IN SILICO DETECTION OF SIGNATURES FOR ADAPTIVE EVOLUTION AT SELECT INNATE IMMUNE AND HEAT STRESS GENES IN INDIGENOUS POULTRY

Abstract

Indigenous poultry such as chickens and ducks have unique embedded adaptive traits which have evolved hence allowed their survival under varied environmental conditions. They provide a cheap source of protein in developing countries especially those in Sub-Saharan Africa. However, indigenous poultry are threatened by emerging disease outbreaks that are virulent and often associated with climate change conditions such as drought. Therefore, the objective of this work was to identify genetic signatures of natural selection at Toll-like Receptor 3 (TLR3), Toll-like Receptor 7 (TLR7), Protein Kinase R (PKR), 2’ 5’- Oligoadenylate Snynthetase 1, Heat Shock Protein 90 (HSP90), Heat Shock Protein 70 (HSP70) and Small Heat Shock Proteins (sHSPs). A reciprocal BlastP algorithm was used to search a non-redudant protein database with an expectation value cut off of 1e-10 so as to obtain homologs. MUSCLE was used to perform Multiple Sequence Alignment, sequences edited in Jalview and MEGA v6 used for evolutionary substitution model selection and rate heterogeneity testing. Phylogeny reconstruction was built using FastME software that implements Nearest Neighbor Interchange and Subtree Pruning and Regrafting (SPR) algorithms. The reliability of the phylogeny tree generated was evaluated using 1000 bootstrap replicates. Codon substitution models in PAML were used to compute the rate of non-synonymous to synonymous substitutions in different amino acid sites and lineages through likelihood Ratio Tests (LRTs). Heat shock protein genes results revealed signatures of negative selection suggestive of high evolutionary conservation. The results from disease-resistant genes revealed signatures of positive selection at several amino acid sites that encode protein domains. This is a good primer towards genetic development of better adapted and highly productive poultry breeds. This will likely reduce disease and drought-related morbidity in poultry, hence alleviation of food insecurity and better economic growth.