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Jhelum H, Papatsiros V, Papakonstantinou G, Krabben L, Kaufer B, Denner J. Screening for Viruses in Indigenous Greek Black Pigs. Microorganisms 2024; 12:315. [PMID: 38399719 PMCID: PMC10893322 DOI: 10.3390/microorganisms12020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/09/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
The successful advancement of xenotransplantation has led to the development of highly sensitive detection systems for the screening of potentially zoonotic viruses in donor pigs and preventing their transmission to the recipient. To validate these methods, genetically modified pigs generated for xenotransplantation, numerous minipigs and other pig breeds have been tested, thereby increasing our knowledge concerning the pig virome and the distribution of pig viruses. Of particular importance are the porcine cytomegalovirus, a porcine roseolovirus (PCMV/PRV) and the hepatitis E virus genotype 3 (HEV3). PCMV/PRV has been shown to reduce the survival time of pig transplants in non-human primates and was also transmitted in the first pig heart transplantation to a human patient. The main aim of this study was to determine the sensitivities of our methods to detect PCMV/PRV, HEV3, porcine lymphotropic herpesvirus-1 (PLHV-1), PLHV-2, PLHV-3, porcine circovirus 2 (PCV2), PCV3, PCV4 and porcine parvovirus 1 (PPV1) and to apply the methods to screen indigenous Greek black pigs. The high number of viruses found in these animals allowed for the evaluation of numerous detection methods. Since porcine endogenous retroviruses (PERVs) type A and B are integrated in the genome of all pigs, but PERV-C is not, the animals were screened for PERV-C and PERV-A/C. Our detection methods were sensitive and detected PCMV/PRV, PLHV-1, PLHV-1, PLHV-3, PVC3 and PERV-C in most animals. PPV1, HEV3, PCV4 and PERV-A/C were not detected. These data are of great interest since the animals are healthy and resistant to diseases.
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Affiliation(s)
- Hina Jhelum
- Institute of Virology, Free University Berlin, 14163 Berlin, Germany; (H.J.); (L.K.); (B.K.)
| | - Vasileios Papatsiros
- Faculty of Veterinary Medicine, Clinic of Medicine (Farm Animal Medicine), University of Thessaly, 43100 Karditsa, Greece; (V.P.); (G.P.)
| | - Georgios Papakonstantinou
- Faculty of Veterinary Medicine, Clinic of Medicine (Farm Animal Medicine), University of Thessaly, 43100 Karditsa, Greece; (V.P.); (G.P.)
| | - Ludwig Krabben
- Institute of Virology, Free University Berlin, 14163 Berlin, Germany; (H.J.); (L.K.); (B.K.)
| | - Benedikt Kaufer
- Institute of Virology, Free University Berlin, 14163 Berlin, Germany; (H.J.); (L.K.); (B.K.)
| | - Joachim Denner
- Institute of Virology, Free University Berlin, 14163 Berlin, Germany; (H.J.); (L.K.); (B.K.)
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Sukhno VV, Vashchenko PA, Saenko AM, Zhukorskyi OM, Tserenyuk OM, Kryhina NV. Association of Fut1 and Slc11a1 gene polymorphisms with productivity traits of Large White pigs. REGULATORY MECHANISMS IN BIOSYSTEMS 2022. [DOI: 10.15421/022229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The purpose of our work was to study the polymorphism of genes associated with disease resistance and to search for their associations with productive traits in the population of the Ukrainian Large White pigs. For this study, 50 pigs were used, observations and measurements were carried out at the age from birth to 180 days. Genetic studies were carried out in a certified laboratory of the Institute of Pig Breeding and Agroindustrial Production. In the study of fucosyltransferase 1 and solute carrier family 11 member 1 genes, polymorphism was found in three of the five analyzed loci. In the Ukrainian Large White subpopulation of pigs the informativeness of these gene polymorphisms was at the optimal level for associative analysis, Polymorphism Information Content was greater than 0.3 in two loci. A sufficiently high level of Polymorphism Information Content indicates the value of this breed to preserve the biodiversity of pigs. The distribution of genotypes at some loci of the solute carrier family 11 member 1 gene was characterized by a deviation from the theoretically expected one due to the increase in the frequency of the heterozygous genotype. There was also a statistically confirmed deviation of the genotypes’ distribution from the normal and polymorphism fucosyltransferase 1 gene, but in this case in the direction of increasing the frequency of both homozygous variants. These results indicate the presence of a certain selection pressure on the mentioned polymorphisms and their possible impact on productive traits. The influence of solute carrier family 11 member 1 gene polymorphism on the weight of pigs at the age of 120 and 180 days, the average daily gain recorded in the period 28–120 days and from birth to 180 days, as well as on the backfat thickness, was established. The preferred genotype is TT, which can be used in breeding to obtain more productive animals with increased disease resistance, but in the selection of animals at this locus, it is necessary to control the backfat thickness and prevent breeding of pigs that may worsen this trait.
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Jeon R, Cheng J, Putz A, Dong Q, Harding J, Dyck M, Plastow G, Fortin F, Lunney J, Rowland R, Canada P, Dekkers J. Effect of a genetic marker for the GBP5 gene on resilience to a polymicrobial natural disease challenge in pigs. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Angthong P, Uengwetwanit T, Pootakham W, Sittikankaew K, Sonthirod C, Sangsrakru D, Yoocha T, Nookaew I, Wongsurawat T, Jenjaroenpun P, Rungrassamee W, Karoonuthaisiri N. Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform. PeerJ 2020; 8:e10340. [PMID: 33240651 PMCID: PMC7668203 DOI: 10.7717/peerj.10340] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.
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Affiliation(s)
- Pacharaporn Angthong
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Tanaporn Uengwetwanit
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Kanchana Sittikankaew
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wanilada Rungrassamee
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Nitsara Karoonuthaisiri
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
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Luc DD, Thinh NH, Bo HX, Vinh NT, Manh TX, Hung NV, Ton VD, Farnir F. Mutation c.307G>A in FUT1 gene has no effect on production performance of Yorkshire pigs in the tropics: the case of Vietnam. CANADIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1139/cjas-2019-0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The alpha (1) fucosyltransferase gene (FUT1) is a candidate gene for controlling the adhesion of Escherichia coli F18 receptor. Indeed, a single-nucleotide polymorphism, c.307G>A, located in the gene is such that pigs with AA genotype are resistant to entero-toxigenic E. coli F18, whereas those with AG and GG genotypes are sensitive. An experiment was carried out in northern Vietnam from March 2016 to May 2017 to determine FUT1 genotype frequencies and the effect of these genotypes on production performance of Yorkshire pigs. A total of 613 animals were genotyped using polymerase chain reaction – restriction fragment length polymorphism method. The body weights at birth, weaning, initial fattening period, and final fattening period were collected from 611, 516, 479, and 418 animals, respectively, whereas backfat thickness, depth of longissimus dorsi, and lean meat percentage were recorded from 328 animals. The frequencies of FUT1 genotypes were found to be in Hardy–Weinberg equilibrium (P = 0.51). Effect of FUT1 genotype was not observed for all production traits (P > 0.05), whereas final body weight and depth of longissimus dorsi were significantly different between females and males (P < 0.05). These results suggest that selection of Yorkshire pigs resistant to entero-toxigenic E. coli F18 could be effective without adversely affecting average daily gain and lean meat.
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Affiliation(s)
- Do Duc Luc
- Department of Animal Breeding and Genetics, Faculty of Animal Science, Vietnam National University of Agriculture, Trau Quy, Gia Lam, Hanoi 12406, Vietnam
| | - Nguyen Hoang Thinh
- Department of Animal Breeding and Genetics, Faculty of Animal Science, Vietnam National University of Agriculture, Trau Quy, Gia Lam, Hanoi 12406, Vietnam
| | - Ha Xuan Bo
- Department of Animal Breeding and Genetics, Faculty of Animal Science, Vietnam National University of Agriculture, Trau Quy, Gia Lam, Hanoi 12406, Vietnam
| | - Nguyen Thi Vinh
- Department of Biology and Zoology, Faculty of Animal Science, Vietnam National University of Agriculture, Trau Quy, Gia Lam, Hanoi 12406, Vietnam
| | - Tran Xuan Manh
- Dabaco Nucleus Breeding Pig Company, Tien Du District, Bac Ninh Province 16416, Vietnam
| | - Nguyen Van Hung
- Dabaco Nucleus Breeding Pig Company, Tien Du District, Bac Ninh Province 16416, Vietnam
| | - Vu Dinh Ton
- Center of Multidiscipline Research for Rural Development, Vietnam National University of Agriculture, Trau Quy, Gia Lam, Hanoi 12406, Vietnam
| | - Frédéric Farnir
- Department of Animal Production, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
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