STR Profiling for Discrimination between Wild and Domestic Swine Specimens and between Main Breeds of Domestic Pigs Reared in Belarus.

Krzysztof Rębała,Svetlana A. Kotova,Alla I. Gandzha,Viachaslau N. Kipen,Alina A. Rabtsava,Iosif S. Tsybovsky,Natalja V. Zhurina,Qin Zhang

doi:10.1371/journal.pone.0166563

Abstract

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.

Highlights

Discrimination between wild and farmed species of animals is of basic importance for assessment of food authenticity, its safety management, assurance of veterinary public health and forensic investigations of wildlife crimes [1,2], and usefulness of molecular genetics in this field is unquestionable [3,4,5]
The aim of the present study was to work out a method based on DNA analysis by polymerase chain reaction (PCR) and on statistical inference of genotypes by likelihood ratios (LRs) for simple discrimination between wild boars and domestic pigs as well as for individualisation of the tested porcine samples and their assignment to regional wild populations or to distinct domestic breeds reared in Belarus
analysis of molecular variance (AMOVA) of 16 tested STR markers did not detect any traces of genetic differentiation between unadmixed and admixed individuals from the Belarusian wild boar population (FST = –0.00207; P = 0.99475)

Summary

Introduction

Discrimination between wild and farmed species of animals is of basic importance for assessment of food authenticity, its safety management, assurance of veterinary public health and forensic investigations of wildlife crimes [1,2], and usefulness of molecular genetics in this field is unquestionable [3,4,5]. In Belarus, an Eastern European state with more than 9.4 million hectares of forests and with 39% forestation, wild boars used to be the most common game mammals, hunted both legally and illegally, with tens of thousands of individuals shot legitimately per year and an unknown number of poaching cases. Tons of wild boar meat were officially introduced to the market, carrying temptation of fraudulent substitution with cheaper domestic pork and the need for reliable speciation and traceability of meat products. Court proceedings of cases of illegal hunting often require species identification and individualisation of biological samples in order to provide indisputable evidence of a crime. Apart from simple species detection, individualisation and/or kinship analysis of porcine samples is essential for parentage control in animal husbandry and for investigation of thefts of livestock or meat products. The need for animal identification and traceability has been further boosted by the recent outbreak of African swine fever in Eastern Europe and the need to control the spread of the epidemic [7]

Objectives

Methods

Results

Conclusion