In silico analysis of candidate genes associated with humoral innate immune response in chicken

BACKGROUND: Production and function of natural antibodies (NAbs) constitutes an important mechanism of the humoral innate immunity in vertebrates. The level of NAbs in chicken is heritable and the genetic background has been partly investigated. However, to date the genetic determination of humoral innate immune response in avian species has not been fully described. The goal of this study was to propose a new set of candidate genes with a potential effect on the NAb phenotype for further SNP association study. METHODS: In silico analysis of positional and functional candidate genes covered 14 QTL regions associated with LPS, LTA & KLH NAbs and located on six chromosomes: GGA5, GGA6, GGA9, GGA14, GGA18 and GGAZ. The function of the genes was subsequently determined based on the NCBI, KEGG, Gene Ontology and InnateDB databases. RESULTS: As a result, the core panel of 38 genes participating in metabolic pathways of innate immune response was proposed. Most of them were assigned to chromosomes: GGA14, GGA5, GGA6 and GGAZ (13, 9, 8 and 5 genes, respectively). These candidate genes encode proteins predicted to play a role in (i) proliferation, differentiation and function of B lymphocytes; (ii) TLR signalling pathway, and (iii) MAP signalling cascade. CONCLUSIONS: Proposed set of candidate genes is recommended to be included in the follow-up studies to model genetic networks of innate humoral immune response in chicken.