Application of open source tools for farm animals welfare

Farm animals represent the key source for human existence. As the other species, they are also attacked by bacterial pathogens and suffer by several diseases. We are focusing on mechanism of the innate immune response of sheep to bacterial infection caused by Corynebacterium pseudotuberculosis, the cause of caseous lymphadenitis disease. For this purpose, we have emploed ovine TLR2 gene long-range amplicon Next-Generation Sequencing (LRA-NGS), FastqQC R package for NGS data quality check, our bash tool kit SheepBam for SNP calling, Integrative Genomic Viewer (IGV) for genome loci visualization, Variant Effect Predictor (VEP) for SNP characterization, Phyre2.2 server for ovine TLR2.pdb protein structure file generation and Pymol open-source software for ovine TLR2 protein visualization. Using these techniques, we have demonstrated negative impact of identified SNP on TLR2 protein structure leading to decrease in ovine immune response against pathogen. These results could help to breed more resistant animals against Corynebacterium pseudotuberculosis infection.