Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Biosciences & Biotechnology Laboratory » Research » Publications at this Location » Publication #320140

Title: RNA-seq profiles of immune related genes in the spleen of Necrotic enteritis-afflicted chicken lines

item TRUONG, ANH DUC - Chung-Ang University
item HONG, JEONG HO - Chung-Ang University
item Lillehoj, Hyun

Submitted to: Asian-Australasian Journal of Animal Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/10/2015
Publication Date: 4/20/2015
Publication URL:
Citation: Truong, A., Hong, J., Lillehoj, H.S. 2015. RNA-seq profiles of immune related genes in the spleen of Necrotic enteritis-afflicted chicken lines. Asian-Australasian Journal of Animal Sciences. 28(10):1496-1511.

Interpretive Summary: Necrotic enteritis (NE) is an economically important disease of the poultry industry worldwide and is caused by the gut bacterium, Clostridium perfringens which produces several toxins. There is no effective treatment method other than antibiotics. With increasing regulations for antibiotic use in animal agriculture, there is a critical need to develop alternative strategies for the treatment of NE. Understanding how host immune system interacts with this gut bacteria is a critical first step towards finding a novel prevention method. ARS scientists collaborated with scientists at Korean universities to characterize the detailed molecular responses of chickens to this disease-causing gut bacterium and identified host immune genes that are responsive to the Clostridium bacterium following NE infection. This was accomplished using a technology to assess genes different between NE- susceptible and unsusceptible chicken lines and to detect those active in the disease process following infection. The hope is to identify factors (genes) that are protective against NE. These new findings will help to understand host-pathogen interaction and guide the future development of novel strategy to control NE.

Technical Abstract: The study aimed to compare the Necrotic enteritis (NE)-induced transcriptome differences in the spleen of two highly inbred White Leghorn chicken lines, line 6.3 that is Marek’s Disease (MD) resistant and line 7.2 that is MD susceptible. Induction of NE in the chickens was achieved by co-infection with E. maxima/C. perfringens. Total RNA from the spleens of two chicken lines was used to make libraries that were sequenced in depth via RNA-seq that yielded 42,736,296 and 42,617,720 usable reads for lines 6.3 and 7.2, respectively. Mapping to the chicken genome resulted in the identification of 29,897 distinct genes for line 6.3 and 29,833 for line 7.2. The transcriptome changes were investigated using the differentially expressed genes (DEGs) package, which indicated 3,255, 2,468 and 2,234 DEGs of line 6.3, line 7.2, and comparison between two lines, respectively (fold change = 2, p < 0.01). Validation of RNA-seq results was done using qRT-PCR. The results of qRT-PCR were consistent with the RNA-seq data. All of the DEGs were analysed using Gene Ontology (GO) terms, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the DEGs in each term were found to be more highly expressed in line 6.3 than in line 7.2. RNA-seq analysis indicated 139 immune related genes, 44 CD molecular genes and 150 cytokines genes which were differentially expressed among chicken lines 6.3 and 7.2 (fold change = 2, p < 0.01). Novel mRNA analysis indicated 15,518 novel genes, for which the expression was shown to be higher in line 6.3 than in line 7.2 including some immune-related targets. These findings will help to understand host-pathogen interaction in the spleen and elucidate the mechanism of host genetic control of NE, and provide basis for future studies that can lead to the development of marker-based selection of highly disease-resistant chickens for molecular breeding.