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1.  Genetic structure of wild boar (Sus scrofa) populations from East Asia based on microsatellite loci analyses 
BMC Genetics  2014;15:85.
Background
Wild boar, Sus scrofa, is an extant wild ancestor of the domestic pig as an agro-economically important mammal. Wild boar has a worldwide distribution with its geographic origin in Southeast Asia, but genetic diversity and genetic structure of wild boar in East Asia are poorly understood. To characterize the pattern and amount of genetic variation and population structure of wild boar in East Asia, we genotyped and analyzed microsatellite loci for a total of 238 wild boar specimens from ten locations across six countries in East and Southeast Asia.
Results
Our data indicated that wild boar populations in East Asia are genetically diverse and structured, showing a significant correlation of genetic distance with geographic distance and implying a low level of gene flow at a regional scale. Bayesian-based clustering analysis was indicative of seven inferred genetic clusters in which wild boars in East Asia are geographically structured. The level of genetic diversity was relatively high in wild boars from Southeast Asia, compared with those from Northeast Asia. This gradient pattern of genetic diversity is consistent with an assumed ancestral population of wild boar in Southeast Asia. Genetic evidences from a relationship tree and structure analysis suggest that wild boar in Jeju Island, South Korea have a distinct genetic background from those in mainland Korea.
Conclusions
Our results reveal a diverse pattern of genetic diversity and the existence of genetic differentiation among wild boar populations inhabiting East Asia. This study highlights the potential contribution of genetic variation of wild boar to the high genetic diversity of local domestic pigs during domestication in East Asia.
doi:10.1186/1471-2156-15-85
PMCID: PMC4112609  PMID: 25034725
Microsatellites; East Asia; Genetic diversity; Genetic structure; Wild boar
2.  STR Profiling for Discrimination between Wild and Domestic Swine Specimens and between Main Breeds of Domestic Pigs Reared in Belarus 
PLoS ONE  2016;11(11):e0166563.
A panel comprising 16 short tandem repeats (STRs) and a gender-specific amelogenin marker was worked out and tested for robustness in discrimination between wild and domestic swine subspecies encountered in Europe, between regional populations of wild boars and between main breeds of domestic pigs reared in Belarus. The STR dataset comprised 310 wild boars, inhabiting all administrative regions of Belarus, and 313 domestic pigs, representing three local and three cosmopolitan lines. Additionally, a total of 835 wild boars were genotyped for the presence of melanocortin 1 receptor (MC1R) alleles specific for domestic pigs. Correctness of assignment of STR profiles to appropriate populations was measured by log-likelihood ratios (log-LRs). All samples were correctly identified as wild boars or domestic pigs with average log-LR of 42.4 (LR = 2.6×1018). On the other hand, as many as 50 out of 835 (6.0%) genotyped wild boars from Belarus possessed MC1R alleles specific to domestic pigs, demonstrating supremacy of our STR profiling system over traditional differentiation between wild boars and domestic pigs, based on single binary markers. Mean log-LRs for allocation of wild boars to their regions of origin and of domestic pigs to appropriate breeds were 2.3 (LR = 9.7) and 13.4 (LR = 6.6×105), respectively. Our results demonstrate the developed STR profiling system to be a highly efficient tool for differentiation between wild and domestic swine subspecies and between diverse breeds of domestic pigs as well as for verification of genetic identity of porcine specimens for the purpose of forensic investigations of wildlife crimes, assurance of veterinary public health, parentage control in animal husbandry, food safety management and traceability of livestock products.
doi:10.1371/journal.pone.0166563
PMCID: PMC5112791  PMID: 27851802
3.  Spatial distribution and risk factors of Brucellosis in Iberian wild ungulates 
Background
The role of wildlife as a brucellosis reservoir for humans and domestic livestock remains to be properly established. The aim of this work was to determine the aetiology, apparent prevalence, spatial distribution and risk factors for brucellosis transmission in several Iberian wild ungulates.
Methods
A multi-species indirect immunosorbent assay (iELISA) using Brucella S-LPS antigen was developed. In several regions having brucellosis in livestock, individual serum samples were taken between 1999 and 2009 from 2,579 wild bovids, 6,448 wild cervids and4,454 Eurasian wild boar (Sus scrofa), and tested to assess brucellosis apparent prevalence. Strains isolated from wild boar were characterized to identify the presence of markers shared with the strains isolated from domestic pigs.
Results
Mean apparent prevalence below 0.5% was identified in chamois (Rupicapra pyrenaica), Iberian wild goat (Capra pyrenaica), and red deer (Cervus elaphus). Roe deer (Capreolus capreolus), fallow deer (Dama dama), mouflon (Ovis aries) and Barbary sheep (Ammotragus lervia) tested were seronegative. Only one red deer and one Iberian wild goat resulted positive in culture, isolating B. abortus biovar 1 and B. melitensis biovar 1, respectively. Apparent prevalence in wild boar ranged from 25% to 46% in the different regions studied, with the highest figures detected in South-Central Spain. The probability of wild boar being positive in the iELISA was also affected by age, age-by-sex interaction, sampling month, and the density of outdoor domestic pigs. A total of 104 bacterial isolates were obtained from wild boar, being all identified as B. suis biovar 2. DNA polymorphisms were similar to those found in domestic pigs.
Conclusions
In conclusion, brucellosis in wild boar is widespread in the Iberian Peninsula, thus representing an important threat for domestic pigs. By contrast, wild ruminants were not identified as a significant brucellosis reservoir for livestock.
doi:10.1186/1471-2334-10-46
PMCID: PMC2841660  PMID: 20205703
4.  Phenotype and animal domestication: A study of dental variation between domestic, wild, captive, hybrid and insular Sus scrofa 
BMC Evolutionary Biology  2015;15(1):6.
Background
Identifying the phenotypic responses to domestication remains a long-standing and important question for researchers studying its early history. The great diversity in domestic animals and plants that exists today bears testament to the profound changes that domestication has induced in their ancestral wild forms over the last millennia. Domestication is a complex evolutionary process in which wild organisms are moved to new anthropogenic environments. Although modern genetics are significantly improving our understanding of domestication and breed formation, little is still known about the associated morphological changes linked to the process itself. In order to explore phenotypic variation induced by different levels of human control, we analysed the diversity of dental size, shape and allometry in modern free-living and captive wild, wild x domestic hybrid, domestic and insular Sus scrofa populations.
Results
We show that domestication has created completely new dental phenotypes not found in wild boar (although the amount of variation amongst domestic pigs does not exceed that found in the wild). Wild boar tooth shape also appears to be biogeographically structured, likely the result of post-glacial recolonisation history. Furthermore, distinct dental phenotypes were also observed among domestic breeds, probably the result of differing types and intensity of past and present husbandry practices. Captivity also appears to impact tooth shape. Wild x domestic hybrids possess second molars that are strictly intermediate in shape between wild boar and domestic pigs (third molars, however, showing greater shape similarity with wild boar) while their size is more similar to domestic pigs. The dental phenotypes of insular Sus scrofa populations found on Corsica and Sardinia today (originally introduced by Neolithic settlers to the islands) can be explained either by feralization of the original introduced domestic swine or that the founding population maintained a wild boar phenotype through time.
Conclusions
Domestication has driven significant phenotypic diversification in Sus scrofa. Captivity (environmental control), hybridization (genome admixture), and introduction to islands all correspond to differing levels of human control and may be considered different stages of the domestication process. The relatively well-known genetic evolutionary history of pigs shows a similar complexity at the phenotypic level.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0269-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0269-x
PMCID: PMC4328033  PMID: 25648385
Teeth; Molars; Geometric morphometrics; Biogeography; Artificial selection; Natural selection
5.  Contemporary Genetic Structure, Phylogeography and Past Demographic Processes of Wild Boar Sus scrofa Population in Central and Eastern Europe 
PLoS ONE  2014;9(3):e91401.
The wild boar (Sus scrofa) is one of the most widely distributed mammals in Europe. Its demography was affected by various events in the past and today populations are increasing throughout Europe. We examined genetic diversity, structure and population dynamics of wild boar in Central and Eastern Europe. MtDNA control region (664 bp) was sequenced in 254 wild boar from six countries (Poland, Hungary, Belarus, Ukraine, Moldova and the European part of Russia). We detected 16 haplotypes, all known from previous studies in Europe; 14 of them belonged to European 1 (E1) clade, including 13 haplotypes from E1-C and one from E1-A lineages. Two haplotypes belonged respectively to the East Asian and the Near Eastern clade. Both haplotypes were found in Russia and most probably originated from the documented translocations of wild boar. The studied populations showed moderate haplotype (0.714±0.023) and low nucleotide diversity (0.003±0.002). SAMOVA grouped the genetic structuring of Central and Eastern European wild boar into three subpopulations, comprising of: (1) north-eastern Belarus and the European part of Russia, (2) Poland, Ukraine, Moldova and most of Belarus, and (3) Hungary. The multimodal mismatch distribution, Fu's Fs index, Bayesian skyline plot and the high occurrence of shared haplotypes among populations did not suggest strong demographic fluctuations in wild boar numbers in the Holocene and pre-Holocene times. This study showed relatively weak genetic diversity and structure in Central and Eastern European wild boar populations and underlined gaps in our knowledge on the role of southern refugia and demographic processes shaping genetic diversity of wild boar in this part of Europe.
doi:10.1371/journal.pone.0091401
PMCID: PMC3951376  PMID: 24622149
6.  Molecular microevolution and epigenetic patterns of the long non-coding gene H19 show its potential function in pig domestication and breed divergence 
Background
The domestic pig Sus scrofa domesticus originated from the wild boar S. scrofa about 10,000 years ago. During domestication, drastic morphological, physiological, and behavioral changes developed between domestic pigs and wild boars through artificial and natural selection. The long non-coding RNA (lncRNA) H19, which is located within the imprinting gene cluster H19-IGF2, plays an important role in regulating muscle development in humans and mice. This study systematically analyzed the molecular evolution of H19 and its possible epigenetic changes during pig domestication and breeding to explore the genetic and epigenetic contributions of H19 to pig domestication.
Results
The molecular evolution of H19 was initially analyzed on a large phylogenetic scale. Results showed that the gene was highly conserved within a broad range, especially in the 5′ terminal sequence. The molecular evolution of the gene was then analyzed using published re-sequencing data of 30 wild boars from Tibet, 3 wild boars from Sichuan, and 15 native pigs from other regions in China. Eight polymorphic sites were identified, and the nucleotide diversity (π) value within the H19 gene body was significantly higher (Z-test, P < 0.05) in domesticated pigs than in wild pigs. However, no significant divergence occurred between domesticated and wild pigs. Single nucleotide polymorphisms in the 3′ terminal sequence were surveyed in other Chinese local breeds and foreign pig breeds. We observed a consistently higher diversity in domesticated pigs than in wild pigs. The methylation pattern of the H19 gene in pigs was subsequently analyzed using published methylated DNA immunoprecipitation data and an unpublished single-base resolution liver methylome. Analysis results showed distinct methylation levels in some tissues. Among the samples surveyed, Landrace showed the lowest methylation level, followed by the Guizhou wild boar, whereas the Enshi pig exhibited the highest methylation level in the 2 kb upstream region of the H19 gene. Liver transcriptome data suggested that Landrace harbored the highest expression of the H19 gene, followed by the Guizhou wild boar, whereas the Enshi pig harbored the lowest expression of the gene. Differential methylation sites (DMSs) among the three breeds were mainly identified in the 2 kb upstream region of the H19 gene. In the Enshi pig, we detected allele-specific methylation (ASM) regions in the 2 kb upstream region of the H19 gene. Most of the DMSs in the upstream 2 kb region of the gene were also located in the ASM region in this breed.
Conclusions
Molecular analyses suggest that the H19 gene was highly conserved during large-scale evolution and exhibited genotype differentiation during domestication and breed differentiation. The drastic diversity pattern between domestic and wild pigs in the H19 gene body, which was highly conserved during large-scale evolution, suggests that this gene might have played roles in the breed differentiation of domestic pigs. Methylation analysis indicates an opposite epigenetic regulation direction between Chinese and European pig (EU) domestication, which resulted in opposite expression changes in this gene between the two domesticated groups. Our preliminary analyses on DMSs among different pig breeds and ASM imply that imprinting was associated with methylation differences. This study systematically demonstrates the genetic and epigenetic patterns of H19 during pig domestication and provide valuable cues and basis for further research on the function of H19 in pig domestication.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-016-0657-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-016-0657-5
PMCID: PMC4841954  PMID: 27107967
Pig; Long non-coding gene; H19; Molecular evolution; Methylation; Domestication; Breed divergence
7.  Detection and molecular characterization of porcine reproductive and respiratory syndrome virus in Lithuanian wild boar populations 
Background
Porcine reproductive and respiratory syndrome virus (PRRSV) is recognized worldwide as an important and economically devastating pathogen in pig production. Although PRRSV is widespread in domestic swine, there is a lack of information regarding PRRSV infection in European wild boars (Sus scrofa). Currently available information does not provide conclusive evidence that wild boars are a reservoir of PRRSV. Nevertheless, wild boars may be likely to become infected by domestic swine through occasional direct or indirect contact. Furthermore, wild boars can act as a reservoir for infectious diseases of domestic pigs. Therefore, the objectives of the present study were to determine the virus prevalence and further explore the epidemiology and diversity of PRRSV strains present in Lithuanian wild boars over a 5-year period. A total of 1597 tissue and serum samples from wild boars inhabiting 44 districts and ten counties in Lithuania were analysed using conventional nested reverse transcription polymerase chain reaction (RT-PCR) and real-time Taqman RT-PCR for the detection of PRRSV-specific open reading frame (ORF) 1 and 6 sequences.
Results
PRRSV was highly prevalent in Lithuanian wild boar populations, with an average rate of 18.66 % using conventional RT-PCR and 19.54 % using real-time RT-PCR. PRRSV was detected in 36.71 and 41.77 % of 237 hunting grounds tested by conventional RT-nPCR and real-time RT-PCR, respectively. No statistically significant differences in PRRSV prevalence were observed by geographic area in the ten Lithuanian counties. Animals infected with PRRSV were identified in all age groups; however, significantly higher prevalence rates were identified in subadult and adult wild boars than in juveniles up to 12 months old. No positive results were obtained using conventional PCR with Type 2 specific primers. Phylogenetic analysis of the partial ORF5 region revealed that ten wild boars harboured virus sequences belonging to genetic subtypes 3 and 4 and may therefore pose a serious threat to Lithuanian pig farms in which only subtype two strains are circulating.
Conclusions
The results of virus prevalence and phylogenetic analyses strongly support the role of wild boars as a possible natural reservoir for PRRSV in Lithuania.
Electronic supplementary material
The online version of this article (doi:10.1186/s13028-016-0232-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s13028-016-0232-5
PMCID: PMC5016999  PMID: 27608974
PRRSV; Wild boar; RT-PCR; Real-time RT-PCR; Virus prevalence; ORF5 sequences
8.  Investigating the Role of Free-Ranging Wild Boar (Sus scrofa) in the Re-Emergence of Enzootic Pneumonia in Domestic Pig Herds: A Pathological, Prevalence and Risk-Factor Study 
PLoS ONE  2015;10(3):e0119060.
Enzootic pneumonia (EP) caused by Mycoplasma hyopneumoniae has a significant economic impact on domestic pig production. A control program carried out from 1999 to 2003 successfully reduced disease occurrence in domestic pigs in Switzerland, but recurrent outbreaks suggested a potential role of free-ranging wild boar (Sus scrofa) as a source of re-infection. Since little is known on the epidemiology of EP in wild boar populations, our aims were: (1) to estimate the prevalence of M. hyopneumoniae infections in wild boar in Switzerland; (2) to identify risk factors for infection in wild boar; and (3) to assess whether infection in wild boar is associated with the same gross and microscopic lesions typical of EP in domestic pigs. Nasal swabs, bronchial swabs and lung samples were collected from 978 wild boar from five study areas in Switzerland between October 2011 and May 2013. Swabs were analyzed by qualitative real time PCR and a histopathological study was conducted on lung tissues. Risk factor analysis was performed using multivariable logistic regression modeling. Overall prevalence in nasal swabs was 26.2% (95% CI 23.3–29.3%) but significant geographical differences were observed. Wild boar density, occurrence of EP outbreaks in domestic pigs and young age were identified as risk factors for infection. There was a significant association between infection and lesions consistent with EP in domestic pigs. We have concluded that M. hyopneumoniae is widespread in the Swiss wild boar population, that the same risk factors for infection of domestic pigs also act as risk factors for infection of wild boar, and that infected wild boar develop lesions similar to those found in domestic pigs. However, based on our data and the outbreak pattern in domestic pigs, we propose that spillover from domestic pigs to wild boar is more likely than transmission from wild boar to pigs.
doi:10.1371/journal.pone.0119060
PMCID: PMC4352045  PMID: 25747151
9.  Effectiveness of 10 polymorphic microsatellite markers for parentage and pedigree analysis in plateau pika (Ochotona curzoniae) 
BMC Genetics  2010;11:101.
Background
The plateau pika (Ochotona curzoniae) is an underground-dwelling mammal, native to the Tibetan plateau of China. A set of 10 polymorphic microsatellite loci has been developed earlier. Its reliability for parentage assignment has been tested in a plateau pika population. Two family groups with a known pedigree were used to validate the power of this set of markers.
Results
The error in parentage assignment using a combination of these 10 loci was very low as indicated by their power of discrimination (0.803 - 0.932), power of exclusion (0.351 - 0.887), and an effectiveness of the combined probability of exclusion in parentage assignment of 99.999%.
Conclusion
All the offspring of a family could be assigned to their biological mother; and their father or relatives could also be identified. This set of markers therefore provides a powerful and efficient tool for parentage assignment and other population analyses in the plateau pika.
doi:10.1186/1471-2156-11-101
PMCID: PMC2994782  PMID: 21062500
10.  Effects of human perturbation on the genetic make-up of an island population: the case of the Sardinian wild boar 
Heredity  2010;106(6):1012-1020.
Game species are often manipulated by human beings, whose activities can deeply affect their genetic make-up and population structure. We focused on a geographically isolated wild boar population (Sardinia, Italy), which is classified, together with the Corsican population, as a separate subspecies (Sus scrofa meridionalis). Two hundred and ten wild boars collected across Sardinia were analysed with a set of 10 microsatellites and compared with 296 reference genotypes from continental wild populations and to a sample of domestic pigs. The Sardinian population showed remarkable diversity and a high proportion of private alleles, and strongly deviated from the equilibrium. A Bayesian cluster analysis of only the Sardinian sample revealed a partition into five subpopulations. However, two different Bayesian approaches to the assignment of individuals, accounting for different possible source populations, produced consistent results and proved the admixed nature of the Sardinian population. Indeed, introgressive hybridization with boars from multiple sources (Italian peninsula, central Europe, domestic stocks) was detected, although poor evidence of crossbreeding with free-ranging domestic pigs was unexpectedly found. After excluding individuals who carried exotic genes, the population re-entered Hardy–Weinberg proportions and a clear population structure with three subpopulations emerged. Therefore, the inclusion of introgressed animals in the Bayesian analysis implied an overestimation of the number of clusters. Nonetheless, two of them were consistent between analyses and corresponded to highly pure stocks, located, respectively, in north-west and south-west Sardinia. This work shows the critical importance of including adequate reference samples when studying the genetic structure of managed wild populations.
doi:10.1038/hdy.2010.155
PMCID: PMC3186246  PMID: 21179064
Sus scrofa; domestic pig; microsatellites; admixture analysis; genetic structure; introgressive hybridization
11.  Identification of a second gene associated with variation in vertebral number in domestic pigs 
BMC Genetics  2011;12:5.
Background
The number of vertebrae in pigs varies and is associated with body size. Wild boars have 19 vertebrae, but European commercial breeds for pork production have 20 to 23 vertebrae. We previously identified two quantitative trait loci (QTLs) for number of vertebrae on Sus scrofa chromosomes (SSC) 1 and 7, and reported that an orphan nuclear receptor, NR6A1, was located at the QTL on SSC1. At the NR6A1 locus, wild boars and Asian local breed pigs had the wild-type allele and European commercial-breed pigs had an allele associated with increased numbers of vertebrae (number-increase allele).
Results
Here, we performed a map-based study to define the other QTL, on SSC7, for which we detected genetic diversity in European commercial breeds. Haplotype analysis with microsatellite markers revealed a 41-kb conserved region within all the number-increase alleles in the present study. We also developed single nucleotide polymorphisms (SNPs) in the 450-kb region around the QTL and used them for a linkage disequilibrium analysis and an association study in 199 independent animals. Three haplotype blocks were detected, and SNPs in the 41-kb region presented the highest associations with the number of vertebrae. This region encodes an uncharacterized hypothetical protein that is not a member of any other known gene family. Orthologs appear to exist not only in mammals but also birds and fish. This gene, which we have named vertnin (VRTN) is a candidate for the gene associated with variation in vertebral number. In pigs, the number-increase allele was expressed more abundantly than the wild-type allele in embryos. Among candidate polymorphisms, there is an insertion of a SINE element (PRE1) into the intron of the Q allele as well as the SNPs in the promoter region.
Conclusions
Genetic diversity of VRTN is the suspected cause of the heterogeneity of the number of vertebrae in commercial-breed pigs, so the polymorphism information should be directly useful for assessing the genetic ability of individual animals. The number-increase allele of swine VRTN was suggested to add an additional thoracic segment to the animal. Functional analysis of VRTN may provide novel findings in the areas of developmental biology.
doi:10.1186/1471-2156-12-5
PMCID: PMC3024977  PMID: 21232157
12.  Reintroductions and genetic introgression from domestic pigs have shaped the genetic population structure of Northwest European wild boar 
BMC Genetics  2013;14:43.
Background
Population genetic studies focus on natural dispersal and isolation by landscape barriers as the main drivers of genetic population structure. However, anthropogenic factors such as reintroductions, translocations and wild x domestic hybridization may also have strong effects on genetic population structure. In this study we genotyped 351 Single Nucleotide Polymorphism markers evenly spread across the genome in 645 wild boar (Sus scrofa) from Northwest Europe to evaluate determinants of genetic population structure.
Results
We show that wild boar genetic population structure is influenced by historical reintroductions and by genetic introgression from domestic pigs. Six genetically distinct and geographically coherent wild boar clusters were identified in the Netherlands and Western Germany. The Dutch Veluwe cluster is known to be reintroduced, and three adjacent Dutch and German clusters are suspected to be a result of reintroduction, based on clustering results, low levels of heterozygosity and relatively high genetic distances to nearby populations. Recent wild x domestic hybrids were found geographically widespread across clusters and at low frequencies (average 3.9%). The relationship between pairwise kinship coefficients and geographic distance showed male-biased dispersal at the population genetic level.
Conclusions
Our results demonstrate that wildlife and landscape management by humans are shaping the genetic diversity of an iconic wildlife species. Historical reintroductions, translocation and recent restocking activities with farmed wild boar have all influenced wild boar genetic population structure. The current trend of wild boar population growth and range expansion has recently led to a number of contact zones between clusters, and further admixture between the different wild boar clusters is to be expected.
doi:10.1186/1471-2156-14-43
PMCID: PMC3663677  PMID: 23688182
13.  Wild boar tuberculosis in Iberian Atlantic Spain: a different picture from Mediterranean habitats 
Background
Infections with Mycobacterium bovis and closely related members of the Mycobacterium tuberculosis complex (MTC) are shared between livestock, wildlife and sporadically human beings. Wildlife reservoirs exist worldwide and can interfere with bovine tuberculosis (TB) eradication efforts. The Eurasian wild boar (Sus scrofa) is a MTC maintenance host in Mediterranean Iberia (Spain and Portugal). However, few systematic studies in wild boar have been carried out in Atlantic regions. We describe the prevalence, distribution, pathology and epidemiology of MTC and other mycobacteria from wild boar in Atlantic Spain. A total of 2,067 wild boar were sampled between 2008 and 2012.
Results
The results provide insight into the current status of wild boar as MTC and Mycobacterium avium complex (MAC) hosts in temperate regions of continental Europe. The main findings were a low TB prevalence (2.6%), a low proportion of MTC infected wild boar displaying generalized TB lesions (16.7%), and a higher proportion of MAC infections (4.5%). Molecular typing revealed epidemiological links between wild boar and domestic – cattle, sheep and goat – and other wildlife – Eurasian badger (Meles meles) and red fox (Vulpes vulpes) – hosts.
Conclusions
This study shows that the likelihood of MTC excretion by wild boar in Atlantic habitats is much lower than in Mediterranean areas. However, wild boar provide a good indicator of MTC circulation and, given the current re-emergence of animal TB, similar large-scale surveys would be advisable in other Atlantic regions of continental Europe.
doi:10.1186/1746-6148-9-176
PMCID: PMC3844463  PMID: 24010539
Wild boar; Tuberculosis; Mycobacterial infections; Atlantic Spain; Cattle
14.  Evidence of shared bovine viral diarrhea infections between red deer and extensively raised cattle in south-central Spain 
Background
Bovine viral diarrhea virus (BVDV) is a pestivirus that affects cattle production worldwide and that can infect other ungulates such as cervids and even wild boar (Sus scrofa). It is believed that domestic livestock can become infected through contact with wild animals, though it is known that infection can spread among wild animals in the absence of contact with livestock. Little is known about the sharing of BVDV infection between wild and domestic animals in the same habitat, which is important for designing eradication campaigns and preventing outbreaks, especially on hunting estates with high animal densities.
Results
We assessed the sharing of BVDV infections among hunted red deer, wild boar and cattle in south-central Spain. Sampled red deer (Cervus elaphus; n = 267) and wild boar (n = 52) were located on 19 hunting estates, and cattle (n = 180) were located on 18 nearby farms. We used ELISA kits for the serological screening, Taqman RT-PCR assay for the virus determination, and subsequent phylogenetic analysis for 17 RT-PCR positive sample amplicons. Fifty-two red deer (19.5 %) and 82 cattle (45.6 %) samples tested positive by ELISA. A high apparent prevalence (22.47 %) was obtained for red deer, while only five cattle farms tested positive by RT-PCR. Conversely, no wild boar tested positive by both ELISA or RT-PCR. Eleven red deer (4.1 %) tested positive by both ELISA and RT-PCR; these animals may have been sampled during the last phase of viremia, or they may represent previously exposed individuals infected by a different BVDV strain. The amplicons shared 92.7–100 % identity and fell within the BVDV subgroup 1b, although nine of these (from four red deer and five cattle pools) formed a separate branch. This suggests that there might be a common BVDV infecting both cattle and red deer. Higher red deer abundance was significantly associated with greater risk that extensively raised cattle would test positive for BVDV by ELISA.
Conclusions
Our findings suggest that BVDV is circulating between cattle and red deer populations in proximity, but further work is required to determine whether they share the same strain(s). These results suggest the potential of BVDV to serve as a surveillance marker in these shared habitats. High seroprevalence of BVDV in red deer from our study area suggests that although BVDV infection is common, animals usually survive the infection. Further research is needed to verify and investigate the role of red deer as a BVDV reservoir.
doi:10.1186/s12917-015-0630-3
PMCID: PMC4712561  PMID: 26767363
Bovine viral diarrhea; Pestivirus; Taqman RT-PCR; ELISA; GLMM; Wild ungulates; Wildlife reservoirs; Spain
15.  A High Throughput Genotyping Approach Reveals Distinctive Autosomal Genetic Signatures for European and Near Eastern Wild Boar 
PLoS ONE  2013;8(2):e55891.
The lack of a Near Eastern genetic signature in modern European porcine breeds indicates that, although domestic pigs from the Fertile Crescent entered Europe during the Neolithic, they were completely replaced by their European counterparts in a short window of time. Whilst the absence of such genetic signature has been convincingly demonstrated at the mitochondrial level, variation at the autosomal genomes of European and Near Eastern Sus scrofa has not been compared yet. Herewith, we have explored the genetic relationships among 43 wild boar from Europe (N = 21), Near East (N = 19) and Korea (N = 3), and 40 Iberian (N = 16), Canarian (N = 4) and Mangalitza (N = 20) pigs by using a high throughput SNP genotyping platform. After data filtering, 37,167 autosomal SNPs were used to perform population genetics analyses. A multidimensional scaling plot based on genome-wide identity-by-state pairwise distances inferred with PLINK showed that Near Eastern and European wild boar populations are genetically differentiated. Maximum likelihood trees built with TreeMix supported this conclusion i.e. an early population split between Near Eastern and European Sus scrofa was observed. Moreover, analysis of the data with Structure evidenced that the sampled Iberian, Canarian and Mangalitza pigs did not carry any autosomal signature compatible with a Near Eastern ancestry, a finding that agrees well with previous mitochondrial studies.
doi:10.1371/journal.pone.0055891
PMCID: PMC3584081  PMID: 23460788
16.  Wild boar: an increasing concern for Aujeszky's disease control in pigs? 
Background
The goal of this study was describing the temporal evolution of Aujeszky's disease virus (ADV) contact prevalence among Eurasian wild boar (Sus scrofa) populations under different management regimes and contact likelihoods with domestic pigs. Given the recent increase in wild boar abundance throughout Europe, we hypothesized that wild boar contact with ADV would remain stable in time even after significant reduction of ADV prevalence in domestic pigs.
Results
Sera from 1659 wild boar were collected from 2000 to 2010 within 6 areas of the Iberian Peninsula and tested for the presence of antibodies against ADV by ELISA. According to sampling date, wild boar were grouped into three time periods. ADV prevalence was compared through period both globally and by geographic area. Overall seroprevalence for the ten-year study period was 49.6 ± 2.4%. The highest seroprevalence was recorded in areas with intense wild boar management. The annual proportion of positive wild boar sampling sites remained stable through the study period, while the percentage of domestic pig AD positive counties decreased from 70% in 2003 to 1.7% in 2010.
Conclusions
Results presented herein confirmed our hypothesis that ADV would remain almost stable in wild boar populations. This evidences the increasing risk wild boar pose in the final stages of ADV eradication in pigs and for wildlife conservation.
doi:10.1186/1746-6148-8-7
PMCID: PMC3274458  PMID: 22251441
Disease control; Monitoring; Pseudorabies; Seroprevalence; Sus scrofa; Wildlife
17.  African swine fever virus transmission cycles in Central Europe: Evaluation of wild boar-soft tick contacts through detection of antibodies against Ornithodoros erraticus saliva antigen 
Background
African swine fever (ASF) is one of the most complex viral diseases affecting both domestic and wild pigs. It is caused by ASF virus (ASFV), the only DNA virus which can be efficiently transmitted by an arthropod vector, soft ticks of the genus Ornithodoros. These ticks can be part of ASFV-transmission cycles, and in Europe, O. erraticus was shown to be responsible for long-term maintenance of ASFV in Spain and Portugal. In 2014, the disease has been reintroduced into the European Union, affecting domestic pigs and, importantly, also the Eurasian wild boar population. In a first attempt to assess the risk of a tick-wild boar transmission cycle in Central Europe that would further complicate eradication of the disease, over 700 pre-existing serum samples from wild boar hunted in four representative German Federal States were investigated for the presence of antibodies directed against salivary antigen of Ornithodoros erraticus ticks using an indirect ELISA format.
Results
Out of these samples, 16 reacted with moderate to high optical densities that could be indicative of tick bites in sampled wild boar. However, these samples did not show a spatial clustering (they were collected from distant geographical regions) and were of bad quality (hemolysis/impurities). Furthermore, all positive samples came from areas with suboptimal climate for soft ticks. For this reason, false positive reactions are likely.
Conclusion
In conclusion, the study did not provide stringent evidence for soft tick-wild boar contact in the investigated German Federal States and thus, a relevant involvement in the epidemiology of ASF in German wild boar is unlikely. This fact would facilitate the eradication of ASF in the area, although other complex relations (wild boar biology and interactions with domestic pigs) need to be considered.
doi:10.1186/s12917-015-0629-9
PMCID: PMC4698789  PMID: 26728767
African swine fever; Transmission cycles; Wild boar; Ornithodoros erraticus; Tick saliva antigen; ELISA
18.  Genetic characterization and phylogeography of the wild boar Sus scrofa introduced into Uruguay 
Genetics and Molecular Biology  2011;34(2):329-337.
The European wild boar Sus scrofa was first introduced into Uruguay, in southern South America during the early decades of the last century. Subsequently, and starting from founder populations, its range spread throughout the country and into the neighbouring Brazilian state Rio Grande do Sul. Due to the subsequent negative impact, it was officially declared a national pest. The main aim in the present study was to provide a more comprehensive scenario of wild boar differentiation in Uruguay, by using mtDNA markers to access the genetic characterization of populations at present undergoing rapid expansion. A high level of haplotype diversity, intermediate levels of nucleotide diversity and considerable population differentiation, were detected among sampled localities throughout major watercourses and catchment dams countrywide. Phylogenetic analysis revealed the existence of two different phylogroups, thereby reflecting two deliberate introduction events forming distantly genetic lineages in local wild boar populations. Our analysis lends support to the hypothesis that the invasive potential of populations emerge from introgressive hybridization with domestic pigs. On taking into account the appreciable differentiation and reduced migration between locales in wild boar populations, management strategies could be effective if each population were to be considered as a single management unit.
doi:10.1590/S1415-47572011005000015
PMCID: PMC3115331  PMID: 21734838
Uruguayan wild boar
19.  Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations 
Ecology and Evolution  2015;5(19):4389-4399.
Abstract
Captive management of ex situ populations of endangered species is traditionally based on pedigree information derived from studbook data. However, molecular methods could provide a powerful set of complementary tools to verify studbook records and also contribute to improving the understanding of the genetic status of captive populations. Here, we compare the utility of single nucleotide polymorphisms (SNPs) and microsatellites (MS) and two analytical methods for assigning parentage in ten families of captive African penguins held in South African facilities. We found that SNPs performed better than microsatellites under both analytical frameworks, but a combination of all markers was most informative. A subset of combined SNP (n = 14) and MS loci (n = 10) provided robust assessments of parentage. Captive or supportive breeding programs will play an important role in future African penguin conservation efforts as a source of individuals for reintroduction. Cooperation among these captive facilities is essential to facilitate this process and improve management. This study provided us with a useful set of SNP and MS markers for parentage and relatedness testing among these captive populations. Further assessment of the utility of these markers over multiple (>3) generations and the incorporation of a larger variety of relationships among individuals (e.g., half‐siblings or cousins) is strongly suggested.
doi:10.1002/ece3.1600
PMCID: PMC4667824  PMID: 26819703
African penguin; ex situ populations; exclusion‐based paternity; pedigree
20.  Hybrid origin of European commercial pigs examined by an in-depth haplotype analysis on chromosome 1 
Frontiers in Genetics  2015;5:442.
Although all farm animals have an original source of domestication, a large variety of modern breeds exist that are phenotypically highly distinct from the ancestral wild population. This phenomenon can be the result of artificial selection or gene flow from other sources into the domesticated population. The Eurasian wild boar (Sus scrofa) has been domesticated at least twice in two geographically distinct regions during the Neolithic revolution when hunting shifted to farming. Prior to the establishment of the commercial European pig breeds we know today, some 200 years ago Chinese pigs were imported into Europe to improve local European pigs. Commercial European domesticated pigs are genetically more diverse than European wild boars, although historically the latter represents the source population for domestication. In this study we examine the cause of the higher diversity within the genomes of European commercial pigs compared to their wild ancestors by testing two different hypotheses. In the first hypothesis we consider that European commercial pigs are a mix of different European wild populations as a result of movement throughout Europe, hereby acquiring haplotypes from all over the European continent. As an alternative hypothesis, we examine whether the introgression of Asian haplotypes into European breeds during the Industrial Revolution caused the observed increase in diversity. By using re-sequence data for chromosome 1 of 136 pigs and wild boars, we show that an Asian introgression of about 20% into the genome of European commercial pigs explains the majority of the increase in genetic diversity. These findings confirm that the Asian hybridization, that was used to improve production traits of local breeds, left its signature in the genome of the commercial pigs we know today.
doi:10.3389/fgene.2014.00442
PMCID: PMC4283659  PMID: 25601878
Sus scrofa; hybridization; domestication; introgression; genetic variation; haplotype homozygosity
21.  Controlling of CSFV in European wild boar using oral vaccination: a review 
Classical swine fever (CSF) is among the most detrimental diseases for the swine industry worldwide. Infected wild boar populations can play a crucial role in CSF epidemiology and controlling wild reservoirs is of utmost importance for preventing domestic outbreaks. Oral mass vaccination (OMV) has been implemented to control CSF in wild boars and limit the spill over to domestic pigs. This retrospective overview of vaccination experiences illustrates the potential for that option. The C-strain live vaccine was confirmed to be highly efficacious and palatable baits were developed for oral delivery in free ranging wild boars. The first field trials were performed in Germany in the 1990’s and allowed deploying oral baits at a large scale. The delivery process was further improved during the 2000’s among different European countries. Optimal deployment has to be early regarding disease emergence and correctly designed regarding the landscape structure and the natural food sources that can compete with oral baits. OMV deployment is also highly dependent on a local veterinary support working closely with hunters, wildlife and forestry agencies. Vaccination has been the most efficient strategy for CSF control in free ranging wild boar when vaccination is wide spread and lasting for a sufficient period of time. Alternative disease control strategies such as intensified hunting or creating physical boundaries such as fences have been, in contrast, seldom satisfactory and reliable. However, monitoring outbreaks has been challenging during and after vaccination deployment since OMV results in a low probability to detect virus-positive animals and the live-vaccine currently available does not allow serological differentiation of infected from vaccinated animals. The development of a new marker vaccine and companion test is thus a promising option for better monitoring outbreaks during OMV deployment as well as help to better determine when to stop vaccination efforts. After rabies in red fox, the use of OMV against CSF in European wild boar can be considered as a second example of successful disease control in wildlife. The 30 years of disease control experience included in this review may provide options for improving future disease management within wild populations.
doi:10.3389/fmicb.2015.01141
PMCID: PMC4615961  PMID: 26557109
Pestivirus; wildlife; diseases; management; surveillance; Sus scrofa
22.  Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape 
PLoS Genetics  2012;8(11):e1003100.
Inbreeding has long been recognized as a primary cause of fitness reduction in both wild and domesticated populations. Consanguineous matings cause inheritance of haplotypes that are identical by descent (IBD) and result in homozygous stretches along the genome of the offspring. Size and position of regions of homozygosity (ROHs) are expected to correlate with genomic features such as GC content and recombination rate, but also direction of selection. Thus, ROHs should be non-randomly distributed across the genome. Therefore, demographic history may not fully predict the effects of inbreeding. The porcine genome has a relatively heterogeneous distribution of recombination rate, making Sus scrofa an excellent model to study the influence of both recombination landscape and demography on genomic variation. This study utilizes next-generation sequencing data for the analysis of genomic ROH patterns, using a comparative sliding window approach. We present an in-depth study of genomic variation based on three different parameters: nucleotide diversity outside ROHs, the number of ROHs in the genome, and the average ROH size. We identified an abundance of ROHs in all genomes of multiple pigs from commercial breeds and wild populations from Eurasia. Size and number of ROHs are in agreement with known demography of the populations, with population bottlenecks highly increasing ROH occurrence. Nucleotide diversity outside ROHs is high in populations derived from a large ancient population, regardless of current population size. In addition, we show an unequal genomic ROH distribution, with strong correlations of ROH size and abundance with recombination rate and GC content. Global gene content does not correlate with ROH frequency, but some ROH hotspots do contain positive selected genes in commercial lines and wild populations. This study highlights the importance of the influence of demography and recombination on homozygosity in the genome to understand the effects of inbreeding.
Author Summary
Small populations have an increased risk of inbreeding depression due to a higher expression of deleterious alleles. This can have major consequences for the viability of these populations. In domesticated species like the pig that are artificially selected in breeding populations, but also in wild populations that experience habitat decline, maintaining genetic diversity is essential. Recent advances in sequence technology enabled us to identify patterns of nucleotide variation in individual genomes. We screened the full genome of wild boars and commercial pigs from Eurasia for regions of homozygosity. We found these regions of homozygosity were caused by the demographic history and effective population size of the pigs. European wild boars are least variable, but also European breeds contain large homozygous stretches in their genome. Moreover, the likelihood of a region becoming depleted depends on its position in the genome, because variation has a high correlation with recombination rate. The telomeric regions are much more variable, and the central region of chromosomes has a higher chance of containing long regions of homozygosity. These findings increase knowledge on the fine-scaled architecture of genomic variation, and they are particularly important for population genetic management.
doi:10.1371/journal.pgen.1003100
PMCID: PMC3510040  PMID: 23209444
23.  Analytical and statistical consideration on the use of the ISAG-ICAR-SNP bovine panel for parentage control, using the Illumina BeadChip technology: example on the German Holstein population 
Background
Parentage control is moving from short tandem repeats- to single nucleotide polymorphism (SNP) systems. For SNP-based parentage control in cattle, the ISAG-ICAR Committee proposes a set of 100/200 SNPs but quality criteria are lacking. Regarding German Holstein-Friesian cattle with only a limited number of evaluated individuals, the exclusion probability is not well-defined. We propose a statistical procedure for excluding single SNPs from parentage control, based on case-by-case evaluation of the GenCall score, to minimize parentage exclusion, based on miscalled genotypes. Exclusion power of the ISAG-ICAR SNPs used for the German Holstein-Friesian population was adjusted based on the results of more than 25 000 individuals.
Results
Experimental data were derived from routine genomic selection analyses of the German Holstein-Friesian population using the Illumina BovineSNP50 v2 BeadChip (20 000 individuals) or the EuroG10K variant (7000 individuals). Averages and standard deviations of GenCall scores for the 200 SNPs of the ISAG-ICAR recommended panel were calculated and used to calculate the downward Z-value. Based on minor allelic frequencies in the Holstein-Friesian population, one minus exclusion probability was equal to 1.4×10−10 and 7.2×10−26, with one and two parents, respectively. Two monomorphic SNPs from the 100-SNP ISAG-ICAR core-panel did not contribute. Simulation of 10 000 parentage control combinations, using the GenCall score data from both BeadChips, showed that with a Z-value greater than 3.66 only about 2.5% parentages were excluded, based on the ISAG-ICAR recommendations (core-panel: ≥ 90 SNPs for one, ≥ 85 SNPs for two parents). When applied to real data from 1750 single parentage assessments, the optimal threshold was determined to be Z = 5.0, with only 34 censored cases and reduction to four (0.2%) doubtful parentages. About 70 parentage exclusions due to weak genotype calls were avoided, whereas true exclusions (n = 34) were unaffected.
Conclusions
Using SNPs for parentage evaluation provides a high exclusion power also for parent identification. SNPs with a low GenCall score show a high tendency towards intra-molecular secondary structures and substantially contribute to false exclusion of parentages. We propose a method that controls this error without excluding too many parent combinations from the evaluation.
Electronic supplementary material
The online version of this article (doi:10.1186/s12711-014-0085-1) contains supplementary material, which is available to authorized users.
doi:10.1186/s12711-014-0085-1
PMCID: PMC4318447  PMID: 25651826
24.  Seroprevalence of porcine proliferative enteropathy among wild boars in the Republic of Korea 
Background
The importance of the wild boar as a reservoir of Lawsonia intracellularis was assessed by investigating the seroprevalence of this pathogen among wild boars in the Republic of Korea. The extent of exposure to L. intracellularis among wild boars (Sus scrofa coreanus) was monitored by a country-wide serological survey using an immunoperoxidase monolayer assay.
Results
In this study, antibodies to L. intracellularis were observed in 165 of 716 clinically healthy wild boars tested. The overall apparent prevalence calculated directly from the sample and the true prevalence calculated based on the accuracy of the test method were 23.0% (95% confidence interval: 20.0-26.3%) and 25.6% (95% confidence interval: 23.9-27.2%), respectively. Serologically positive animals were found in all the tested provinces.
Conclusions
Our results confirm that L. intracellularis is present in the wild boar population worldwide, even in Far East Asia. Despite the high seroprevalence shown in wild boars, further studies are warranted to evaluate their potential as a reservoir species because seroprevalence does not prove ongoing infection nor shedding of the bacteria in amounts sufficient to infect other animals. It should also be determined whether the wild boar, like the domestic pig, is a natural host of L. intracellularis.
doi:10.1186/1746-6148-10-5
PMCID: PMC3883484  PMID: 24393381
Lawsonia intracellularis; Serology; Wild boar
25.  Risk factors for contacts between wild boar and outdoor pigs in Switzerland and investigations on potential Brucella suis spill-over 
Background
Due to the parallel increase of the number of free-ranging wild boar and domestic pigs reared outdoor, the risk that they interact has become higher. Contacts with wild boar can be the origin of disease outbreaks in pigs, as it has been documented for brucellosis in some European countries. This study aimed at quantifying the occurrence of contacts between wild boar and outdoor domestic pigs in Switzerland, and identifying risk factors for these contacts. Furthermore, exposed pigs were tested for pathogen spill-over, taking Brucella suis as an example because B. suis is widespread in Swiss wild boar while domestic pigs are officially free of brucellosis.
Results
Thirty-one percent of the game-wardens and 25% of the pig owners participating to a country-wide questionnaire survey reported contacts, including approaches of wild boar outside the fence, intrusions, and mating. Seventeen piggeries (5%) reported the birth of cross-bred animals. Risk factors for contacts identified by a uni- and multivariable logistic regression approach were: distance between pigs enclosure and houses, proximity of a forest, electric fences, and fences ≤ 60 cm. Pigs of the Mangalitza breed were most at risk for mating with wild boar (births of cross-bred animals). Blood and tissues of 218 outdoor pigs from 13 piggeries were tested for an infection with Brucella suis, using rose bengal test, complement fixation test, and an IS711-based real-time PCR. One piggery with previous wild boar contacts was found infected with B. suis, however, epidemiological investigations failed to identify the direct source of infection.
Conclusions
Results show that interactions between wild boar and outdoor pigs are not uncommon, pointing at the existing risk of pathogen spill-over. Provided data on risk factors for these interactions could help the risk-based implementation of protection measures for piggeries. The documentation of a brucellosis outbreak in pigs despite the freedom-of-disease status underlines the importance of improving pathogen surveillance strategies and increasing disease awareness of farmers and veterinary practitioners.
doi:10.1186/1746-6148-8-116
PMCID: PMC3464720  PMID: 22817843
Brucella suis; Brucellosis; Interactions; Outdoor pigs; Risk factors; Spill-over; Wild boar

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