Genetic Polymorphism of TAP1, TAP2 and Tapasin Genes in Exotic and Indian Native Chicken Breeds

Background: Indigenous chicken breeds have shown resilience to common poultry diseases due to their genetic background. Research has highlighted the role of certain genes in the immune response and disease resistance in poultry. Among these, Tapasin and Transporter associated with antigen processing (TAP) genes have been identified as crucial players in the immune surveillance of avian species. However, very diminutive information is available on the genetic polymorphism of TAP1, TAP2 and Tapasin genes in Indian native chicken breeds Methods: A total of 362 birds from three distinct breeds, namely Brown Nicobari (female: 55, male:64), Ghagus (female: 58; male:60)and Dahlem Red (female: 57; male:68), were used in the study. DNA isolation was performed, followed by PCR amplification using various primers from the three genes. Single-Strand Confirmation Polymorphism (SSCP) analysis was carried out on the PCR products to identify any potential single nucleotide polymorphisms (SNPs). These SNPs were then confirmed through sequencing. Result: The study has confirmed that these genes are polymorphic in all the three studied chicken breeds. In the exon 7 of TAP1 gene, a polymorphic SNP at nucleotide position 3698 (GAG 336 AAG) was identified. A non-synonymous substitution at nucleotide position 4209 (GCA 371 ACA) in the exon8 of TAP1 gene was observed. In exon 6 of TAP2 gene, three variations were observed and of which the variation at nucleotide position 2658 (GAC 446 AAC) is non-synonymous. In exon 7 and 8 of TAP2 gene, a total of three SNPs were observed of which a non-synonymous substitution was observed at nucleotide position 3125(AGG 579AAG) in exon 7. In exon 5 of Tapasin gene, three non-synonymous substitution at nucleotide 3226 (ACG 293ATG), 3292 (CAC 315 CGC) and 3466 (ATT 373ACT) were identified.