Matching STR and SNP genotyping to discriminate between wild boar, domestic pigs and their recent hybrids for forensic purposes

Abstract

the genetic discrimination between phylogenetically close taxa can be challenging if their gene pools are not differentiated and there are many shared polymorphisms. The gene flow between wild boar (Sus scrofa) and domestic pig (S. s. domesticus) has never been interrupted from domestication onwards, due to non-stop natural and human-mediated crossbreeding. To date there are no individual genetic markers that are able to distinguish between the two forms, nor even to identify effectively their hybrids. We developed a combined molecular protocol based on multiplex porcine-specific STR-profiling system and new real time pcR-based assays of single polymorphisms in the NR6A1 and MC1R genes to gain high diagnostic power in the differentiation of wild boar, pig and hybrids for forensic purposes. The combined approach correctly assigned individuals to one or the other parental gene pool and identified admixed genotypes. Evidence was found for substantial reduction of false negative results by using multiple marker systems jointly, compared to their use individually. Our protocol is a powerful and costeffective diagnostic tool that can easily be adopted by most forensic laboratories to assist authorities contrast food adulteration, assure veterinary public health and fight against wildlife crimes, like poaching and illegal detention of wild animals.

Comparative Pathology of Domestic Pigs and Wild Boar Infected with the Moderately Virulent African Swine Fever Virus Strain “Estonia 2014”

“…Different clinical signs, immunological responses, and pathological outcomes are also known for highly pathogenic porcine reproductive and respiratory syndrome virus infection in wild boar and domestic pigs [ 32 ]. So far, genetic discrimination between domestic pigs and wild boar has been challenging since there have been only few genetic markers identified to distinguish between domestic pigs and wild boar [ 33 ], and even immunogenetic investigation of domestic pigs and wild boar could not identify any statistically significant differences in allele frequency and heterozygosity across SNPs [ 34 ]. However, very recently SLA-1 diversity was investigated in different domestic pig breeds showing significant distribution of SLA-1 alleles among pig breeds which could explain differences in the immune response [ 35 ].…”

NR6A1Allelic Frequencies as an Index for both Miniaturizing and Increasing Pig Body Size

“…The NR6A1 gene, encoding an orphan nuclear receptor, is located in a 300-kb region that is fixed in a variety of European commercial breeds (Landrace, LW, Yorkshire, Duroc, and Berkshire) (1). This gene has been focused on as a means of controlling economically important traits in the swine market or as a tool to discriminate between wild boar and domestic pigs (19,27,28). We found that the Microminipig was homozygous for the NR6A1 C/C genotype, with a vertebrae number of lower than the 19 vertebrae uniformly found in wild boar (3,23).…”

Combination of Multiple Microsatellite Analysis and Genome-Wide SNP Genotyping Helps to Solve Wildlife Crime: A Case Study of Poaching of a Caucasian tur (Capra caucasica) in Russian Mountain National Park

“…A combination of the mitochondrial Cytochrome-b gene ( Cyt-b ) with 12 microsatellite loci was beneficial and allowed a successful investigation of poaching of the Cypriot mouflon ( Ovis orientalis ophion ), wherein three shot mouflon were discovered, and bloodstained items were seized from a suspect’s vehicle [ 5 ]. Use of a porcine-specific STR system and real time PCR-based assays of single nucleotide polymorphisms in the NR6A1 and MC1R genes was proposed for discrimination of wild boars from domestic pigs, and validated for forensic purposes [ 7 ].…”