Comparison of Skin Tissue Gene Expression Between Tick-Susceptible and Tick-Resistant Cattle Using Transcriptomics Data

Tick infestation is one of the major challenges facing the livestock industry. The present study aimed to identify key differentially expressed genes (DEGs) and perform gene ontology (GO) analysis between two groups of tick-resistant and tick-susceptible cattle using RNA-sequencing (RNA-seq) data from skin tissue (10 samples in two groups, with 5 biological replicates each). Cattle were classified into resistant and susceptible groups based on the number of adult female ticks attached to the animal’s body surface under natural infestation conditions. Preprocessing, alignment, and differential expression analysis of the reads were performed using FastQC, Trimmomatic, Hisat2, Samtools, and Cufflinks, respectively, while gene ontology analysis was carried out using the DAVID database. After quality control, and with an alignment rate to the reference genome exceeding 99.9%, 44 genes out of 37,820 annotated gene IDs were identified as significantly differentially expressed (q-value2 ultimately yielded 19 key candidate genes. The results of gene ontology and KEGG pathway analyses revealed the key genes such as MX2, ISG15, IFI27, RSAD2, CCL20, IL1B, and CXCL3 play essential roles in the innate immune response, interferon signaling pathway, regulation of inflammatory cytokines, apoptosis, and immune cell chemotaxis. In resistant breeds, the rapid, targeted, and controlled activation of these genes appears to prevent chronic inflammation and tissue damage at the bit site. The identified key interferon-responsive genes and cytokines (particularly ISG15, MX2, and IL1B) can be considered as molecular candidates for explaining the differential response of resistant and susceptible cattle to tick infestation.