Copy number variation within CLEC4E locus as a molecular tool for distinguishing DNA from domestic pigs and wild boars

Wild boar, the primary wild ancestor of the domestic pig, frequently interbreeds with its domesticated counterpart. Distinguishing between the domestic pig (Sus scrofa domestica), wild boar (Sus scrofa), and their hybrids is ambitious due to their close evolutionary relationship and the various genetic markers they have in common. The aim of the study was to develop a reliable and straightforward method to distinguish pig and wild boar DNA based on CNV in the CLEC4E gene, preventing food fraud and ensuring product safety.

The study population consisted of domestic pigs (n=42), wild boars (n=40) and their hybrids (n=6). The domestic pig group is comprised of four breeds: Polish Large White, Duroc, Polish Landrace and Puławska. Wild boars were sampled from the South West region of Poland. The pair of primers (F/R) designed for the CLEC4E gene were used for analysis. A quantitative-comparative CT reaction with a melting curve (SybrGreen) was performed for the tested samples.

The obtained results indicate different CT values for pigs and wild boars. The CT values below 18.70 cycles and melting temperature equal or above 90°C indicate wild origin, while the CT below 17.67, and melting temperature lower than 89.20°C additionally supported by the shape of the melting curve, indicate the presence of a domestic pig or hybrid. The analysis of 85 out of 88 tested samples, supported the assumptions based on the CT value, while for the remaining 3 the result was doubtful due to inconsistent interpretation for CT and / or Tm.