DNA single nucleotide polymorphism analysis for differentiation of Sus scrofa scrofa and Sus scrofa domesticus

Objective: to develop a new model for differentiating between domestic pigs and wild boars based on autosomal SNP analysis, thereby improving the accuracy of species identification.
Materials and Methods: using the SRA-BLAST and GENIS bioinformatics algorithms, 1,639 genomes were analyzed: 91 wild boar (Sus scrofa scrofa) and 1,548 domestic pig (Sus scrofa domesticus). The differentiating potential of the studied polymorphisms was assessed, and a classification model for wild boar and domestic pig was calculated based on three SNPs (Sscrofa11.1 (GCF_000003025.6)): rs330419406 (Chr.5:55839440A>G), rs81293059 (Chr.8:52261272C>T), and rs326780270 (Chr.1:265347265A>G, NR6A1).
Conclusion. The model demonstrated high accuracy (99,84 %), specificity (100 %), and sensitivity (100 %). The model was successfully tested on a sample of 95 wild boars and 95 domestic pigs, with classification accuracy reaching 100 %. Testing on DNA from wild boar and domestic pigs confirmed the high discriminatory potential of the proposed polymorphisms. Of 190 samples, 100 % were correctly classified. Since the genetic similarity between wild boar and domestic pigs reaches 99 %, specialized methods and genetic markers are necessary for reliable differentiation of their samples, highlighting the particular importance of our developed model for precision scientific research.

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