Identification and characterisation of single nucleotide polymorphisms in interferon regulatory factor‑5 gene of Nigerian local chickens
2021
Durosaro, Samuel Olutunde | Ozoje, Michael Ohiokhuaobo | Adebambo, Ayotunde Olutumininu et al.
The interferon regulatory factor gene family encodes transcription factors with multiple biological functions, which include reproduction, cell differentiation and immunity. Interferon regulatory factor‑5 (IRF‑5) gene is involved in immune defence against virus, stress response, activation of type I interferon genes, cell differentiation and growth. This experiment was conducted to identify and characterise single nucleotide polymorphisms in exons 3, 4, 5 and 7 of IRF‑5 gene in Nigerian local chickens. Exons 3, 4, 5 and 7 of IRF‑5 gene were amplified and sequenced. Single nucleotide polymorphisms (SNPs) present in exons 3, 4, 5 and 7 of IRF‑5 gene were identified and analysed using Clustal W, DnaSp and SNAP2 software packages. Four SNPs, rs317511101, rs312902332, rs315149141 and rs739389464, were identified in exon 3 of IRF‑5 gene in all the three genotypes. Exon 4 of the gene was conserved while three of the SNPs (rs736423928, 170C>T and rs740736761) identified in exon 7 were shared among the three genotypes. Linkage disequilibrium of 1.00 existed between rs317511101 and rs315149141 polymorphisms identified in exon 3 of normal feathered and frizzle feathered chickens. Mutation rs740736761 identified in exon 7 had the highest polymorphism information content obtainable for any biallelic marker. Most of the SNPs identified in exons 3, 5 and 7 were synonymous and singletons which could not be used for association study. The study concluded that only haplotypes in exons 3 and 7 of IRF‑5 gene can be used in marker‑assisted selection when improving Nigerian local chickens.
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