Cis-eQTL analysis reveals genes involved in biological processes of the immune system in Nelore cattle

•Cis-eQTLs are predominantly found in intronic and intergenic regions.•eQTLs were linked to genes involved in susceptibility and resistance to infections.•eGenes play a critical role in negatively regulating the NF-κB pathway. The combination of transcriptional profiling and genotype data analyses enables the identification of genetic variants that may affect gene expression (eQTL – expression quantitative trait loci). This study aimed to identify cis-eQTL in Nellore cattle muscle tissue and determine their biological processes related to the immune system and involved eGenes. Genotypic data (SNP-Chip) and gene expression data (RNA-Seq) from a commercial population of 80 Nellore animals were evaluated. For the cis-eQTL identification, association tests were conducted for all variants near the gene (cis variants), followed by permutation tests to correct for multiple comparisons. Our analyses revealed 828 top cis-eQTL related to 1,062 genes of which most of these variants were in intronic and intergenic regions. The eQTLs rs109525554, rs109589165, rs110192253, rs133127698, rs137742430, rs41803313, rs43366333, and rs43711242 were associated with susceptibility and resistance to infections in cattle. Additionally, interferon family eGenes, such as IFNT3, IFN-TAU, IFNK, FYN, and IFNW1, and endothelial leukocyte migration, such as PRKCG and CXCL10 were found. These eGene families were linked to biological processes of innate and adaptive immune responses and associated with somatic cell scores in cattle, respectively. Our results may have implications for selecting desirable resistance traits in animals bred for production and highlight the importance of studying genetic variants involved in quantitative traits to improve our understanding of genetic mechanisms underlying gene expression regulation of adaptive traits in cattle.