Edinburgh Zoo, Edinburgh, United Kingdom
| | - Michael W. Miller
- Wildlife Research Center, Colorado Division of Parks and Wildlife, Fort Collins, Colorado, United States of America
| | - Michael A. Tranulis
- Norwegian School of Veterinary Science, Dept. Basic Sciences & Aquatic Medicine, Oslo, Norway
| | - Wilfred Goldmann
- Neurobiology Division, The Roslin Institute & R(D)SVS, University of Edinburgh, Roslin, United Kingdom
- * E-mail:
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Abstract
The UK national scrapie plan (NSP) for sheep is based on selection for the resistant ARR/ARR genotype and elimination of susceptible types of the ovine prion protein (PrP) gene. The aim of this study was to estimate the possible association of the PrP genotype and performance traits by using data from the CAMDA Welsh Mountain flock. Four alleles (ARH, ARQ, ARR and VRQ) and 10 genotypes covering all five NSP risk groups were present in the CAMDA flock. Overall, the most common allele was ARR (35.2%), and VRQ was the least common (5.4%). The commonest genotypes were ARR/ARQ (23.7%) and ARR/AHQ (23.1%). The most resistant genotype, ARR/ARR, and the most susceptible genotype, VRQ/VRQ, were found in 10.2% and 0.3%, respectively, of the population tested. The associations of PrP genotypes with weight and ultrasonically scanned traits were investigated in three analyses, the first using genotypes, the second using risk categories and the third using number of alleles. These associations were evaluated by univariate analysis of each trait using an animal model with maternal effects where appropriate, and PrP was included as a fixed effect. Selection for scrapie resistance will not adversely affect progress in the traits considered and is consistent with improvements in muscle depth.
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Goldmann W, Ryan K, Stewart P, Parnham D, Xicohtencatl R, Fernandez N, Saunders G, Windl O, González L, Bossers A, Foster J. Caprine prion gene polymorphisms are associated with decreased incidence of classical scrapie in goat herds in the United Kingdom. Vet Res 2011; 42:110. [PMID: 22040234 PMCID: PMC3224758 DOI: 10.1186/1297-9716-42-110] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 10/31/2011] [Indexed: 12/31/2022] Open
Abstract
The application of genetic breeding programmes to eradicate transmissible spongiform encephalopathies in goats is an important aim for reasons of animal welfare as well as human food safety and food security. Based on the positive impact of Prnp genetics on sheep scrapie in Europe in the past decade, we have established caprine Prnp gene variation in more than 1100 goats from the United Kingdom and studied the association of Prnp alleles with disease phenotypes in 150 scrapie-positive goats. This investigation confirms the association of the Met142 encoding Prnp allele with increased resistance to preclinical and clinical scrapie. It reveals a novel association of the Ser127 encoding allele with a reduced probability to develop clinical signs of scrapie in goats that are already positive for the accumulation of disease-specific prion protein in brain or periphery. A United Kingdom survey of Prnp genotypes in eight common breeds revealed eleven alleles in over thirty genotypes. The Met142 encoding allele had a high overall mean allele frequency of 22.6%, whereas the Ser127 encoding allele frequency was considerably lower with 6.4%. In contrast, a well known resistance associated allele encoding Lys222 was found to be rare (0.9%) in this survey. The analysis of Prnp genotypes in Mexican Criollas goats revealed nine alleles, including a novel Phe to Leu substitution in codon 201, confirming that high genetic variability of Prnp can be found in scrapie-free populations. Our study implies that it should be feasible to lower scrapie prevalence in goat herds in the United Kingdom by genetic selection.
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Affiliation(s)
- Wilfred Goldmann
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Kelly Ryan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Paula Stewart
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - David Parnham
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Rosa Xicohtencatl
- Facultad de Medicina Veterinaria y Zootecnia, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Nora Fernandez
- Facultad de Medicina Veterinaria y Zootecnia, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Ginny Saunders
- Animal Health and Veterinary Laboratories Agency, Weybridge, New Haw, Addlestone, Surrey, UK
| | - Otto Windl
- Animal Health and Veterinary Laboratories Agency, Weybridge, New Haw, Addlestone, Surrey, UK
| | - Lorenzo González
- Animal Health and Veterinary Laboratories Agency, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, UK
| | - Alex Bossers
- Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands
| | - James Foster
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
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Fediaevsky A, Calavas D, Gasqui P, Moazami-Goudarzi K, Laurent P, Arsac JN, Ducrot C, Moreno C. Quantitative estimation of genetic risk for atypical scrapie in French sheep and potential consequences of the current breeding programme for resistance to scrapie on the risk of atypical scrapie. Genet Sel Evol 2010; 42:14. [PMID: 20482755 PMCID: PMC2880962 DOI: 10.1186/1297-9686-42-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 05/18/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since 2002, active surveillance programmes have detected numerous atypical scrapie (AS) and classical scrapie cases (CS) in French sheep with almost all the PrP genotypes. The aim of this study was 1) to quantify the genetic risk of AS in French sheep and to compare it with the risk of CS, 2) to quantify the risk of AS associated with the increase of the ARR allele frequency as a result of the current genetic breeding programme against CS. METHODS We obtained genotypes at codons 136, 141, 154 and 171 of the PRNP gene for representative samples of 248 AS and 245 CS cases. We used a random sample of 3,317 scrapie negative animals genotyped at codons 136, 154 and 171 and we made inferences on the position 141 by multiple imputations, using external data. To estimate the risk associated with PrP genotypes, we fitted multivariate logistic regression models and we estimated the prevalence of AS for the different genotypes. Then, we used the risk of AS estimated for the ALRR-ALRR genotype to analyse the risk of detecting an AS case in a flock homogenous for this genotype. RESULTS Genotypes most at risk for AS were those including an AFRQ or ALHQ allele while genotypes including a VLRQ allele were less commonly associated with AS. Compared to ALRQ-ALRQ, the ALRR-ALRR genotype was significantly at risk for AS and was very significantly protective for CS. The prevalence of AS among ALRR-ALRR animals was 0.6 per thousand and was not different from the prevalence in the general population. CONCLUSION In conclusion, further selection of ALRR-ALRR animals will not result in an overall increase of AS prevalence in the French sheep population although this genotype is clearly susceptible to AS. However the probability of detecting AS cases in flocks participating in genetic breeding programme against CS should be considered.
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Evidence for maternal transmission of scrapie in naturally affected flocks. Prev Vet Med 2009; 93:121-8. [PMID: 19945758 DOI: 10.1016/j.prevetmed.2009.10.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 10/14/2009] [Accepted: 10/16/2009] [Indexed: 11/24/2022]
Abstract
It has been known for many years that the offspring of scrapie affected ewes are at increased risk of developing scrapie but whether this is simply the result of an increased genetic susceptibility or transmission of infection has always been unclear. To contribute to clarify this we analysed the data collected in a detailed study of scrapie occurrence in a number of naturally affected commercial sheep flocks in Great Britain (GB) to investigate the association between PrP genotype and parental scrapie status and the incidence of scrapie. Our analyses confirmed the strong association between PrP genotype and the incidence of scrapie found in previous studies and a low incidence of scrapie in animals carrying the ARR allele and a high risk in homozygous VRQ animals. However, we also demonstrate an increased incidence of scrapie in the offspring of scrapie affected ewes controlling for the confounding effect of PrP genotype, but no increased scrapie incidence in the offspring of scrapie affected sires. Our results suggest that some of the increased incidence of scrapie in the offspring of scrapie affected ewes is the result of transmission of infection from mother to offspring. Our results confirm that a breeding policy aimed at decreasing the genetic susceptibility of the population should decrease the incidence of scrapie and that removing the offspring of scrapie affected animals from affected flocks could contribute to the control of this disease.
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Tongue SC, Pfeiffer DU, Shearn PD, Wilesmith JW. PrP genotype: a flock-level risk factor for scrapie? Prev Vet Med 2009; 92:309-23. [PMID: 19783057 DOI: 10.1016/j.prevetmed.2009.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Revised: 08/07/2009] [Accepted: 08/16/2009] [Indexed: 11/26/2022]
Abstract
Previous epidemiological studies of risk factors for classical scrapie at flock level have identified a variety of management and purchase related variables, along with increased flock size and, in some cases, breed effects. Although known as a risk factor at the individual animal level, PrP genotype frequencies at flock level have not yet been studied. In an unmatched case-control study, three measures of flock-level prion protein (PrP) frequency estimates were investigated with respect to the scrapie status of the flock in 293 British sheep flocks (195 control flocks and 98 case flocks). Flocks with positive frequencies (more than 0 per cent) of two genotypes (VRQ/VRQ and AHQ/VRQ), large frequencies (more than 10 per cent) of the ARR/VRQ genotype, and large frequencies (more than 5.2 per cent) of the VRQ allele were at increased odds of being affected with clinical classical scrapie. When adjusted for flock size, breed and sampling strategy the genotype and allele effects remained, except that for flocks with positive frequencies of VRQ/VRQ. The known effect of increased risk with increased flock size was confirmed. A measure of the flock PrP genotype frequency profile should thus be included in studies of risk factors for scrapie. It could also be integrated into risk-based surveillance strategies for identification of "at-risk-of scrapie" flocks.
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Affiliation(s)
- Sue C Tongue
- Centre for Epidemiology and Risk Analysis, Veterinary Laboratories Agency - Weybridge, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK.
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Vaccari G, Scavia G, Sala M, Cosseddu G, Chiappini B, Conte M, Esposito E, Lorenzetti R, Perfetti G, Marconi P, Scholl F, Barbaro K, Bella A, Nonno R, Agrimi U. Protective effect of the AT137RQ and ARQK176 PrP allele against classical scrapie in Sarda breed sheep. Vet Res 2009; 40:19. [PMID: 19171116 PMCID: PMC2695041 DOI: 10.1051/vetres/2009002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Accepted: 01/22/2009] [Indexed: 12/03/2022] Open
Abstract
The susceptibility of sheep to scrapie is under the control of the host’s prion protein (PrP) gene and is also influenced by the strain of the agent. PrP polymorphisms at codons 136 (A/V), 154 (R/H) and 171 (Q/R/H) are the main determinants of susceptibility/resistance of sheep to classical scrapie. They are combined in four main variants of the wild-type ARQ allele: VRQ, AHQ, ARH and ARR. Breeding programmes have been undertaken on this basis in the European Union and the USA to increase the frequency of the resistant ARR allele in sheep populations. Herein, we report the results of a multi-flock study showing the protective effect of polymorphisms other than those at codons 136, 154 and 171 in Sarda breed sheep. All ARQ/ARQ affected sheep (n = 154) and 378 negative ARQ/ARQ controls from four scrapie outbreaks were submitted to sequencing of the PrP gene. The distribution of variations other than those at the standard three codons, between scrapie cases and negative controls, was statistically different in all flocks. In particular, the AT137RQ and ARQK176 alleles showed a clear protective effect. This is the first study demonstrating a protective influence of alleles other than ARR under field conditions. If further investigations in other sheep breeds and with other scrapie sources confirm these findings, the availability of various protective alleles in breeding programmes of sheep for scrapie resistance could be useful in breeds with a low frequency of the ARR allele and would allow maintaining a wider variability of the PrP gene.
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Complete genomic sequence of the goat prion protein gene (PRNP). Virus Genes 2008; 38:189-92. [DOI: 10.1007/s11262-008-0288-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2008] [Accepted: 09/10/2008] [Indexed: 11/26/2022]
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Hickford JGH, Zhou H, Fang Q, Byun SO, Gong H. Frequency of PRNP genotypes in common New Zealand sheep breeds. Vet Rec 2008; 163:453-4. [PMID: 18849578 DOI: 10.1136/vr.163.15.453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- J G H Hickford
- Gene-Marker Laboratory, Agriculture and Life Sciences Division, po Box 84, Lincoln University, Lincoln 7647, Canterbury, New Zealand
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Rongyan Z, Xianglong L, Lanhui L, Xiangyun L, Fujun F. Evolution and differentiation of the prion protein gene (PRNP) among species. ACTA ACUST UNITED AC 2008; 99:647-52. [PMID: 18799453 DOI: 10.1093/jhered/esn073] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A total of 937 prion protein gene (PRNP) sequences belonging to 83 species in 56 genera of 26 families were analyzed in order to investigate its evolution and differentiation among species. The length of PRNP coding sequence for all species analyzed varied from 567 to 825 bp, which was mainly because of insertion or deletion in the repeat region within and among the species. TGA and TAG are the main stop codons in the PRNP gene. Bos taurus had the smallest variation in terms of average number of nucleotide differences (0.811), nucleotide diversity (0.0011), and nonsynonymous nucleotide diversity (0.0002) among all the ruminants. The reconstructed phylogenetic tree of PRNP of families and species was basically consistent with the taxonomy of National Center for Biotechnology Information except for Felidae (Felis catus), which was initially clustered with Moschidae rather than Mustelidae or Canidae.
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Affiliation(s)
- Zhou Rongyan
- Department of Animal Science, College of Animal Science and Technology, Agricultural University of Hebei, Baoding 071001, China
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Sawalha RM, Brotherstone S, Conington J, Villanueva B. Lambs with scrapie susceptible genotypes have higher postnatal survival. PLoS One 2007; 2:e1236. [PMID: 18043743 PMCID: PMC2077931 DOI: 10.1371/journal.pone.0001236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 11/02/2007] [Indexed: 11/20/2022] Open
Abstract
Background Prion protein (PrP) alleles associated with scrapie susceptibility persist in many sheep populations even with high frequencies despite centuries of selection against them. This suggests that scrapie susceptibility alleles have a pleiotropic effect or are associated with fitness or other traits that have been subject to selection. Methodology/Principal Findings We genotyped all lambs in two scrapie-free Scottish Blackface sheep flocks for polymorphisms at codons 136, 154 and 171 of the PrP gene. We tested potential associations of the PrP genotype with lamb viability at birth and postnatal survival using a complementary log-log link function and a Weibull proportional hazard model, respectively. Here we show there is an association between PrP genotype, as defined by polymorphisms at codons 154 ad 171, and postnatal lamb survival in the absence of scrapie. Sheep carrying the wild-type ARQ allele have higher postnatal survival rates than sheep carrying the more scrapie-resistant alleles (ARR or AHQ). Conclusion The PrP genotypes associated with higher susceptibility to scrapie are associated with improved postnatal survival in the absence of the disease. This association helps to explain the existence, and in many instances the high frequency, of the ARQ allele in sheep populations.
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Affiliation(s)
- Rami M Sawalha
- Scottish Agricultural College, Edinburgh, United Kingdom.
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Obbard DJ, Linton YM, Jiggins FM, Yan G, Little TJ. Population genetics of Plasmodium resistance genes in Anopheles gambiae: no evidence for strong selection. Mol Ecol 2007; 16:3497-510. [PMID: 17688548 DOI: 10.1111/j.1365-294x.2007.03395.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Anopheles mosquitoes are the primary vectors for malaria in Africa, transmitting the disease to more than 100 million people annually. Recent functional studies have revealed mosquito genes that are crucial for Plasmodium development, but there is presently little understanding of which genes mediate vector competence in the wild, or evolve in response to parasite-mediated selection. Here, we use population genetic approaches to study the strength and mode of natural selection on a suite of mosquito immune system genes, CTL4, CTLMA2, LRIM1, and APL2 (LRRD7), which have been shown to affect Plasmodium development in functional studies. We sampled these genes from two African populations of An. gambiae s.s., along with several closely related species, and conclude that there is no evidence for either strong directional or balancing selection on these genes. We highlight a number of challenges that need to be met in order to apply population genetic tests for selection in Anopheles mosquitoes; in particular the dearth of suitable outgroup species and the potential difficulties that arise when working within a closely-related species complex.
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Affiliation(s)
- D J Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh, UK.
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Opinion of the Scientific Panel on biological hazards (BIOHAZ) on the Breeding programme for TSE resistance in sheep. EFSA J 2006. [DOI: 10.2903/j.efsa.2006.382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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