RNA-seq Analysis Revealed Functional Genes Associated With Resistance To Salmonella Enterica In Chicken

Salmonella enteritidis(SE) is a non-host-specific pathogenic bacterium which can lead to public health issues. Controlling and avoiding SE infection is one of the crux in poultry breeding and industry. To study the immune mechanism of chicken resistance to SE and identify major genes will provide us theory principle for the breeding of resistant strain.Two hundred and ten SPF White Leghorn chickens were maintained in SPF condition and orally infected with SE at 3-day-old.Then a total of 9 chickens were sampled at 24h-48 h post infection, which include 3 susceptible chickens(close to die) with high blood SE load, 3 resistant chickens(survive well) with low blood SE load and 3 non-infected chickens as cnotrol. Total RNA of spleens were used for RNA-seq. The results showed that:(1) The infected chickens showed lower body weight growth rate than controls. And the infected chicken has a significantly lower body weight than controls at 7d post infection(P<0.05). We obtained 15279 genes that can be annotated in chicken gnome. Differencially expressed gene lists were obtained using a criteria of FPKM≥2, ︱fold_change︱≥2 and P≤0.05. There were 137 genes between the control and resistant group, 176 genes between susceptible and resistant chickens and 270 genes between control and susceptible chickens differetially expressed using the above criteria. Significantly enriched GO term involved in the biological process of positive regulation of caspase activity, protein binding, cytokine binding, positive regulation of interleukin-10 biosynthetic process and germinal center B cell differentiation. Significantly enriched immune related pathway include Cytokine-cytokine receptor interaction, NOD-like receptor signaling pathway, ABC transporters and PI3K-Akt signaling pathway.(2) Seventeen immune related gene were selected for RT-q PCR based on pathway analysis,and only two gene showed different expression pattern between groups when compared with the pattern detected by RNA-seq. Meanwhile, fold-change of gene expression level between groups detected by RNA-seq and RT-q PCR has a high positive correlation(R2=0.85, P<0.01), indicating the m RNA expression profile from RNA-seq was reliable. In addition, CTLA4、ICOS、SOCS1、IL10RA、IL-8 and AVD were selected as candidate gene to study its temporal expression pattern using RT-q PCR. The results showed that CTLA4、ICOS、SOCS1 and AVD genes were highly expressed in susceptible group than that in other group(P<0.05). Further study reavealed that candidate gene CTLA4 has significantly higher expression level in infected chickens than controls at 48 h post infection.Conclusion: The transcriptom of chicken spleen significantly changed after challenge with SE. The differentially expressed gene CTLA4、ICOS and AVD may be involved in the progress of the anti-infection. This study can provide theory principle for the understanding of chicken resistant to SE infection.