Patel SM, Koringa PG, Nathani NM, Patel NV, Shah TM, Joshi CG. Exploring genetic polymorphism in innate immune genes in Indian cattle (Bos indicus) and buffalo (Bubalus bubalis) using next generation sequencing technology.
Meta Gene 2015;
3:50-8. [PMID:
26925373 PMCID:
PMC4722485 DOI:
10.1016/j.mgene.2015.01.002]
[Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/17/2014] [Accepted: 01/25/2015] [Indexed: 11/28/2022] Open
Abstract
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.
Sequencing of exonic regions of 10 selected innate immune genes, 895.60 Mb data was generated.
Variant analysis using GATK pipeline revealed 278 SNPs, 32 SNVs and from these 24 were found to be reported.
43, 36 and 11 SNPs were observed in chromagranin genes viz. CHGA, CHGB and CHGC respectively.
32 and 81 SNPs were identified in NRAMP genes viz. NRAMP1 and NRAMP2 respectively.
21 and 22 SNPs were observed in β-defensin genes viz. DEFB1 and TAP respectively.
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