Activation of innate immunity initiates various cascades of reactions that largely contribute to defense against physical, microbial or chemical damage, prompt for damage repair and removal of causative organisms as well as restoration of tissue homeostasis. Genetic polymorphism in innate immune genes plays prominent role in disease resistance capabilities in various breeds of cattle and buffalo. Here we studied single nucleotide variations (SNP/SNV) and haplotype structure in innate immune genes viz CHGA, CHGB, CHGC, NRAMP1, NRAMP2, DEFB1, BNBD4, BNBD5, TAP and LAP in Gir cattle and Murrah buffalo. Targeted sequencing of exonic regions of these genes was performed by Ion Torrent PGM sequencing platform. The sequence reads obtained corresponding to coding regions of these genes were mapped to reference genome of cattle BosTau7 by BWA program using genome analysis tool kit (GATK). Further variant analysis by Unified Genotyper revealed 54 and 224 SNPs in Gir and Murrah respectively and also 32 SNVs was identified. Among these SNPs 43, 36, 11,32,81,21 and 22 variations were in CHGA, CHGB, CHGC, NRAMP1, NRAMP2, DEFB1 and TAP genes respectively. Among these identified 278 SNPs, 24 were found to be reported in the dbSNP database. Variant analysis was followed by structure formation of haplotypes based on multiple SNPs using SAS software revealed a large number of haplotypes. The SNP discovery in innate immune genes in cattle and buffalo breeds of India would advance our understanding of role of these genes in determining the disease resistance/susceptibility in Indian breeds. The identified SNPs and haplotype data would also provide a wealth of sequence information for conservation studies, selective breeding and designing future strategies for identifying disease associations involving samples from distinct populations.
Keywords: BAM, Binary Alignment Map; BNBD4, Neutrophil beta-defensin 4; BNBD5, Neutrophil beta-defensin 5; BWA, Burrows–Wheeler Aligner; CHGA, Chromagranin A; CHGB, Chromagranin B; CHGC, Chromagranin C; DEFB1, Beta defensin 1; EM, Expectation Maximization; GATK, Genome Analysis Tool Kit; Haplotype; Indian cattle and buffalo; Innate immune genes; LAP, Lingual Antimicrobial Peptide; LD, Linkage Disequilibrium; NCBI, National Center for Biotechnology Information; NRAMP1, Natural Resistance associated macrophage protein 1; NRAMP2, Natural Resistance associated macrophage protein 2; Next generation sequencing; PCR, Polymerase Chain Reaction; PGM, Personal Genome Machine; RFLP, Restriction Fragment Length Polymorphism; SAM, Sequence Alignment Map; SAS, Statistical Analysis System; SLC11, Solute Carrier Family 11; SNP, Single Nucleotide Polymorphism; SNV, Single Nucleotide Variant; Single nucleotide polymorphism; TAP, Tracheal Antimicrobial Peptide; TLR, Toll Like Receptor; UTR, Untranslated Region.