title: RNA sequencing-based analysis of the spleen transcriptome following infectious bronchitis virus infection of chickens selected for different mannose-binding lectin serum concentrations.
abstract: BACKGROUND
  Avian infectious bronchitis is a highly contagious disease of the upper-respiratory tract caused by infectious bronchitis virus (IBV). Understanding the molecular mechanisms involved in the interaction between innate and adaptive immune responses to IBV infection is a crucial element for further improvements in strategies to control IB. To this end, two chicken lines, selected for high (L10H line) and low (L10L line) serum concentration of mannose-binding lectin (MBL) were studied. In total, 32 birds from each line were used. Sixteen birds from each line were infected with IBV and sixteen were left uninfected. Eight uninfected and infected birds from each line were euthanized at 1 and 3 weeks post infection. RNA sequencing was performed on spleen samples from all 64 birds and differential gene expression analysis was performed for four comparisons: L10L line versus L10H line for uninfected birds at weeks 1 and 3, respectively, and in the same way for infected birds. Functional analysis was performed using Gene Ontology (GO) Immune System Process terms specific for Gallus gallus.
  
  
  RESULTS
  Comparing uninfected L10H and L10L birds, we identified 1698 and 1424 differentially expressed (DE) genes at weeks 1 and 3, respectively. For the IBV-infected birds, 1934 and 866 DE genes were identified between the two lines at weeks 1 and 3, respectively. The two most enriched GO terms emerging from the comparison of uninfected birds between the two lines were "Lymphocyte activation involved in immune response" and "Somatic recombination of immunoglobulin genes involved in immune response" at weeks 1 and 3, respectively. When comparing IBV-infected birds between the two lines, the most enriched GO terms were "Alpha-beta T cell activation" and "Positive regulation of leukocyte activation" at weeks 1 and 3, respectively.
  
  
  CONCLUSIONS
  Healthy birds from the two lines showed significant differences in expression profiles for subsets of adaptive and innate immunity-related genes, whereas comparison of the IBV-infected birds from the two lines showed differences in expression of immunity-related genes involved in T cell activation and proliferation. The observed transcriptome differences between the two lines indicate that selection for MBL had influenced innate as well as adaptive immunity.
authors.affiliation: UMR1313 Animal Genetics and Integrative Biology Unit, AgroParisTech, Université Paris-Saclay, 16 rue Claude Bernard, 75005, Paris, France. edin.hamzic@jouy.inra.fr.|UMR1313 Animal Genetics and Integrative Biology Unit, INRA, Université Paris-Saclay, Domaine de Vilvert, 78350, Jouy-en-Josas, France. edin.hamzic@jouy.inra.fr.|Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark. edin.hamzic@jouy.inra.fr.
authors.forename: Edin
authors.initials: E
authors.lastname: Hamzić
authors.affiliation: Department of Animal Science, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark. rikke.kjaerup@anis.au.dk.
authors.forename: Rikke Brødsgaard
authors.initials: RB
authors.lastname: Kjærup
authors.affiliation: UMR1313 Animal Genetics and Integrative Biology Unit, INRA, Université Paris-Saclay, Domaine de Vilvert, 78350, Jouy-en-Josas, France. nuria.mach@jouy.inra.fr.
authors.forename: Núria
authors.initials: N
authors.lastname: Mach
authors.affiliation: Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy. giulietta.minozzi@unimi.it.|University of Milan, DIVET, Via Celoria 10, 20133, Milan, Italy. giulietta.minozzi@unimi.it.
authors.forename: Guilietta
authors.initials: G
authors.lastname: Minozzi
authors.affiliation: Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy. francesco.strozzi@ptp.it.
authors.forename: Francesco
authors.initials: F
authors.lastname: Strozzi
authors.affiliation: Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy. valentina.gualdi@ptp.it.
authors.forename: Valentina
authors.initials: V
authors.lastname: Gualdi
authors.affiliation: Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy. john.williams01@adelaide.edu.au.|School of Animal and Veterinary Sciences, University of Adelaide, SA, 5371, Roseworthy, Australia. john.williams01@adelaide.edu.au.
authors.forename: John L
authors.initials: JL
authors.lastname: Williams
authors.affiliation: Cobb-Vantress Inc, US-412 Road, Siloam Springs, AR, 72761, USA. jun.chen@cobb-vantress.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Chen
authors.affiliation: National Veterinary Institute, Ulls väg 2B, 751 89, Uppsala, Sweden. eva.wattrang@sva.se.
authors.forename: Eva
authors.initials: E
authors.lastname: Wattrang
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark. bart.buitenhuis@mbg.au.dk.
authors.forename: Bart
authors.initials: B
authors.lastname: Buitenhuis
authors.affiliation: Department of Animal Science, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark. helle.juulmadsen@anis.au.dk.
authors.forename: Helle Risdahl
authors.initials: HR
authors.lastname: Juul-Madsen
authors.affiliation: Department of Animal Science, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark. tina.dalgaard@anis.au.dk.
authors.forename: Tina Sørensen
authors.initials: TS
authors.lastname: Dalgaard
mesh_terms: D000818:Animals; D002645:Chickens; D018352:Coronavirus Infections / Q000503:physiopathology / Q000662:veterinary*; D001351:Infectious bronchitis virus / Q000235:genetics*; D037601:Mannose-Binding Lectin / Q000097:blood* / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D037601:Mannose-Binding Lectin
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