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

<div><p>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 (<i>MC1R</i>) 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 <i>MC1R</i> 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.</p></div

Impact of the tested STR markers sorted in an ascending order of F_ST values on discrimination between wild boars and domestic pigs.

<p>Impact of the tested STR markers sorted in an ascending order of F_ST values on discrimination between wild boars and domestic pigs.</p

Geographic location of 6 administrative regions of Belarus, in which wild boar samples were collected (adapted from http://www.d-maps.com/carte.php?num_car=4238&lang=en), compared with a two-dimensional plot obtained from MDS based on pairwise F_ST values for 6 regional wild boar populations from Belarus and for 16 STR markers analysed in the study.

<p>Geographic location of 6 administrative regions of Belarus, in which wild boar samples were collected (adapted from <a href="http://www.d-maps.com/carte.php?num_car=4238&lang=en" target="_blank">http://www.d-maps.com/carte.php?num_car=4238&lang=en</a>), compared with a two-dimensional plot obtained from MDS based on pairwise F_ST values for 6 regional wild boar populations from Belarus and for 16 STR markers analysed in the study.</p

Comparison of the mean number of detected alleles, mean observed (Ho) and expected (He) heterozygosity as well as the number of statistically significant deviations from HWE at the tested loci in the studied swine populations.

<p>Comparison of the mean number of detected alleles, mean observed (Ho) and expected (He) heterozygosity as well as the number of statistically significant deviations from HWE at the tested loci in the studied swine populations.</p

Characterisation of DNA markers used in the study.

<p>Characterisation of DNA markers used in the study.</p