先天免疫的激活引发了各种级联反应,这些反应在很大程度上有助于防御身体,微生物或化学损害,提示损伤修复和去除致病生物以及恢复组织稳态。先天免疫基因的遗传多态性在不同品种的牛和水牛的抗病能力中起着重要作用。在这里,我们研究了先天免疫基因(CHGA)中的单核苷酸变异(SNP/SNV)和单倍型结构,CHGB,CHGC,Gir牛和Murrah水牛的NRAMP1,NRAMP2,DEFB1,BNBD4,BNBD5,TAP和LAP。这些基因的外显子区域的靶向测序通过IonTorrentPGM测序平台进行。通过BWA程序使用基因组分析工具试剂盒(GATK)将对应于这些基因的编码区获得的序列读段映射到牛BosTau7的参考基因组。统一基因型仪的进一步变异分析显示,Gir和Murrah中分别有54和224个SNP,还鉴定了32个SNV。在这些SNPs中,有43、36、11、32、81、21和22个变异在CHGA中,CHGB,CHGC,NRAMP1、NRAMP2、DEFB1和TAP基因分别。在这些确定的278个SNP中,在dbSNP数据库中发现了24例。在变异分析之后,使用SAS软件基于多个SNP的单倍型的结构形成揭示了大量的单倍型。在印度牛和水牛品种的先天免疫基因中发现SNP将增进我们对这些基因在确定印度品种的抗病性/易感性中的作用的理解。确定的SNP和单倍型数据也将为保护研究提供丰富的序列信息,选择性育种和设计未来的策略,以识别涉及不同种群样本的疾病关联。
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.