Evaluating variability in interferon gamma and toll like receptor 4 in the chicken (gallus gallus, linnaeus, 1758) for comparison of known breeds with the native Philippine chicken

• Main Authors: Hernandez, Jed Allyn T., Suficiencia, Zaki L
• Format: text
• Language: English
• Published: Animo Repository 2022
• Subjects: Chickens > Philippines; Chickens—Diseases > Philippines; Chicken breeds; Immune response; Animal Sciences; Biology; Poultry or Avian Science
• Online Access: https://animorepository.dlsu.edu.ph/etdb_bio/9; https://animorepository.dlsu.edu.ph/cgi/viewcontent.cgi?article=1009&context=etdb_bio
• Institution: De La Salle University

Breeding programs for chickens will benefit from the identification of genes which may increase resistance to a variety of diseases because pathogenic diseases are the source of major losses for the global chicken industry. For breeding programs which involve the native Philippine chickens, screening variability in their disease resistance related genes would be extremely valuable, for very little is known about their genetic variability or disease resistance genes. Breeding in the Philippine chicken will benefit from a study that (1) consolidates the information on genes across diseases and determines those that are involved in immune response to several diseases and have substantial data in the information repositories (2) compares the evolutionary descent of the candidate genes as an indication of species specificity of the immune response given the propensity of pathogen transfer in Aves and (3) evaluates mutation rates across genes based on a haplotype networks to achieve rational design of primers suitable for detection of variation in the Philippine chicken populations. Gene ontology analysis on themes across 75 papers indicated that many of the gene products are localized to extracellular regions, with functions related to immune response, stress response, cell signaling and cytokines. Only 6 of the 428 genes were related to 5 or more of the 15 diseases suggesting disease responses were pathogen specific. Of these genes, TLR4 and IFNG were chosen for evaluation given the number of sequences available from different laboratories. Comparative phylogenetic analysis of trees from forty-three RefSeq sequences of the taxonomy related COX1 gene for Aves, with the trees generated by a similar number of sequences of the functional genes IFNG and TLR4 indicated the similarity in evolutionary forces acting on these genes. This suggests species specificity of immune responses in Aves. Polyphyly in Gallus gallus was observed across 142 and 152 TLR4 and IFNG sequences from GenBank indicating the absence of structure in these genes geographically separated populations. Thirty SNP sites were observed in TLR4 and seven in IFNG. TLR4 registered 92 haplotypes and IFNG had 7. The contrasting abundances of haplotypes suggests that either mutation rates were faster in TLR4 than IFNG or that mutation was better tolerated in TLR4 than IFNG. The variation was reflective of the contrasting functions of the two genes as pathogen recognition and immune response regulation. Finally, primers were designed for each gene using NCBI Primer-BLAST. The primers are theoretically able to amplify all variable regions in both genes and can be used in the genetic characterization of Philippine chickens.