U.S. flagAn official website of the United States government
                    Here's how you know **Official websites use .gov**
                            
                            A **.gov** website belongs to an official government organization in the United States.
 **Secure .gov websites use HTTPS**
                            
                            A **lock** (                            
                              A locked padlock                                                      
                            
                            ) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.


Menu Agricultural Research Service
						
                    U.S. DEPARTMENT OF AGRICULTURE
 Animal Biosciences & Biotechnology Laboratory: Beltsville, MD
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                People

                    Staff Listing
                                    Careers


        


                    Announcements
                        ABBL Journal Club
                    USDA Civil Rights Policy StatementSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Northeast Area Beltsville, Maryland (BARC) Beltsville Agricultural Research Center Animal Biosciences & Biotechnology Laboratory Research Publications at this Location





- ARS National Programs
- Search for a scientific manuscript
- Search for a research project
- ARS Software
- Programs and Projects
- Collaborations
- Subjects of Investigation
- Publications

Title:   Author  item
                                            TRUONG, AHN DUC - Chung-Ang Universityitem
                                            HONG, YEOJIN - Chung-Ang Universityitem
                                            PARK, BOYEONG - Chung-Ang Universityitem
                                            HOANG, CONG THANH - Chung-Ang Universityitem
                                            Lillehoj, Hyunitem
                                            HONG, YEONG HO - Chung-Ang University
  Submitted to: Poultry Science
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 10/24/2016
                                    Publication  Date: 4/25/2017
                                    Publication URL: http://handle.nal.usda.gov/10113/5695444Citation: Truong, A., Hong, Y., Park, B., Hoang, C., Lillehoj, H.S., Hong, Y. 2017. Analysis of differentially expressed genes in Necrotic Enteritis-infected Fayoumi chicken using RNA-Seq: next generation sequencing mRNA in Fayoumi chickens. Poultry Science. 54(2):121-133. https://doi.org/10.12141/jpsa.0160053.DOI: https://doi.org/10.12141/jpsa.0160053                                                              
                                Interpretive Summary: Necrotic enteritis (NE) is an enteric disease caused by Clostridium perfringens and represents a global problem that costs over USD 2 billion per year in production losses.  High-throughput RNA sequencing (RNA-Seq) which is a powerful tool was used in this study to identify genes that control poultry response to this infection.  Genomic analysis of the expressed genes located  different functional categories of poultry genes in the intestinal mucosa of the NE-afflicted chickens.  These new data identified many host genes associated with immune response and host defense against pathogens and strongly suggest important role of cell-mediated immunity in protective host response to NE.  Application of high technology in genomic analysis will continue to impact our understanding the mechanisms of disease resistance to NE, and will foster the development of effective control strategies against these enteric pathogens.
                                Technical Abstract: We identified and evaluated differentially expressed genes (DEGs) by RNA-Seq in the intestinal mucosa of two Fayoumi chicken lines, M5.1 and M15.2, that are affected by necrotic enteritis (NE); these chicken lines share the same genetic background but have different major histocompatibility complexes (MHC).  RNA-Seq generated over 49 and 40 million reads for lines M5.1 and M15.2, respectively.  The alignment of these sequences with the Gallus gallus genome database revealed the expression of more than 14,500 gene transcripts in the two lines, among which 581 DEGs (308 were upregulated and 273 were downregulated), 1270 DEGs (1078 were upregulated and 192 were downregulated), and 1140 DEGs (1065 were upregulated and 75 were downregulated) were detected when lines M15.2 and M5.1 were compared with the control and compared between each other.  The analysis of all DEGs using the gene ontology database revealed annotations for 111 biological processes, 32 cellular components, and 17 molecular functions, and KEGG pathway mapping indicated that the DEGs were primarily involved in immunity, responses to various stimuli, and signal transduction.  In addition, we analyzed 183 innate immune genes that were differentially expressed in the NE-induced chicken lines, including 46 CD molecular genes, 89 immune-related genes, and 13 ß-defensin genes with three lineage-specific duplications.  Taken together, the transcriptional profiles showed that line M5.1 was more resistant to NE than line M15.2 and that differential gene expression patterns were associated with host genetic differences in resistance to NE. qRT-PCR and RNA-Seq analyses showed that all the genes examined had similar responses to NE (correlation coefficient R = 0.84 to 0.88, p < 0.01) in both lines M5.1 and M15.2.  To the best of our knowledge, this is the first study that describes NE-induced DEGs using RNA-seq in two Fayoumi chicken lines with different levels of susceptibility to NE.  These results will lead to increased insights on NE disease resistance mechanisms and the role of host genes in the control of the host immune response.


Return to top


Connect with ARS Sign up


ARS Home
                            USDA.gov
                            Plain Writing
                            Policies & Links
                            Civil Rights Statements
                            FOIA
                            Accessibility Statement
                            Privacy Policy
                            Non-Discrimination Statement
                            Quality of Information
                            USA.gov
                            WhiteHouse.gov