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 nonsynonymous 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.

Key words: Signatures, toll-like receptor, heat shock proteins, p rotein kinaseR, dN/dS, oligoadenylate Synthase 1