Sequence characterization and screening for polymorphism in the caspase recruitment domain 15 gene of goat (Capra hircus)

•New sequence information and polymorphism in the CARD15 gene of indigenous breeds of goats.•Two non-synonymous substitutions R2441H (Barbari, Tellicherry) and A2492G (Tellicherry, Kanni).•MDP inductions resulted in significantly higher levels of IL1-β mRNA in Kanni.•Host genetic background for differential response might be a contributing factor.

The NOD-like receptors (NLRs) are a group of intracellular germline encoded innate immune receptors that recognize conserved microbial structures in various invasive pathogens. Atleast 23 different NLRs have been identified with CARD15 being the major NLR playing an important role in the co-ordination of adaptive immune response induced by the CARD15 agonist Muramyl dipeptide (MDP). CARD15 has been reported to confer resistance or susceptibility to Crohn's disease in humans and Johne's disease in animals. We amplified and sequenced the major region of the CARD15 gene (3042 bp) from three native goat breeds (Barbari, Tellicherry and Kanni), screened for polymorphisms and correlated the expression levels of MDP induced CARD15 mRNA and downstream cytokines with that of the polymorphisms. The different exons that contribute to the LRR domain of the CARD15 gene were screened from a 3 breed panel with twenty un-related animals each. Four polymorphisms were located in the coding region of the gene (one each in exon 5 and 10 and two in exon 6) and one in the non-coding region of the gene (Intron 5–6). Two nonsynonymous substitutions R2441H (in Barbari and Tellicherry) and A2492G (in Tellicherry and Kanni) were observed in exons 5 and 6 respectively.The major genotype in exon 5 was GG across Barbari, Tellicherry and Kanni. The polymorphism at position 2492 with respect to mRNA in exon 6 revealed the major genotypes GG, CC and GC in Barbari, Tellicherry and Kanni respectively. Upon MDP stimulation, there was no significant change in the expression levels of CARD15 and TNF-α mRNA across the three breeds while the IL1-β mRNA levels were significantly higher in Kanni breed of goat. The results provide us some basic data on the genotypes and the polymorphisms in the CARD15 gene in native breeds of goat. Future studies with an increased sample number, screening for paratuberculosis and understanding the host genetic background would help in disease association.