In silico analysis of Beta-Lactoglobulin gene in some selected mammalian species
2015
Momoh, O. M. (University of Agriculture, Makurdi (Nigeria). College of Animal Science, Department of Animal Breeding and Physiology) | Vincent, S. T. (University of Agriculture, Makurdi (Nigeria). College of Animal Science, Department of Animal Breeding and Physiology) | Yakubu, A. (Nasarawa State University, Lafia (Nigeria). Faculty of Agriculture, Department of Animal Science)
This study investigated in silico, the genetic diversity of Beta- Lactoglobulin (β-Lg) and their evolutionary and differentiation within and among selected mammalian species; and also examined the attendant effects of polymorphism on the functionality of the gene. A total of 21 β-Lg gene sequences with corresponding amino acids belonging to 6 species [cattle (4), buffalo (4), sheep (3), goat (3), pig (3) and horse (4)] were retrieved from GenBank (www.ncbi.nlm.nih.gov). All sequences were trimmed to equal length (500bp) corresponding to the same region. Sequences’ alignment, translation and comparison were done with ClustalW using IUB substitution matrix, gap open penalty of 15 and gap extension penalty of 6.66. The alignment revealed high polymorphism of sequences among extant species. The Dxy inferred using p- distance revealed that sheep and goat had the lowest distance of 0.05 with a maximum distance of 0.65 between goat and horse. The hypothesis of strict neutrality (dN = dS) was rejected for all extant species as allelic sequence evolution was driven by both purifying and positive selection. Only those of pig and buffalo were driven by positive selection. In-silico functional analysis of non-synonymous mutations using PANTHER revealed that, all the 12 amino acid substitutions (10 in cattle and 2 in sheep) did not impair protein function. The Neighbour-Joining phylogeny revealed trans-species evolution, but a species-wise phylogeny was obtained for UPGMA with consensus sequences. Thus, all probed SNPs from this study have no deleterious effect and can be tolerated by breeders when selecting stocks for milk improvement.
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