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A Botner - One of the best experts on this subject based on the ideXlab platform.
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potential routes for indirect transmission of african swine fever virus into Domestic Pig herds
Transboundary and Emerging Diseases, 2020Co-Authors: Ann Sofie Olesen, Anette Boklund, Graham J Belsham, Thomas Bruun Rasmussen, Louise Lohse, Rene Bodker, Tariq Hisham Beshara Halasa, A BotnerAbstract:Following its introduction into Georgia in 2007, African swine fever virus (ASFV) has become widespread on the European continent and in Asia. In many cases, the exact route of introduction into Domestic Pig herds cannot be determined, but most introductions are attributed to indirect virus transmission. In this review, we describe knowledge gained about different matrices that may allow introduction of the virus into Pig herds. These matrices include uncooked Pig meat, processed Pig-derived products, feed, matrices contaminated with the virus and blood-feeding invertebrates. Knowledge gaps still exist, and both field studies and laboratory research are needed to enhance understanding of the risks for ASFV introductions, especially via virus-contaminated materials, including bedding and feed, and via blood-feeding, flying insects. Knowledge obtained from such studies can be applied to epidemiological risk assessments for the different transmission routes. Such assessments can be utilized to help predict the most effective biosecurity and control strategies.
Claus Jørgensen - One of the best experts on this subject based on the ideXlab platform.
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inaugural article by a recently elected academy member strong signatures of selection in the Domestic Pig genome
Proceedings of the National Academy of Sciences of the United States of America, 2012Co-Authors: Carl-johan Rubin, Orjan Carlborg, Hendrik-jan Megens, Alvaro Martinez Barrio, Khurram Maqbool, Shumaila Sayyab, Doreen Schwochow, Chao Wang, Patric Jern, Claus JørgensenAbstract:Several subspecies of wild boars have contributed to the development of the Domestic Pig, and there is a considerable divergence time between them (on the order of 1 million y) (1–4). The Domestication process has, to a large extent, been going on in parallel in Asia and Europe. For instance, black coat color in Asian and European Domestic Pigs is caused by independent missense mutations in the melanocortin 1 receptor (MC1R) that occurred on haplotypes originating from the Asian and European wild boar, respectively (5). Since animal breeding became more organized in the 18th century, the selection goals in Pigs have evolved in response to demand. The early focus on selection for fatness was driven by demand for energy-rich food and tallow for candles. In contrast, there has been very strong selection for lean growth (high protein and low fat content) during the last 60 y, driven by the demand for reduced caloric intake in modern society. Several mutations with major effects on lean growth have already been identified, including a missense mutation in Ryanodine receptor 1 (RYR1) (6), a missense mutation in PRKAG3 encoding the gamma 3 subunit of AMP-activated protein kinase (7), and a single base change at a repressor binding site in intron 3 of insulin-like growth factor 2 (IGF2) (8). Here we used the Pig draft genome sequence (Sscrofa10.2) (4) and whole-genome resequencing to reveal loci that have been under selection during and since Pig Domestication. We searched for selective sweeps and genetic variants showing marked allele frequency differences between Pig and wild boar populations. The results are based on the combined analyses of two datasets: (i) mate pair reads from eight different pools of Pigs and wild boars sequenced to ∼5× coverage/pool, and (ii) paired-end fragment reads (100 + 100 bp) from 37 individual Pigs and 11 wild boars, each sequenced to ∼10× coverage (Table 1). Table 1. Samples used for whole-genome shotgun sequencing
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Strong signatures of selection in the Domestic Pig genome
Proceedings of the National Academy of Sciences of the United States of America, 2012Co-Authors: Carl-johan Rubin, Orjan Carlborg, Hendrik-jan Megens, Alvaro Martinez Barrio, Khurram Maqbool, Shumaila Sayyab, Doreen Schwochow, Chao Wang, Patric Jern, Claus JørgensenAbstract:Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in Domestic Pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci that underlie phenotypic evolution in European Domestic Pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the Domestic Pig—the elongation of the back and an increased number of vertebrae. The three loci were associated with the NR6A1, PLAG1, and LCORL genes. The latter two have repeatedly been associated with loci controlling stature in other Domestic animals and in humans. Most European Domestic Pigs are homozygous for the same haplotype at these three loci. We found an excess of derived nonsynonymous substitutions in Domestic Pigs, most likely reflecting both positive selection and relaxed purifying selection after Domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white or white-spotted Pigs, carrying the Dominant white, Patch, or Belt alleles. This discovery illustrates how structural changes have contributed to rapid phenotypic evolution in Domestic animals and how alleles in Domestic animals may evolve by the accumulation of multiple causative mutations as a response to strong directional selection.
Anette Boklund - One of the best experts on this subject based on the ideXlab platform.
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potential routes for indirect transmission of african swine fever virus into Domestic Pig herds
Transboundary and Emerging Diseases, 2020Co-Authors: Ann Sofie Olesen, Anette Boklund, Graham J Belsham, Thomas Bruun Rasmussen, Louise Lohse, Rene Bodker, Tariq Hisham Beshara Halasa, A BotnerAbstract:Following its introduction into Georgia in 2007, African swine fever virus (ASFV) has become widespread on the European continent and in Asia. In many cases, the exact route of introduction into Domestic Pig herds cannot be determined, but most introductions are attributed to indirect virus transmission. In this review, we describe knowledge gained about different matrices that may allow introduction of the virus into Pig herds. These matrices include uncooked Pig meat, processed Pig-derived products, feed, matrices contaminated with the virus and blood-feeding invertebrates. Knowledge gaps still exist, and both field studies and laboratory research are needed to enhance understanding of the risks for ASFV introductions, especially via virus-contaminated materials, including bedding and feed, and via blood-feeding, flying insects. Knowledge obtained from such studies can be applied to epidemiological risk assessments for the different transmission routes. Such assessments can be utilized to help predict the most effective biosecurity and control strategies.
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simulating the spread of classical swine fever virus between a hypothetical wild boar population and Domestic Pig herds in denmark
Preventive Veterinary Medicine, 2008Co-Authors: Anette Boklund, Stine Gissel Goldbach, Ase Uttenthal, Lis AlbanAbstract:Denmark has no free-range wild-boar population. However, Danish wildlife organizations have suggested that wild boar should be reintroduced into the wild to broaden national biodiversity. Danish Pig farmers fear that this would lead to a higher risk of introduction of classical swine fever virus (CSFV), which could have enormous consequences in terms of loss of pork exports. We conducted a risk assessment to address the additional risk of introducing and spreading CSFV due to the reintroduction of wild boar. In this paper, we present the part of the risk assessment that deals with the spread of CSFV between the hypothetical wild-boar population and the Domestic population. Furthermore, the economic impact is assessed taking the perspective of the Danish national budget and the Danish Pig industry. We used InterSpreadPlus to model the differential classical swine fever (CSF) risk due to wild boar. Nine scenarios were run to elucidate the effect of: (a) presence of wild boar (yes/no), (b) locations for the index case (Domestic Pig herd/wild-boar group), (c) type of control strategy for wild boar (hunting/vaccination) and (d) presence of free-range Domestic Pigs. The presence of free-range wild boar was simulated in two large forests using data from wildlife studies and Danish habitat data. For each scenario, we estimated (1) the control costs borne by the veterinary authorities, (2) the control-related costs to farmers and (3) the loss of exports associated with an epidemic. Our simulations predict that CSFV will be transmitted from the Domestic Pig population to wild boar if the infected Domestic Pig herd is located close to an area with wild boar (<5 km). If an outbreak begins in the wild-boar population, the epidemic will last longer and will occasionally lead to several epidemics because of periodic transfer of virus from groups of infected wild boar to Domestic Pig herds. The size and duration of the epidemic will be reduced if there are no free-range Domestic Pig herds in the area with CSF-infected wild boar. The economic calculations showed that the total national costs for Denmark (i.e. the direct costs to the national budget and the costs to the Pig industry) related to an outbreak of CSF in Denmark will be highly driven by the reactions of the export markets and in particular of the non-EU markets. Unfortunately, there is a substantial amount of uncertainty surrounding this issue. If hunting is used as a control measure, the average expenses related to a CSF outbreak will be 40% higher if wild boar are present compared with not present. However, a vaccination strategy for wild boar will double the total costs compared with a hunting strategy.
Rupert Hochegger - One of the best experts on this subject based on the ideXlab platform.
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applicability of a duplex and four singleplex real time pcr assays for the qualitative and quantitative determination of wild boar and Domestic Pig meat in processed food products
Scientific Reports, 2020Co-Authors: Maria Kaltenbrunner, Walter Mayer, Rupert Hochegger, Kirsten Kerkhoff, Rita Epp, Hermann Ruggeberg, Margit CichnamarklAbstract:Appropriate analytical methods are needed for the detection of food authentication. We investigated the applicability of a duplex real-time PCR assay targeting chromosome 1 and two singleplex real-time PCR assays targeting chromosome 9, both published recently, for the qualitative and quantitative determination of wild boar and Domestic Pig in processed food products. In addition, two singleplex real-time PCR assays targeting chromosome 7 were tested for their suitability to differentiate the two subspecies. Even by targeting the three genome loci, the probability of misclassification was not completely eliminated. Application of the real-time PCR assays to a total of 35 commercial meat products, including 22 goulash products, revealed that Domestic Pig DNA was frequently present, even in 14 out of 15 products declared to consist of 100% wild boar. Quantitative results obtained with the real-time PCR assays for wild boar (p < 0.001) and those for Domestic Pig (p < 0.001) were significantly different. However, the results obtained with the real-time PCR assays for wild boar (r = 0.673; p < 0.001) and those for Domestic Pig (r = 0.505; p = 0.002) were found to be significantly correlated. If the rules given in the paper are followed, the real-time PCR assays are applicable for routine analysis.
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differentiation between wild boar and Domestic Pig in food by targeting two gene loci by real time pcr
Scientific Reports, 2019Co-Authors: Maria Kaltenbrunner, Walter Mayer, Rupert Hochegger, Kirsten Kerkhoff, Rita Epp, Hermann Ruggeberg, Margit CichnamarklAbstract:Studies indicate that many meat products are not authentic, most frequently because the meat species differ from those given on the food labels. At present, DNA based methods play the most important role in meat species authentication. Discrimination of wild boar and Domestic Pig meat in food is challenging because it is differentiation on the subspecies level. We developed and validated two singleplex real-time PCR assays targeting SNP rs81416363 on chromosome 9 and a duplex real-time PCR assay targeting SNP g.299084751 C > T in the NR6A1 gene located on chromosome 1. The singleplex real-time PCR assays led to some ambiguous results for Mangalica and Krskopolje Pig breeds and wild boar individuals from Germany, the duplex real-time PCR assay particularly for the Turopolje Pig breed. We demonstrate that the probability of misclassification can be substantially reduced if the results of both the singleplex real-time PCR assays and the duplex real-time PCR assay are taken into consideration. 86 (91.5%) of a total of 94 individuals, comprising 64 Domestic Pigs (14 different breeds and 6 cross-breeds) and 30 wild boars (from Austria, Germany, Romania, USA and Estonia), were classified correctly.
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discrimination of two alleles of the melanocortin receptor 1 gene to discern european wild boar sus scrofa scrofa and Domestic Pig sus scrofa Domestica in meat products by real time pcr
European Food Research and Technology, 2011Co-Authors: Walter Mayer, Rupert HocheggerAbstract:A duplex real-time polymerase chain reaction (PCR) technique for the discrimination of two subspecies of sus scrofa in meat products has been developed. Primers and probes target at a sequence in the melanocortin receptor 1 (MCR1) gene being associated in the expression of wild-type coat color. Both PCRs amplify a 56-bp product of DNA from wild boar (Sus scrofa scrofa) and Domestic Pig (Sus scrofa Domestica) likewise. One of the TaqMan probes specifically anneals to the wild boar sequence and the other one to the Domestic Pig sequence, their base sequence differing only in a single nucleotide (single nucleotide polymorphism, SNP). This qualitative-method allows the detection of genomic DNA from wild boar and Domestic Pig as low as 25 pg in a 25-μl reaction volume. No cross reactivities were found with either genomic DNA from various other meat species, or with other ingredients of meat products (e.g. spices). The PCR efficiency is >95% for both targets. Although both PCRs are impaired by the presence of bovine and porcine DNA (wild boar detection is impaired by Domestic Pig DNA and vice versa), the method is applicable for the detection of low levels of wild boar and Domestic Pig meat simultaneously in commercial meat products. The limit of detection (LOD) in meat samples is 2% for wild boar and 5% for Domestic Pig.
Orjan Carlborg - One of the best experts on this subject based on the ideXlab platform.
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inaugural article by a recently elected academy member strong signatures of selection in the Domestic Pig genome
Proceedings of the National Academy of Sciences of the United States of America, 2012Co-Authors: Carl-johan Rubin, Orjan Carlborg, Hendrik-jan Megens, Alvaro Martinez Barrio, Khurram Maqbool, Shumaila Sayyab, Doreen Schwochow, Chao Wang, Patric Jern, Claus JørgensenAbstract:Several subspecies of wild boars have contributed to the development of the Domestic Pig, and there is a considerable divergence time between them (on the order of 1 million y) (1–4). The Domestication process has, to a large extent, been going on in parallel in Asia and Europe. For instance, black coat color in Asian and European Domestic Pigs is caused by independent missense mutations in the melanocortin 1 receptor (MC1R) that occurred on haplotypes originating from the Asian and European wild boar, respectively (5). Since animal breeding became more organized in the 18th century, the selection goals in Pigs have evolved in response to demand. The early focus on selection for fatness was driven by demand for energy-rich food and tallow for candles. In contrast, there has been very strong selection for lean growth (high protein and low fat content) during the last 60 y, driven by the demand for reduced caloric intake in modern society. Several mutations with major effects on lean growth have already been identified, including a missense mutation in Ryanodine receptor 1 (RYR1) (6), a missense mutation in PRKAG3 encoding the gamma 3 subunit of AMP-activated protein kinase (7), and a single base change at a repressor binding site in intron 3 of insulin-like growth factor 2 (IGF2) (8). Here we used the Pig draft genome sequence (Sscrofa10.2) (4) and whole-genome resequencing to reveal loci that have been under selection during and since Pig Domestication. We searched for selective sweeps and genetic variants showing marked allele frequency differences between Pig and wild boar populations. The results are based on the combined analyses of two datasets: (i) mate pair reads from eight different pools of Pigs and wild boars sequenced to ∼5× coverage/pool, and (ii) paired-end fragment reads (100 + 100 bp) from 37 individual Pigs and 11 wild boars, each sequenced to ∼10× coverage (Table 1). Table 1. Samples used for whole-genome shotgun sequencing
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Strong signatures of selection in the Domestic Pig genome
Proceedings of the National Academy of Sciences of the United States of America, 2012Co-Authors: Carl-johan Rubin, Orjan Carlborg, Hendrik-jan Megens, Alvaro Martinez Barrio, Khurram Maqbool, Shumaila Sayyab, Doreen Schwochow, Chao Wang, Patric Jern, Claus JørgensenAbstract:Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in Domestic Pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci that underlie phenotypic evolution in European Domestic Pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the Domestic Pig—the elongation of the back and an increased number of vertebrae. The three loci were associated with the NR6A1, PLAG1, and LCORL genes. The latter two have repeatedly been associated with loci controlling stature in other Domestic animals and in humans. Most European Domestic Pigs are homozygous for the same haplotype at these three loci. We found an excess of derived nonsynonymous substitutions in Domestic Pigs, most likely reflecting both positive selection and relaxed purifying selection after Domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white or white-spotted Pigs, carrying the Dominant white, Patch, or Belt alleles. This discovery illustrates how structural changes have contributed to rapid phenotypic evolution in Domestic animals and how alleles in Domestic animals may evolve by the accumulation of multiple causative mutations as a response to strong directional selection.
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the origin of the Domestic Pig independent Domestication and subsequent introgression
Genetics, 2000Co-Authors: Elisabetta Giuffra, James Kijas, Orjan Carlborg, J T Jeon, Leif AnderssonAbstract:The Domestic Pig originates from the Eurasian wild boar (Sus scrofa). We have sequenced mitochondrial DNA and nuclear genes from wild and Domestic Pigs from Asia and Europe. Clear evidence was obtained for Domestication to have occurred independently from wild boar subspecies in Europe and Asia. The time since divergence of the ancestral forms was estimated at approximately 500,000 years, well before Domestication approximately 9,000 years ago. Historical records indicate that Asian Pigs were introduced into Europe during the 18th and early 19th centuries. We found molecular evidence for this introgression and the data indicated a hybrid origin of some major "European" Pig breeds. The study is an advance in Pig genetics and has important implications for the maintenance and utilization of genetic diversity in this livestock species.