Trachea transcriptome analysis in SPF broiler chickens infected with avian infectious bronchitis

Avian infectious bronchitis (IB) is an acute and highly contagious disease of the upper-respiratory tract caused by the infectious bronchitis virus (IBV). The virus is a member of the Coronaviridae family and has numerous serotypes and strains. Rapid replication combined with high mutation rate and recombination are the main causes of the observed high diversity.Feed conversion and average daily gain are affected in broilers, and infection is often followed by secondary bacterial infections. In layers, IBV causes a reduction in egg production.Today, IB is one of the most economically important diseases in the poultry industry. Transcriptional profiles of trachea tissue of the infected group (IBV) were studied with control group to evaluate changes in transcriptome profile at the early stages of infection. After the challenge of SPF chickens with IBV IS-1494 like (GI-23, the trachea tissue was used for RNA extraction, and changes in the transcriptome were investigated by Illumina RNA-seq technique. Up-regulated and down-regulated differentially expressed genes (DEGs) in the transcriptome of trachea were identified. Gene ontology category, KEGG pathway were analyzed to identify relationships among differentially expressed genes. In general, the numbers of up-regulated genes were higher than of down-regulated genes in experimental group. In the experimental group, a more severe immune response occurred; an important up-regulated genes in this group’s was Toll-like receptor signaling pathway, apoptotic pathway, MAPK signaling pathway. Results of this study could provide a general overview of transcriptome changes in the trachea at the early stage of infection with avian infectious bronchitis (IBV) virus.