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Riggio S, Tolone M, Sottile G, Tumino S, Portolano B, Sutera AM, Sardina MT, Cesarani A, Mastrangelo S. A high-density genome-wide approach reveals novel genetic markers linked to small ruminant lentivirus susceptibility in sheep. Front Genet 2024; 15:1376883. [PMID: 38911298 PMCID: PMC11191640 DOI: 10.3389/fgene.2024.1376883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/10/2024] [Indexed: 06/25/2024] Open
Abstract
Visna/Maedi virus (VMV) is lentiviral disease of sheep responsible for severe production losses. Multiple genomic regions associated with infection were reported indicating genetic complexity. In this study, a combined genome-wide approach using a high-density SNP array has been performed, comparing VMV-infected (n = 78) and non-infected (n = 66) individuals of the Valle del Belice breed. The serological tests showed a seroprevalence of 26%. The comparison among results from different approaches (GWAS, Fisher's exact test and the FST analysis) revealed two association signals: on OAR03 close to the GRIN2B gene and on OAR05 close to the TMEM232 gene. To the best of our knowledge, there has been no previous association between these genes and lentiviral infection in any species. The GRIN2B gene plays a role in pain response, synaptic transmission, and receptor clustering, while TMEM232 is involved in the development of immune-related disorders. The results highlighted new aspects of the genetic complexity related to the resistance/susceptibility to VMV in sheep, confirming that studies on different breeds can lead to different results. The ideal approach for validation of the markers identified in our study is to use samples from a population independent from the discovery population with the same phenotype used in the discovery stage.
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Affiliation(s)
- Silvia Riggio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Marco Tolone
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, University of Messina, Messina, Italy
| | - Gianluca Sottile
- Dipartimento Scienze Economiche, Aziendali e Statistiche, University of Palermo, Palermo, Italy
| | - Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Anna Maria Sutera
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, University of Messina, Messina, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
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Impact of Four Ovine TMEM154 Haplotypes on Ewes during Multiyear Lentivirus Exposure. Int J Mol Sci 2022; 23:ijms232314966. [PMID: 36499292 PMCID: PMC9741230 DOI: 10.3390/ijms232314966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/08/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Polypeptide variation encoded by the ovine transmembrane protein 154 gene (TMEM154) is associated with susceptibility to ovine lentivirus, the causative agent of Ovine Progressive Pneumonia (OPP) and Visna/Maedi. Our aim was to compare the four most prevalent TMEM154 haplotypes on the incidence of infection and ewe productivity during natural multiyear virus exposure. Prospective cohort studies were designed to test gene action and estimate effects of TMEM154 haplotypes encoding distinctive variant residues: K35 (“1”), I70 (“2”), ancestral (“3”), and A4del/M44 (“4”). Exposure consisted of co-mingling infected ewes at a rate greater than 30% with serological status evaluated every four months. For ewes with one or two copies of the highly susceptible haplotypes “2” and ”3”, the infection prevalence steadily increased to nearly 100% at 55 months. Haplotypes “2” and “3” were equally susceptible and dominant to haplotype “1”. A difference was not detected (p < 0.53) in the magnitude of effect with haplotype combinations of “1” and ”4”. The ewe infection prevalence with “1,1”; “1,4”; and “4,4” was 10% to 40% at 55 months. The latter suggested that two copies of the K35 amino acid substitution (“1”) were as effective as a homozygous TMEM154 “knockout” with the frame-shift deletion mutation (“4”) in reducing infection susceptibility. When considering ewe reproductive performance, a difference was not detected when comparing haplotypes “2”, and “3” to each other, or “1” and “4” to each other. Our study indicated that ewes with two copies of the severely truncated versions of TMEM154 (“4,4”) had normal lamb productivity. Without complete understanding of the natural function of TMEM154 our recommendations to producers interested in using TMEM154 selection to reduce their flock’s genetic predisposition to OPP are encouraged to increase the frequency of TMEM154 haplotype K35 (“1”) since it encodes a full-length protein with minimal difference to the ancestral polypeptide.
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Moretti R, Sartore S, Colitti B, Profiti M, Chessa S, Rosati S, Sacchi P. Susceptibility of different TMEM154 genotypes in three Italian sheep breeds infected by different SRLV genotypes. Vet Res 2022; 53:60. [PMID: 35906709 PMCID: PMC9335956 DOI: 10.1186/s13567-022-01079-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/11/2022] [Indexed: 11/25/2022] Open
Abstract
Small ruminant lentiviruses (SRLV) belong to the Retroviridae family and can cause various diseases. One of the most impacting diseases is visna-maedi, a complex disease characterized by long latencies and chronic progressive inflammatory events affecting the nervous system, lungs, mammary gland, and articular joints. A single nucleotide polymorphism (rs408593969, c.103G>A, missense mutation E35K) in the ovine transmembrane protein gene 154 (TMEM154) was identified as protective against small ruminant lentivirus infection in different herds worldwide. However, there is evidence in the scientific literature of a breed-specificity of this protective effect and, furthermore, there are still limited studies regarding the association between the animal genotype and the infecting virus genotype. Thus, the aim of this study was to further investigate the association between the animal genotype for the suggested protective mutation and the infecting virus genotype, in three different sheep breeds reared in northern Italy. The results obtained only partially confirmed the data available in the literature, as the protective effect was confirmed only for SRLV genotype A clusters, while other genotypes (namely B and E) infected AA and GA animals. Further studies with an experimental infection of specific virus genotypes in hosts with specific genotypes are required to confirm the larger number of cases the results obtained in this study.
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Affiliation(s)
- Riccardo Moretti
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095, Grugliasco, TO, Italy
| | - Stefano Sartore
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095, Grugliasco, TO, Italy
| | - Barbara Colitti
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095, Grugliasco, TO, Italy
| | - Margherita Profiti
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095, Grugliasco, TO, Italy
| | - Stefania Chessa
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095, Grugliasco, TO, Italy.
| | - Sergio Rosati
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095, Grugliasco, TO, Italy
| | - Paola Sacchi
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095, Grugliasco, TO, Italy
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Alternative Molecular Tools for the Fight against Infectious Diseases of Small Ruminants: Native Sicilian Sheep Breeds and Maedi-Visna Genetic Susceptibility. Animals (Basel) 2022; 12:ani12131630. [PMID: 35804527 PMCID: PMC9264923 DOI: 10.3390/ani12131630] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Local breeds represent a precious reservoir of genetic diversity, crucial to adapting to environmental and climate changes and reacting to evolving diseases. In Sicily, four native dairy breeds, namely Valle del Belìce, Comisana, Barbaresca, and Pinzirita, have adapted to low-input farming systems and semiarid environments, having an essential role in producing high-quality milk and typical dairy products. Maedi-visna (MV) is one of the most important chronic diseases affecting the sheep sector worldwide, causing production losses. Different target genes play an important role in immunity and in genetic resilience to MV, such as TMEM154, TLR9, MYD88, and CCR5. A major host genetic component to sheep MV susceptibility was identified in the ovine TMEM154 gene. Animals with either of TMEM154 haplotypes that encode glutamate at position 35 (E35) of the protein are at higher risk of MV infection than those homozygous with lysine at position 35 (K35). In the tested Sicilian breeds, animals carrying the allele E35 showed a greater risk of being serologically positive. Comisana, Barbaresca, and Pinzirita breeds showed a good frequency of the protective allele K35, whilst a high frequency of risk allele was found in the Valle del Belìce breed, related to the selection strategies addressed to obtain a productive dairy sheep. Our results highlight the importance of the preservation of autochthonous breeds as a reservoir of natural resistance against infectious disease. Abstract Maedi-visna (MV) is a disease caused by small ruminant lentiviruses. It is included in the list of notifiable terrestrial animal diseases due to economic losses and animal welfare harm in the sheep sector. To date, control programs remain the onliest approach to avoiding infection. The allelic variant p.Glu35Lys (E35K) of the TMEM154 gene has been strongly associated with host vulnerability to MV illness. The present study aimed to investigate the association of TMEM154 E35K allele frequencies with MV susceptibility in native Sicilian sheep breeds. More than 400 animals from 14 local sheep were serologically tested and genotyped for the TMEM154 E35K polymorphism. The local breeds displayed different values of MV seroprevalence, with the lowest antibody prevalence in Barbaresca and Pinzirita breeds. TMEM154 protective allele (K35) was less frequent than the risk allele (E35) in Valle del Belìce breed, whereas the other three breeds showed a more balanced alleles distribution. A positive association between seroprevalence and genotype was found in the entire sample set. The risk of infection resulted in more than 3-fold times as high in sheep with EK and EE genotype compared to the KK genotype. Our data could be helpful in establishing selection breeding programs aimed at reducing MV infection in Sicilian sheep farming and encouraging the breeding of native breeds.
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Genetic Characterization of Small Ruminant Lentiviruses (SRLVs) Circulating in Naturally Infected Sheep in Central Italy. Viruses 2022; 14:v14040686. [PMID: 35458416 PMCID: PMC9032261 DOI: 10.3390/v14040686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 12/21/2022] Open
Abstract
Small ruminant lentiviruses (SRLVs) represent a very heterogeneous group of ss-RNA viruses that infect sheep and goats worldwide. They cause important, deleterious effects on animal production and limit the animal trade. SRLVs show a high genetic variability due to high mutation rate and frequent recombination events. Indeed, five genotypes (A–E) and several subtypes have been detected. The aim of this work was to genetically characterize SRLVs circulating in central Italy. On this basis, a phylogenetic study on the gag-pol genetic region of 133 sheep, collected from 19 naturally infected flocks, was conducted. In addition, to evaluate the frequency of mutation and the selective pressure on this region, a WebLogo 3 analysis was performed, and the dN/dS ratio was computed. The results showed that 26 samples out of 133 were clustered in genotype A and 106 samples belonged to genotype B, as follows: A9 (n = 8), A11 (n = 10), A24 (n = 7), B1 (n = 2), B2 (n = 59), and B3 (n = 45). No recombination events were found. Mutations were localized mainly in the VR-2 region, and the dN/dS ratio of 0.028 indicated the existence of purifying selection. Since the genetic diversity of SRLVs could make serological identification difficult, it is important to perform molecular characterization to ensure a more reliable diagnosis, to maintain flock health status, and for the application of local and national control programs.
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Jones S, McKay H, Eden L, Bollard N, Dunham S, Davies P, Tarlinton R. Clearance of Maedi-visna infection in a longitudinal study of naturally infected rams is associated with homozygosity for the TMEM154 resistance allele. J Med Microbiol 2022; 71. [PMID: 35144720 PMCID: PMC8941955 DOI: 10.1099/jmm.0.001506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Maedi-visna (MV) is a lentiviral disease of sheep responsible for severe production losses in affected flocks. There are no vaccination or treatment options with control reliant on test and cull strategies. The most common diagnostic methods used at present are combination ELISAs for Gag and Env proteins with virus variability making PCR diagnostics still largely an experimental tool. To assess variability in viral loads and diagnostic tests results, serology, DNA and RNA viral loads were measured in the blood of 12 naturally infected rams repeatedly blood sampled over 16 months. Six animals tested negative in one or more tests at one or more time points and would have been missed on screening programmes reliant on one test method or a single time point. In addition the one animal homozygous for the ‘K’ allele of the TMEM154 E35K SNP maintained very low viral loads in all assays and apparently cleared infection to below detectable limits at the final time point it was sampled. This adds crucial data to the strong epidemiological evidence that this locus represents a genuine resistance marker for MV infection and is a strong candidate for selective breeding of sheep for resistance to disease.
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Affiliation(s)
- Scott Jones
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.,Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Heather McKay
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.,Three Valleys Veterinary, 107 Kesh Road, Irvinestown, Enniskillen BT94FX, UK
| | - Laura Eden
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.,Bishopton Veterinary Group, Mill Farm, Studley Road, Ripon, North Yorkshire, HG4 2QR, UK
| | - Nicola Bollard
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Stephen Dunham
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Peers Davies
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.,Department of Livestock and One Health, University of Liverpool, Liverpool, CH64 7TE, UK
| | - Rachael Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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Ovine Toll-like Receptor 9 ( TLR9) Gene Variation and Its Association with Flystrike Susceptibility. Animals (Basel) 2021; 11:ani11123549. [PMID: 34944323 PMCID: PMC8697942 DOI: 10.3390/ani11123549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/09/2021] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Flystrike is a major ectoparasitic disease of sheep and it creates both an economic impact and welfare issue for the sheep industry. Several factors control the responses of sheep to flystrike, and among these, immune response is regarded as an important factor. Toll-like receptors (TLRs) plays a crucial role in the innate immune system by recognizing pathogen-associated molecular patterns derived from various microbes. Of these receptors, TLR9 recognises unmethylated cytosine-phosphate-guanine (CpG) motifs that are known to be prevalent in bacterial genomes and are also reported in Dipteran insects, including Lucilia cuprina, one of the main species associated with flystrike in sheep. In this study, we used a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique to investigate TLR9 variation in sheep with and without flystrike, and found that variation in a gene region containing the coding sequence of the putative CpG-DNA binding domain was associated with the likelihood of flystrike occurrence. This suggests that variation in ovine TLR9 may affect a sheep’s response to flystrike. Abstract Toll-like receptors (TLRs) are a family of proteins that play a role in innate immune responses by recognising pathogen-associated molecular patterns derived from various microbes. Of these receptors, TLR9 recognises bacterial and viral DNA containing unmethylated cytosine-phosphate-guanine (CpG) motifs, and variation in TLR9 has been associated with resistance to various infectious diseases. Flystrike is a problem affecting the sheep industry globally and the immune response of the sheep has been suggested as one factor that influences the response to the disease. In this study, variation in ovine TLR9 from 178 sheep with flystrike and 134 sheep without flystrike was investigated using a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) approach. These sheep were collected from both commercial and stud farms throughout New Zealand and they were of 13 different breeds, cross-breds and composites. Four alleles of TLR9 were detected, including three previously identified alleles (*01, *02 and *03) and a new allele (*04). In total six single nucleotide polymorphisms (SNPs) were found. Of the three common alleles in the sheep studied, the presence of *03 was found to be associated with a reduced likelihood of flystrike being present (OR = 0.499, p = 0.024). This suggests that variation in ovine TLR9 may affect a sheep’s response to flystrike, and thus the gene may have value as a genetic marker for improving resistance to the disease.
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Murphy TW, Chitko-McKown CG, Heaton MP, Freking BA. Effect of TMEM154 E35K variant (haplotypes 1 and 3) on the incidence of ovine lentivirus infection and ewe productivity during lifetime exposure. J Anim Sci 2021; 99:6407712. [PMID: 34673957 DOI: 10.1093/jas/skab304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/18/2021] [Indexed: 01/18/2023] Open
Abstract
Ovine progressive pneumonia virus (OPPV) is a small ruminant lentivirus that is widespread throughout U.S. sheep flocks. Infections with OPPV are lifelong and effects are multi-systemic with significant implications for animal well-being and productivity. A protein isoform with lysine at position 35 (K35, haplotype "1") encoded by the ovine transmembrane protein 154 (TMEM154) gene has been associated with reduced susceptibility to infection when two copies are present (i.e., diplotype "1,1"). Conversely, the ancestral protein isoform with glutamate at position 35 (E35, haplotype "3") is associated with high susceptibility to infection when at least one copy is present. The beneficial effect of TMEM154 K35 alleles on ewe productivity has not been previously measured in controlled challenge experiments and was a major objective of this study. Ewes with TMEM154 diplotypes "1,1"; "1,3"; and "3,3" (n = 31, 47, and 30, respectively) were born and reared by OPPV-infected dams and managed under continual natural exposure to OPPV. Ewes were tested for serological status at 4-mo intervals for up to 5.5 yr. The incidence of infection in ewes with diplotype "1,1" was 6.5% to 9.7% and significantly lower (P < 0.001) than ewes with diplotype "1,3" (60.5 to 97.3%) or "3,3" (64.0 to 91.4%). Furthermore, the incidence among ewes with diplotype "1,1" did not increase from 10 to 67 mo of age (P > 0.99), whereas the incidence among diplotype "1,3" and "3,3" ewes increased steadily until reaching an asymptote at approximately 52 mo of age. Total number and weight of lamb weaned per ewe exposed through 5.5 yr from ewes with diplotype "1,1" far exceeded (P ≤ 0.05) those with diplotypes "1,3" and "3,3" by, on average, 2.1 lambs and 40 kg, respectively. The present study confirmed that TMEM154 diplotype "1,1" animals have reduced incidence of OPPV infection and, correspondingly, improved productivity. In flocks with a high frequency of TMEM154 haplotype "3," selection for haplotype "1" appears to be a cost-effective approach to mitigate the impact of this economically important disease.
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Affiliation(s)
- Thomas W Murphy
- USDA, ARS, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Carol G Chitko-McKown
- USDA, ARS, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Mike P Heaton
- USDA, ARS, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Brad A Freking
- USDA, ARS, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
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