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The interferon regulatory factor gene family encodes transcription factors with multiple biological functions, which include reproduction, cell differentiation and immunity. Interferon regulatory factor-5 (IRF-5) gene is involved in immune defence against virus, stress response, activation of type I interferon genes, cell differentiation and growth. This experiment was conducted to identify and characterise single nucleotide polymorphisms in exons 3, 4, 5 and 7 of IRF-5 gene in Nigerian local chickens. Exons 3, 4, 5 and 7 of IRF-5 gene were amplified and sequenced. Single nucleotide polymorphisms (SNPs) present in exons 3, 4, 5 and 7 of IRF-5 gene were identified and analysed using Clustal W, DnaSp and SNAP2 software packages. Four SNPs, rs317511101, rs312902332, rs315149141 and rs739389464, were identified in exon 3 of IRF-5 gene in all the three genotypes. Exon 4 of the gene was conserved while three of the SNPs (rs736423928, 170C>T and rs740736761) identified in exon 7 were shared among the three genotypes. Linkage disequilibrium of 1.00 existed between rs317511101 and rs315149141 polymorphisms identified in exon 3 of normal feathered and frizzle feathered chickens. Mutation rs740736761 identified in exon 7 had the highest polymorphism information content obtainable for any biallelic marker. Most of the SNPs identified in exons 3, 5 and 7 were synonymous and singletons which could not be used for association study. The study concluded that only haplotypes in exons 3 and 7 of IRF-5 gene can be used in marker-assisted selection when improving Nigerian local chickens.

Improvement in fertility is possible through gene assisted selection. Cattle fertility and genes underlying it should be thoroughly studied and exploited to find solution to declining cattle fertility. Reprimo (RPRM) gene is a pleiotropic gene involved in suppression of cancer, regulation of mitotic cell cycle, cell cycle arrest and regulation of survival. Comparison of protein tertiary structures is important in inferring functional characteristics of new proteins. This study used computational approach to identify some fertility functions of bovine RPRM gene using motif prediction and protein structure comparison. Amino acid sequences of bovine RPRM gene and some other cattle fertility genes were retrieved from GenBank. Motifs in the amino acid sequence of bovine RPRM gene were predicted using PROSITE software. The domain structure of bovine RPRM protein was predicted using simple modular architecture research tool (SMART). Protein tertiary structures (3D structures) of bovine RPRM gene and other cattle fertility genes were predicted with Phyre 2 software. To have structural and functional similarity, it has been found that protein structure after superimposition should have Root Mean Square Deviation (RMSD) value less than or equal to 2A. The protein 3D structures of other cattle fertility genes were superposed against the protein 3D structure of bovine RPRM gene using SuperPose web server and the proteins with RMSD value of 2A or less were predicted as proteins with similar functions and structures as bovine RPRM gene. The predicted motifs (N-glycosylation site, N-myristoylation site, and cAMP and cGMP-dependent protein kinase phosphorylation site) and protein structure comparison revealed that, bovine RPRM gene and bovine growth hormone gene have the same fertility function with alpha carbon and backbone root mean square deviations of 1.94 A and 1.81 A, respectively. It follows therefore that other fertility functions of bovine RPRM gene included sexual maturation, steroidogenesis, gametogenesis, gonadal differentiation and gonadotrophin secretion which are the functions of growth hormone gene. Keywords : Reprimo gene, fertility, growth hormone gene, motifs, root mean square deviation

Immune genes are under acute selective pressure in order to resist pathogenic attacks. It is not really clear the type of selective force that acts on immune genes because of diverse pathogen load and host population density, so this experiment studied the selective force acting on exon 3 of IRF-5 gene in Nigerian indigenous chickens. DNA was extracted from 90 Nigerian indigenous chickens and exon 3 of IRF-5 gene was sequenced. The region was tested for deviation from neutrality using DnaSP. The Mean non-synonymous substitutions per non-synonymous site (dN) and mean synonymous substitutions per synonymous site (dS) were calculated to predict likely selective force/event acting on the region using HyPhy software implemented inside MEGA6 software. All the test of neutrality indices obtained for exon 3 of IRF-5 gene in Nigerian indigenous chickens were greater than 1 except Tajima’s D value of normal feather chickens (0.93) and Fu’s Fs value of naked neck chickens (0.71). The dN of 0.00 and negative dS were estimated for exon 3 of IRF-5 gene in all the three genotypes. This study therefore concluded that purifying selective forces are acting on exon 3 of IRF-5 gene in Nigerian indigenous chickens. Keywords: Chickens, co-evolution, immunity, pathogens, selection.

Deciphering genomic information requires markers that are polymorphic and sufficient enough to capture its vast array of genetic data. Polymorphic loci can differ greatly between breeds of the same species and the exclusion of the Nigerian and some African sheep breeds during the development of the OvineSNP50 chip necessitated the validation of SNPs included on the chip to allow for genomic applications of the excluded breeds. A total of sixty sheep samples were genotyped [10 each of the Balami, Uda, West African Dwarf and Yankasa from Nigeria, Dorper and Red Maasai from Kenya (East Africa)] using the Ovine 50k Illumina SNP bead chip. Results revealed that 33,994 SNPs (97.47%) of the called 34,876 SNPs were validated for downstream analysis. Mean heterozygosity values of 0.154 and 0.153 were obtained for polymorphic SNPs on sex and autosomal chromosomes respectively, while the values of 0.662 and 0.054 were obtained on the sex and autosomal chromosomes respectively for the mean identity-bystate (IBS). Six and three individuals violated the per ID and identity-by-state (IBS) thresholds, respectively. It was observed that the Ovine 50k Illumina SNP bead chip was informative in the Nigerian and East African sheep that were studied, and should be useful in examining the underlying genetic variation. Keywords: Sheep, OvineSNP50, genome-wide, call rate, minor allele frequency

In this study, the maternal genetic diversity, phylogenetic relationship and effect of natural selection on indigenous chickens from Nigeria were assessed. A total of 397-bp fragment of the mitochondrial DNA (mtDNA) D-loop region of 171 indigenous chickens from four populations of Nigeria and four commercial egg line strains (two Anak titan, one Giriraja and one Yaffa) as out-groups were analysed. Thirty-one haplotypes (28 from Nigerian chickens and three from commercial strains) and 34 polymorphic sites were identified. The mean haplotypic and nucleotide diversity were found to be 0.39 ± 0.05 and 0.02 ± 0.02, respectively. Majority of Nigerian chicken haplotypes observed were grouped into haplogroup D which originated from Indian subcontinent, suggesting a single maternal lineage. Genetic variation within and between populations accounted for 97.30 and 2.70% of the total genetic variation, respectively, which is in agreement with a recent and maternal founding effect. High number (4) of negatively selected sites observed based on single likelihood ancestral counting (SLAC) model indicated that the sampled Nigerian chicken populations were undergoing purifying selection. This study concluded that there was relatively high genetic diversity and differentiation, thus, this information will probably paveway for further evaluation studies, preservation and improvement of Nigerian chickens as genetic resources towards ensuring food security.

Mitochondrial DNA (mtDNA) hypervariable region 1 ( HV1) sequences of three Nigerian indigenous goat breeds; West African Dwarf (WAD), Red Sokoto (RS) and Sahel were used to investigate the genetic diversity and effect of selection between and among these populations. Deoxyribonucleic acid (DNA) of Nigerian indigenous chicken was extracted from blood samples collected and preserved on Fast Technology for Analysis (FTA) paper. The extracted DNA were amplified and sequenced with predefined mitochondria (mtDNA) primer sets for HV1. Eighty-seven (87) polymorphic sites were found in 115 sequences which were grouped into 92 haplotypes. The mean haplotypic and nucleotide diversity were found to be 0.996±0.002 and 0.092±0.04 respectively. Genetic variation within population and between populations accounted for 97.26% and 2.74% of the total maternal variation respectively, with FST value of 0.0274. The Tajima's (D) and Fu's (F) test of neutrality were significant (P

Egeria radiata is a benthic species of bivalves which inhabits freshwater bodies along the coast of Nigeria. It’s an edible species with shells of nutrient value used in animal feeds and healthcare industries. This research was undertaken to investigate its species diversity in some coastal populations in Nigeria. Partial sequence of Cytochrome b region of mitochondrial DNA extracted from 53 samples from three locations (Itu 17, Southern Ijaw 18 and Burutu 18) in the Niger delta region of Nigeria were sequenced, aligned and subjected to haplotype network analysis. Afterwards, MEGA 6.06 was used in the analysis of genetic distance, selection and some diversity-based parameters. Results showed high transversion and non-synonymous substitution in Itu population. Polymorphic sites and haplotype diversity was high across the populations (0.88 [Image: see text] ” 0.96), indicating considerable diversity of the sequences. Nucleotide diversity was highest in Itu population. Graphical display of relationship among the haplotypes of pooled samples did not show population-based discrimination. Within-population genetic distance was least in Burutu (0.003), while between-population genetic distance was least between Burutu and Southern Ijaw (0.014). In addition, diversity indicated by genetic distance and diversity indices was not severe. Phylogenetics and median-joining network analyses did not segregate the populations into well-defined clades. Selection analysis revealed large site indices for both positive and negative selection in Itu, but more of neutral selection in the other two populations. Tajima’s D and Fu’s F values for neutrality test showed no significance difference (P>0.01) in each case. However, negative D value was obtained for the three populations. The rate of population growth or expansion was higher in Burutu than Itu and Southern Ijaw. Egeria radiata showed no maternal relationship with the other bivalve species based on the cytochrome b gene region used in this study.

Pregnancy associated glycoptotein-1 (PAG-1) gene belong to a large family of aspartic peptidases expressed exclusively by different placental cells of mammalian species. This study was conducted to characterize exon 4 (the most polymorphic exon) of PAG-l gene in White Fulani, Muturu and N’Dama breeds of cattle. Blood samples from seventy-four (74) animals (25 Muturu, 25 White Fulani and 24 from N’Dama) were collected from two farms in Southwest, Nigeria. Exon 4 and the surrounding intron 5 of bovine PAG-l gene were amplified and sequenced. Single nucleotide polymorphisms (SNPs) in the gene were detected using codon code aligner. Estimates of population genetic statistics and diversity were obtained using Arlequin 2.0 and DnaSP respectively. The protein motifs and its secondary structure were predicted. Four SNPs: 173G>A (χ2 =1.75), 244C>A (χ2=11.11), 377C>A, (χ2=0.89) and 392G>A (χ2=0.51) were observed in exon 4 of White Fulani, while two, 620A>G (χ2=0.01) and 630G>A (χ2=17.38), were observed in intron 5 of Muturu. Mutation 244C>A (χ2=10.41) was shared by White Fulani and N’Dama. Eight haplotypes were identified in exon 4 and the surrounding intron 5 of bovine PAG-l gene with White Fulani having the highest haplotype diversity (0.82), nucleotide diversity (2.7 x 10–3) and average number of nucleotide differences (1.74). The AMOVA results revealed that the percentage of variation within the population for gene in the three breeds was greater than variation among the populations. The result indicated no genetic differentiation between Muturu and N’Dama. Three motifs (Protein kinase C-phosphorylation, N-myristoylation and Casein Kinase II phosphorylation sites) were shared by the three cattle breeds. Protein structure prediction analysis classified exon 4 of bovine PAG-l as mixed folding consisting of 25.97% alpha helix among the three cattle breeds. The SNPs observed in these cattle breeds could be used for association studies with pregnancy related traits.