In Silico Identification and Analysis of Signatures for Adaptive Evolution at Selected Innate Immune and Heat-stress Genes in Poultry

Abstract

Poultry represents a diverse population of birds that are ubiquitously distributed across all continents. Indigenous poultry are particularly important as a cheap source of income and protein for the resource-poor populace such as those living in Sub-saharan Africa. However, these birds are threatened by virulent disease outbreaks and heat-stress conditions associated with climate change. In addition, inbreeding and crossbreeding with commercial poultry have also led to genetic dilution and erosion of the adaptive traits in indigenous poultry. This study aimed to identify signatures of adaptive evolution in four innate immune genes and three heat-stress genes through an in silico approach. Based on the availability of genomic sequences in public databases, genes were selected and a reciprocal BLASTp performed to select inter-species homologs for comparative analysis. MUSCLE software was used to perform Multiple Sequence Alignments prior to phylogeny reconstruction using MEGA. To detect signatures, nested codon substitution models of PAML package were used to compute the rate of non-synonymous (dN) to synonymous (dS) substitutions in different lineages and amino acid sites through likelihood Ratio Tests and Bayes Empirical Bayes posterior probabilities. The dN/dS ratios obtained revealed strong purifying selection for heat-stress genes with values ranging from 0.00 to 0.73. In contrast, lineage and codon site analyses of innate immune genes revealed signatures of adaptive evolution in the Leucine Rich Repeats ectodomains of Toll-like Receptor 7 and Toll-like Receptor 3, the 2’-5’-oligoadenylate synthetase 1 C-terminus domain of 2’-5’-oligoadenylate synthetase and the double-stranded RNA Binding Motif and Protein Kinase domains of Protein Kinase R. Adaptive dN/dS values from lineage analysis ranged from 1.01 to 8.07 whereas Bayes Empirical Bayes values ranged from 0.956 to 1.000. In conclusion, this study successfully identified signatures associated with heat-stress tolerance and resistance to avian viral diseases. These results can be applied in marker-assisted selection, transgenics and introgression of the resistant alleles into susceptible populations while conserving indigenous poultry genetic resources. Successful genetic breeding will significantly reduce viral disease and heat-stress related morbidity in poultry which will translate to improved productivity, economic growth and food security.