Computational Analysis of the Sequences of LIPE Gene of Selected Ruminants and Non-ruminants

Abstract

Tropically adapted farm animals are characterized by low meat and milk productivity. Traditionally, mass selection has been widely employed in breeding for improved animal performance. However, improving animal productivity using mass selection is laborious and usually less effective. Advances in molecular techniques such as DNA sequencing analysis provide the opportunity to characterize meat and milk influencing genes, which can lead to faster genetic improvement but often unaffordable and expensive particularly in developing countries. Unlike the wet laboratory analysis, computational molecular analyses is comparatively cheaper in pre-screening of the functional impacts of nonsynonymous single-nucleotide variants of some performance traits-related genes such as hormone-sensitive lipase (LIPE).
 A total of fifteen (15) LIPE nucleotide sequences comprising pig (3), cattle (3), water buffalo (2), camel (2), goat (2) and sheep (3) were retrieved from the Genbank. Also, twenty (20) functionally associated genes with the LIPE gene including perilipin 1, 2 & 5 protein kinase cAMP-activated catalytic subunit alpha, protein kinase X-linked were determined using the GeneMANIA.
 Functional analysis of non-synonymous single nucleotide polymorphism using PROVEAN showed that ten amino acid substitutions (S216C, P107del, Q28_P29insRATHVA, S41_S44dup, A640M, S940A, L660I, D86delinsWA, S1000F) in water buffalo and pig (X678E, V789K, G987del, T218K, Q2234del, L278H, Q321del, L1023delinsPKL, P1452V, H1267delinsRFT), nine in sheep (F67_P68delinsVQ, R24G, A247_R248dup, L122L, L144P, S149K, S125S, S224H, G148M) and goats (A450Y, P480H, G490delinsPHQ, L500R, R550del, S100_S101dup, E600S, A700Q, P754delinsQAW) and five in camel (A320A, S210S, L130L, T400T, L440I) were found neutral indicating their beneficial effect while only T110A out of the fifteen amino acid substitutions was found deleterious in cattle. The obtained phylogenetic trees from the nucleotide sequences showed a closer relationship among the members of the Bovidae family particularly the sheep and cattle.
 This information may aid future research that aims at the selection of the studied animals for improved meat and milk quality traits.

In silico Analysis of Single Nucleotide Polymorphism in INHA Gene of Sheep and Goats

“…Details of the downloaded sequences are presented in Table 1. The amino acid sequence alignment of the two species was carried out using ClustalW algorithm of Molecular Evolutionary Genetic Analysis software version 6.0 [15].…”