Comparative transcriptome analysis of Salmonella resistance in Beijing-You chickens and Guang Ming broilers

Background: Salmonella is a food-borne pathogen that can infect animals and humans. It is currently the most common bacterial pathogen that negatively affects poultry industry. Although different chicken breeds have been observed to exhibit diverse resistance to Salmonella infection, the underlying genetic mechanisms remain unclear and the genes involved in this differential disease resistance need to be identified. To overcome this knowledge gap, we used a liver transcriptome analysis to screen differentially expressed genes (DEGs) in two different chicken breeds (local Beijing You (BY) and commercial Guangming No. 2 broiler line B (GM)) before and after Salmonella infection. We also performed weighted gene co-expression network analysis (WGCNA) to detect hub genes, and employed selection signal analysis of candidate genes. Results: Transcriptome analysis showed that there were 329 differentially expressed genes in Guang Ming (GM) broilers Salmonella infection group and control group, of which 173 were up-regulated and 156 were down regulated. In Beijing You (BY) chickens, there were 563 DEGs between the Salmonella infection group and control group , including 220 up-regulated and 343 down-regulated genes. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we found that some genes were significantly enriched in immune-related signaling pathways, such as Toll-like receptor signaling pathway, Salmonella infection. Three promising genes ( EGR1 , JUN and FOS ) were eventually identified, which were significantly and differentially expressed in the same breed under different conditions, and in the two breeds after Salmonella infection. Hub genes, such as PPFIA4 and ZNF395, were also identified using WGCNA, which were associated with the heterophils/lymphocytes ratio, an indicator of disease resistance. Conclusions: the present study identified several genes and pathways associated with resistance to Salmonella infection, and found that BY had greater resistance to Salmonella infection than GM. The results obtained provide valuable resources for investigating the mechanisms of resistance to Salmonella infection in different chicken breeds.