Cloning and characterization of 414 polymorphic porcine microsatellites

Identifying a hunter responsible for killing a hunting dog by individual-specific genetic profiling of wild boar DNA transferred to the canine during the accidental shooting

While genetic profiling can be a powerful tool to solve wildlife crime, comparably few examples of individual identification in wildlife forensics are available in the literature. Here, we report a case of an accidental shooting of a hunting dog during a wild boar drive hunt. The market value of trained hunting dogs can reach several thousand euro. No one admitted to killing the dog. Wild boar hairs were found in the dog's wound, suggesting that the bullet first hit a wild boar and then the dog. Since it was known who harvested each boar, we aimed to use individual-specific genetic profiles to link these hairs to a bagged animal and to identify the culprit. We genotyped 19 harvested boar and the unknown hair sample using 13 STRs. In the case of the hair sample, we performed multiple genotyping to ensure the reliability of the genetic profile. We showed that we genotyped sufficient loci to distinguish between separate individuals with certainty. While the three most informative loci were enough to differentiate the 19 reference individuals, we did find a perfect match at all 13 STRs between the hair DNA and one tissue sample. Since our methods were reliable and reproducible, we passed the relevant information on to forestry officials who will use the information we have provided to attempt to find an amicable solution.

Multiple Origins and Admixture of Recently Expanding Japanese Wild Boar (Sus scrofa leucomystax) Populations in Toyama Prefecture of Japan

Japanese wild boar (Sus scrofa leucomystax) populations have expanded drastically throughout the Japanese Archipelago in recent decades. To elucidate the dispersal patterns of Japanese wild boar in Toyama Prefecture in central Japan, we used a multi-locus microsatellite DNA analysis to determine its population structure and the degree of admixture. The deviation from Hardy-Weinberg equilibrium was detected in either total or separate regional wild boar samples from Toyama Prefecture. This result could be explained by the Wahlund effect resulting from the mixture of samples from different sources. Bayesian structure analysis, assignment test, and factorial correspondence analysis suggested that wild boars around Toyama Prefecture derive from at least two ancestral sources. The migration and possible mating of each individual may have occurred recently and continued in each geographically neighboring region. The present genetic results may be useful for prediction of future dispersal patterns of Japanese wild boar, as well as other animals in expansion.

Feral pig populations are structured at fine spatial scales in tropical Queensland, Australia

Feral pigs occur throughout tropical far north Queensland, Australia and are a significant threat to biodiversity and World Heritage values, agriculture and are a vector of infectious diseases. One of the constraints on long-lasting, local eradication of feral pigs is the process of reinvasion into recently controlled areas. This study examined the population genetic structure of feral pigs in far north Queensland to identify the extent of movement and the scale at which demographically independent management units exist. Genetic analysis of 328 feral pigs from the Innisfail to Tully region of tropical Queensland was undertaken. Seven microsatellite loci were screened and Bayesian clustering methods used to infer population clusters. Sequence variation at the mitochondrial DNA control region was examined to identify pig breed. Significant population structure was identified in the study area at a scale of 25 to 35 km, corresponding to three demographically independent management units (MUs). Distinct natural or anthropogenic barriers were not found, but environmental features such as topography and land use appear to influence patterns of gene flow. Despite the strong, overall pattern of structure, some feral pigs clearly exhibited ancestry from a MU outside of that from which they were sampled indicating isolated long distance dispersal or translocation events. Furthermore, our results suggest that gene flow is restricted among pigs of domestic Asian and European origin and non-random mating influences management unit boundaries. We conclude that the three MUs identified in this study should be considered as operational units for feral pig control in far north Queensland. Within a MU, coordinated and simultaneous control is required across farms, rainforest areas and National Park Estates to prevent recolonisation from adjacent localities.

Monitoring wild pig populations: a review of methods

Wild pigs (Sus scrofa) are widespread across many landscapes throughout the world and are considered to be an invasive pest to agriculture and the environment, or conversely a native or desired game species and resource for hunting. Wild pig population monitoring is often required for a variety of management or research objectives, and many methods and analyses for monitoring abundance are available. Here, we describe monitoring methods that have proven or potential applications to wild pig management. We describe the advantages and disadvantages of methods so that potential users can efficiently consider and identify the option(s) best suited to their combination of objectives, circumstances, and resources. This paper offers guidance to wildlife managers, researchers, and stakeholders considering population monitoring of wild pigs and will help ensure that they can fulfill their monitoring objectives while optimizing their use of resources.

Development of a microsatellite-based method for the differentiation of European wild boar (Sus scrofa scrofa) from domestic pig breeds (Sus scrofa domestica) in food

Twenty microsatellites (simple sequence repeats, SSR) were used to discriminate wild boar from domestic pig and to identify mixtures of the two. Reference groups of wild boar and pig samples were collected from the UK and Europe for genetic assignment tests. Bayesian Analysis of Populations software (BAPs) gave 100% correct assignment for blind wild boar and pig samples and correctly identified mixed samples. DNA was extracted from 12 commercial food samples (11 labeled as containing wild boar) including patés, salamis, and sausage, and good SSR profiles were obtained. Eleven samples were correctly assigned as pig, and two as mixed meats. One sample sold as wild boar meat was clearly assigned as pig. A further 10 blind samples of meat cuts were analyzed, eight wild boar and two pig, and all were correctly assigned.

Genetic structure of pig breeds from Korea and China using microsatellite loci analysis

To understand molecular genetic characteristics of Korean pigs, the genetic relationships of nine pig breeds including two Korean pigs (Korean native pig and Korean wild pig), three Chinese pigs (Min pig, Xiang pig, and Wuzhishan pig), and four European breeds (Berkshire, Duroc, Landrace, and Yorkshire) were characterized from a 16-microsatellite loci analysis. The mean heterozygosity within breeds ranged from 0.494 to 0.703. Across multiple loci, significant deviation from Hardy-Weinberg equilibrium was observed in most pig breeds, except for two Chinese pigs (Min pig and Wuzhishan pig). This deviation was in the direction of heterozygote deficit. Across population loci, 36 of 144 significantly deviated (P < 0.05) from Hardy-Weinberg equilibrium. The mean FST, a measure of genetic divergence among subpopulations, of all loci indicated that 26.1% of total variation could be attributed to the breed difference. Relationship trees based on the Nei's DA genetic distance and scatter diagram from principal component analysis consistently displayed pronounced genetic differentiation among the Korean wild pig, Xiang pig, and Wuzhishan pig. Individual assignment test using a Bayesian method showed 100% success in assigning Korean and Chinese individual pigs into their correct breeds of origin and 100% exclusion success from all alternative reference populations at P < 0.001. These findings indicate that the Korean native pig has been experiencing progressive interbreeding with Western pig breeds after originating from a North China pig breed with a black coat color. Considering the close genetic relationship of Korean pigs to the Western breeds such as Berkshire and Landrace, our findings can be used as valuable genetic information for the preservation and further genetic improvement of the Korean native pig.

Porcine IL12A and IL12B gene mapping, variation and evidence of association with lytic complement and blood leucocyte proliferation traits

Interleukin-12, a heterodimeric cytokine consisting of glycosylated subunits of 35 and 40 kDa, is a central molecule in controlling innate as well as adaptive immunity. This study was aimed to investigate the role of IL12A and IL12B as candidate genes for immune competence in pigs. The porcine genes were screened for polymorphism and association analysis was carried out by mixed model analysis with parameters of innate immunity, in vitro haemolytic complement activity in the classical and alternative pathways, in vivo complement activation expressed as C3c serum concentration, and blood leucocyte proliferation measured in F2 animals of a pig resource population based on cross of Duroc and Berlin miniature pig (DUMI resource population). A single nucleotide polymorphism (SNP) in the promoter region (C > A) of IL12A was identified. Two SNPs were detected in intron 4 of IL12B at positions 192 (A > G) and 437 (C > T). Significant effects of IL12 genotypes on complement activity traits and mitogen-induced leucocyte proliferation were found. The IL12A and IL12B genes were assigned to chromosome13 and 16, respectively, by using radiation hybrid analysis and genetic mapping in the DUMI resource population. Mapping and association analyses promote the IL12 genes as functional and positional candidate gene for disease resistance in pigs.

Mapping of QTL on chromosome X for fat deposition, muscling and growth traits in a wild boar x Meishan F2 family using a high-density gene map

Quantitative trait loci (QTL) for fat deposition, growth and muscling traits have been previously mapped on the basis of low-density linkage maps in a wild boar x Meishan F2family to the chromosome X region flanked by SW2456 and SW1943. Improved QTL resolution was possible using data for F2 animals with a marker density of 2.7 cM distance in the SW2456 to SW1943 region, including AR, SERPINA7 and ACSL4 as candidate genes. The resolution of the QTL scan was increased substantially, as evidenced by the higher F-ratio values for all QTL. Maxima of F-ratio values for fat deposition, muscling and growth traits were 28.6, 18.2 and 16.5 respectively, and those QTL positions accounted for 7.9%, 5.0% and 4.5% of the F2 phenotypic variance (VF2) respectively. QTL for fatness and growth and for most muscling traits mapped near ACSL4, with the exception of the QTL for ham traits that mapped proximally, in the vicinity of AR. An analysis performed separately for F2 male animals showed the predominant QTL affecting fat deposition traits (up to 13.6% VF2) near AR and two QTL for muscling traits (up to 9.9% VF2) mapped close to ACSL4. In the F2 female animals, QTL affecting muscling (up to 12.1% VF2) mapped at ACSL4 and SW2456, and QTL for fat deposition (10% VF2) and growth (up to 10.5% VF2) mapped at ACSL4.

Mapping of quantitative trait loci affecting resistance/susceptibility to Sarcocystis miescheriana in swine

The outcome of infectious diseases in vertebrates is under genetic control at least to some extent. In swine, e.g., marked differences in resistance/susceptibility to Sarcocystis miescheriana have been shown between Chinese Meishan and European Pietrain pigs, and these differences are associated with high heritabilities. A first step toward the identification of genes and polymorphisms causal for these differences may be the mapping of quantitative trait loci (QTLs). Considering clinical, immunological, and parasitological traits in the above model system, this survey represents the first QTL study on parasite resistance in pigs. QTL mapping was performed in 139 F(2) pigs of a Meishan/Pietrain family infected with S. miescheriana. Fourteen genome-wide significant QTLs were mapped to several chromosomal areas. Among others, major QTLs were identified for bradyzoite numbers in skeletal muscles (F = 17.4; p < 0.001) and for S. miescheriana-specific plasma IgG(2) levels determined 42 days p.i. (F = 20.9; p < 0.001). The QTLs were mapped to different regions of chromosome 7, i.e., to the region of the major histocompatibility complex (bradyzoites) and to an immunoglobulin heavy chain cluster, respectively. These results provide evidence for a direct and causal role for gene variants within these gene clusters (cis-acting) in differences in resistance to S. miescheriana.

Cloning, mapping and association study with carcass traits of the porcine SDHD gene

A 1320-bp cDNA containing the full coding region of the porcine succinate dehydrogenase complex, subunit D (SDHD) gene was obtained by random sequencing of clones from a Chinese Tongcheng pig 55-day fetal longissimus dorsi muscle cDNA library. Analysis of the SDHD gene across the INRA-University of Minnesota porcine radiation hybrid panel indicated close linkage with microsatellite marker SW2401, located on SSC9p21. The open reading frame of this cDNA covers 480 bp and encodes 159 amino acids. The deduced porcine amino acid sequence showed greater similarity with human and bovine protein sequences than with those from mouse and rat. The BLAST analysis of the porcine SDHD to NCBI identified Unigene Cluster Ssc.2586. Possible single nucleotide polymorphisms (SNP) were identified by alignment of expressed sequence tags in the cluster. The polymerase chain reaction (PCR) single strand conformation polymorphism, sequencing, and PCR restriction fragment length polymorphism were used to confirm and detect a synonymous polymorphic MboI site within the open-reading frame. Allele frequencies of this SNP were investigated in two commercial and five Chinese local pig breeds. These five Chinese breeds had very high frequencies for one allele, whereas frequencies of both alleles were intermediate in Large White and Duroc. An association analysis suggested that different SDHD genotypes have significant differences in loin-muscle area (P < 0.01).

Successful production of piglets derived from vitrified morulae and early blastocysts using a microdroplet method

This study was conducted to determine the efficiency of vitrification using the microdroplet (MD) method for early stage porcine embryos. Embryos at compacted morulae to early blastocyst stage were vitrified in a vitrification solution containing 40% (v/v) ethylene glycol, 0.6M sucrose and 2% (w/v) polyethylene glycol in M2 (ESP) without any pretreatment. The equilibration and dilution were carried out in third and fourth steps, respectively, at 38 degrees C. The survivability of the cryopreserved embryos was assessed for both in vitro culture (Experiment 1) and by embryo transfer (Experiment 2). In Experiment 1, the embryos were vitrified within a microdroplet or 0.25 ml straw (ST) and fresh embryos were used as a control group. The survival rates after 24h culture in the MD, ST and control groups were 21/23, 14/20 and 20/20, respectively. The hatching rates of the embryos after 48 h incubation were 14/23, 4/20 and 16/20, respectively. In Experiment 2, 171 vitrified embryos were transferred to 5 recipient gilts, and 17 healthy piglets were produced from 2 recipients (3 recipients aborted) in Group 1. In Group 2, 81 vitrified embryos and 16 fresh embryos in total were transferred to 4 recipient gilts, and 10 healthy piglets from the vitrified embryos were produced from 3 recipients. These results indicated that porcine embryos of compacted morulae to early blastocyst stage can survive cryopreservation using the microdroplet method without any special intracellular manipulation or treatment.

The genetic impact of demographic decline and reintroduction in the wild boar (Sus scrofa): a microsatellite analysis

The reintroduction of wild boar from central Europe after World War II has contributed substantially to the range expansion of this species in Italy, where indiscriminate hunting in earlier times resulted in extreme demographic reduction. However, the genetic impact of such processes is not well-understood. In this study, 105 individuals from Italian and Hungarian wild boar populations were characterized for nine autosomal microsatellite loci. The Hungarian samples, and two central Italian samples from protected areas (parks) where reintroduction is not documented, were assumed to be representative of the genetic composition of the source and the target populations in the reintroduction process, respectively. Animals hunted in the wild in the Florence area of Tuscany (Italy) were then studied to identify the effects of reintroduction. The results we obtained can be summarized as follows: (i) none of the populations analysed shows genetic evidence of demographic decline; (ii) the three parental populations from Italy and Hungary are genetically distinct; however, the low level of divergence appears in conflict with the naming of the Italian and the European subspecies (Sus scrofa majori and Sus scrofa scrofa, respectively); in addition, the Italian groups appear to be as divergent from each other as they are from the Hungarian population; (iii) most of the individuals hunted near Florence are genetically intermediate between the parental groups, suggesting that hybridization has occurred in this area, the average introgression of Hungarian genotypes is 13%, but approximately 45% of the genetic pool of these individuals can not be directly attributed to any of the parental populations we analysed; (iv) analysis of microsatellite loci, though in a limited number, is an important tool for estimating the genetic effect of reintroduction in the wild boar, and therefore for the development of conservation and management strategies for this species.

Mapping microsatellite markers identified in porcine EST sequences

A sequence search of swine expressed sequence tags (EST) data in GenBank identified over 100 sequence files which contained a microsatellite repeat or simple sequence repeat (SSR). Most of these repeat motifs were dinucleotide (CA/GT) repeats; however, a number of tri-, tetra-, penta- and hexa-nucleotide repeats were also detected. An initial assessment of six dinucleotide and 14 higher-order repeat markers indicated that only dinucleotide markers yielded a sufficient number of informative markers (100% vs. 14% for dinucleotide and higher order repeats, respectively). Primers were designed for an additional 50 di- and one tri-nucleotide SSRs. Overall, 42 markers were polymorphic in the US Meat Animal Research Center (MARC) reference population, 17 markers were uninformative and 12 primer pairs failed to satisfactorily amplify genomic DNA. A comparison of di-nucleotide repeat vs. markers with repeat motifs of three to six bases demonstrated that 72% of dinucleotide markers were informative relative to only 7% of other repeat motifs. The difference was the result of a much higher percentage of monomorphic markers in the three to six base repeat motif markers than in the dinucleotide markers (64% vs. 14%). Either higher order repeat motifs are less polymorphic in the porcine genome or our selection criteria for repeat length of more than 17 contiguous bases was too low. The mapped microsatellite markers add to the porcine genetic map and provide valuable links between the porcine and human genome.

Ordering three microsatellites on porcine chromosome 12 by single sperm typing

Three microsatellite loci on porcine chromosome 12 were ordered by single sperm typing to expand the limited genetic map of this region. Individual sperm cells from a Chinese indigenous Qingping boar triply heterozygous at SW874, SW1350 and SW1553 were amplified using PEP and heminesting primer design at each locus. Analysis of the sperm typing data by the SPERM.FOR program showed that the most likely order was SW1553-SW1350-SW874.