Detection of Molecular Signatures of Selection at Production Genes for Eggs and Meat Production using dN/dS

Abstract

Livestock are widely reared in Africa. The livestock are variable phenotypically due to Natural Selection. However, improvement of their productivity is still a challenge. The aim of this study was to perform analysis for signatures of selection at candidate genes for egg and meat production. Genes for egg production were prolactin (prl), vasoactive intestinal peptide 1(vip1) and vasoactive intestinal peptide receptor 1(vipr1) while genes for meat production were growth hormone (gh), growth hormone receptor (ghr), insulin like growth factor I (igf1) and insulin like growth factor I receptor (igf1r). A reciprocal BLASTp using BLOSUM 62 substitution matrix was performed. Thereafter, Multiple Sequence Alignment using MUSCLE was performed and phylogenetic trees inferred using FastME. Finally, Phylogenetic analysis was done by estimating the rate of non-synonymous to synonymous substitution in the lineages and amino acid sites using codon-based substitution models of PAML4. Likelihood Ratio Tests were performed to compare the models followed by Bayes Empirical Bayes analysis to predict signatures of selection. In vipr1 and growth hormone receptor, all the lineages were shown to be under purifying selection while in prolactin, the lineages leading to poultry and other birds were under positive selection. In growth hormone, positive selection was detected in the artiodactyls. Insulin like growth factor I receptor had positive selection on amino acid isoleucine at position 460 located on Receptor L domain. The positive selection on igf1r may be used as a molecular marker in genetic improvement of growth of livestock.