Bioinformatic analyses of kappa casein gene in mammalian livestock species

Abstract

Kappa casein (CSN3) gene is a variant of the milk protein highly conserved in mammalian species. Genetic variations in CSN3 gene of six mammalian livestock species were investigated using bioinformatics approach. A total of twenty-seven CSN3 gene sequences with corresponding amino acids belonging to the six species studied were retrieved from GenBank. Using a comparative genomic approach, we obtained 1797 bp of the CSN3 sequences from cattle, goat, horse, pig, rabbit and sheep. Alignment of twenty-seven sequences within the region of 1713 bp and containing gaps was carried out using Clustal W. The sequence alignment revealed high polymorphisms of CSN3 sequences among the six species. The percent identity and similarity between species were determined by conducting pair-wise comparisons of the sequences. Results revealed high level of identity and similarity among the ruminant animals (84-97% and 86-99%) which implied the gene is conserved in all the ruminants. However, percent identity and similarity between pig and rabbit were relatively low (45%, 61%). This revealed that CSN3 protein from them might be functionally different and divergence between them is more ancient. Higher polymorphism of amino acids was observed among the species than within species. Four non-synonymous mutations occurred in cattle, six in goat, four in horse, three in rabbit and seven in sheep. The results of DnaSP analysis indicated that the selected region (1-1797 bp) of the twenty-seven sequences from all the species had 1298 nucleotide sites excluding sites with gaps (499). There are invariable and variable sites that include 185 singleton variable sites and 56 parsimony informative sites. The nucleotide diversity (ð= 0.212) and average number of nucleotide diversity (k = 94.84) for all sequences which were lower than the highest values in rabbit (ð = 0.557, k = 229) were estimated. Divergence of the species could be inferred from high genetic diversity of the CSN3 gene. The haplotype diversity was 1.00 in goat, horse and sheep indicating abundant genetic diversity in those species. Close relationship between goat and sheep was observed in phylogenetic tree of CSN3 gene which showed that the comparability of CSN3 gene sequences was highest between the goat and sheep and they evolved from a most recent common ancestor. A more detailed study involving more divergent taxa and complete amino acid sequence will help to delineate how the mutations affect the functions of the gene.

Keywords: Diversity, Haplotype, Kappa casein, Non-synonymous, Polymorphism