Comparison and differential expression of immune system genes of indigenous and commercial poultry by RNA Seq analysis

The immune system plays a key role in the health maintenance and pathogenesis of a wide range of diseases. The avian immune system is divided into two types of immunity innate and adaptive. Innate immunity is considered the first line of defense and lacks specificity, protecting against multiple types of pathogens. Recently, next-generation sequencing technology (RNA-Seq) has become available as a powerful tool to investigate transcriptional profiles for gene expression analysis of many organisms. The main use of RNA-Seq in agriculture species is focusing on finding the immune-related genes or pathways by comparison of the whole transcriptome following pathogen challenge. Disease control and prevention was a critical factor in the dramatic growth of the poultry industry. This study used RNA sequencing to comparison transcripts of two breeds. The results of the transcriptome study revealed 1327, 310, 759, and 258 differential expressed (DE) genes, isoforms, transcription start sites (TSS), and coding sequences (CDS), respectively. Among 18 pathways was significantly different, Natural killer cell-mediated cytotoxicity, Cytokine-cytokine receptor interaction, Toll-like receptor signaling pathway, Jak-STAT signaling pathway, and Apoptosis related to partial innate immune. In the gene networking of the immune system, the PTPN6 gene which exists in most of the innate immune system pathways and related to many genes is considered a key gene in this network. SYK and VAV3 related to Natural Killer Cell, MAPK11 and MAPK12 related to Toll-like receptor signaling pathway play an important role in the innate immune system. These genes have been associated with other genes that determined their highly interaction with other pathways.