Polymorphisms, Haplotype Variability and Neutrality Test of Bronze Locus in Turkey (Meleagris gallopavo)

The bronze locus, identified as melanocortin-1 receptor (MC1R) gene, is involved in body coloration. We examined polymorphisms, haplotype variability and deviation from neutrality of bronze locus in Nigerian Indigenous Turkeys (NIT) using British United Turkeys (BUT) as control breed. Single-exon coding region of MC1R was sequenced. Polymorphisms were identified using MEGA v6 and CodonCode Aligner. In silico prediction of the functional effects of amino acid substitutions was done using SNAP2. Haplotypes were reconstructed using DnaSp v5. Eight polymorphisms were identified in MC1R gene of the birds with two novel polymorphisms: c.37C>A (neutral effect) and c.866T>G (gain-of-function) in NIT and BUT, respectively. Mutations c.450C>T and c.866T>G were unique to lavender NIT while c.186C>G was present in all birds. Two polymorphisms, c.866T>G and c.887C>T, were predicted to have functional effects. The highest genetic diversity was observed in lavender NIT while the least was observed in BUT. Fifteen (15) haplotypes were reconstructed, with MC1RBUT1 and MC1RBUT2 unique to BUT. Haplotype MC1R*4 was absent in all the birds used in this study while MC1R*5 was present in all NIT. Our study confirmed that MC1R*2 carried black (B) allele. Two novel haplotypes (MC1RNig1 and MC1RNig2) identified in this study also carried B allele. MC1RNig6, MC1RNig7 and MC1RNig8 were found to be unique to lavender. The novel polymorphisms and haplotypes identified in NIT and BUT could be used in differentiating them from other turkey breeds with the same plumage colours. Also, various polymorphisms and haplotypes identified in bronze locus of turkey are useful in breeding programmes aimed at developing or conserving different plumage colour types

Polymorphisms, Haplotype Variability and Neutrality Test of Bronze Locus in Turkey (Meleagris gallopavo)

The bronze locus, identified as melanocortin-1 receptor (MC1R) gene, is involved in body coloration. We examined polymorphisms, haplotype variability and deviation from neutrality of bronze locus in Nigerian Indigenous Turkeys (NIT) using British United Turkeys (BUT) as control breed. Single-exon coding region of MC1R was sequenced. Polymorphisms were identified using MEGA v6 and CodonCode Aligner. In silico prediction of the functional effects of amino acid substitutions was done using SNAP2. Haplotypes were reconstructed using DnaSp v5. Eight polymorphisms were identified in MC1R gene of the birds with two novel polymorphisms: c.37C>A (neutral effect) and c.866T>G (gain-of-function) in NIT and BUT, respectively. Mutations c.450C>T and c.866T>G were unique to lavender NIT while c.186C>G was present in all birds. Two polymorphisms, c.866T>G and c.887C>T, were predicted to have functional effects. The highest genetic diversity was observed in lavender NIT while the least was observed in BUT. Fifteen (15) haplotypes were reconstructed, with MC1RBUT1 and MC1RBUT2 unique to BUT. Haplotype MC1R*4 was absent in all the birds used in this study while MC1R*5 was present in all NIT. Our study confirmed that MC1R*2 carried black (B) allele. Two novel haplotypes (MC1RNig1 and MC1RNig2) identified in this study also carried B allele. MC1RNig6, MC1RNig7 and MC1RNig8 were found to be unique to lavender. The novel polymorphisms and haplotypes identified in NIT and BUT could be used in differentiating them from other turkey breeds with the same plumage colours. Also, various polymorphisms and haplotypes identified in bronze locus of turkey are useful in breeding programmes aimed at developing or conserving different plumage colour types

Genetic Diversity and Gene Flow among Three Chicken Populations in Nigeria Using Microsatellite Markers

To understand the level of genetic diversity among and within three improved locally adapted chicken populations in Nigeria, six microsatellite markers were used with 100 genomic DNA from Shika Brown (SB = 34), FUNAAB Alpha (FA = 33), and Noiler (NL = 33). The allelic and genotypic profiles of each representative from each population were determined through polymerase chain reaction amplification of the repeat region. Genetic diversity, genetic distance, level of inbreeding, polymorphism information content, and combined exclusion probabilities of markers (CPE/CPF) were analyzed using Microsoft Excel microsatellite toolkit, GenAlex, Microsatellite Analyser, FSTAT, and Poptree2. 416 alleles with 18.99% rare and 81.01% fixed alleles were observed across populations. The mean number of alleles was 23.111 ± 0.43, mean effective number of alleles was 16.975 ± 0.75, the expected heterozygosity was 0.940 ± 0.00, observed heterozygosity was 0.396 ± 0.02, mean PIC value was 0.937, and mean gene flow rate was 10.874 ± 0.817. The mean FIS was 0.579 ± 0.037 and the global FST was 0.023 ± 0.002. Nei’s genetic distance revealed that Shika Brown and the Noiler chicken populations were related (0.6985). The combined exclusion probability (CPE) across markers and populations was 0.999 (excluding a parent) and CPF was 1.000 (excluding both parents). The PIC/marker values across populations were greater than the minimum value of 0.5. High FIS and low FST value indicated a high inbreeding level within and low degree of genetic differentiation among the chicken populations. In conclusion, the microsatellite markers used are highly polymorphic and suitable for parentage analysis, control inbreeding, and could be used as baseline genetic information in conservation programs

Genetic Diversity and Gene Flow among Three Chicken Populations in Nigeria Using Microsatellite Markers

To understand the level of genetic diversity among and within three improved locally adapted chicken populations in Nigeria, six microsatellite markers were used with 100 genomic DNA from Shika Brown (SB = 34), FUNAAB Alpha (FA = 33), and Noiler (NL = 33). The allelic and genotypic profiles of each representative from each population were determined through polymerase chain reaction amplification of the repeat region. Genetic diversity, genetic distance, level of inbreeding, polymorphism information content, and combined exclusion probabilities of markers (CPE/CPF) were analyzed using Microsoft Excel microsatellite toolkit, GenAlex, Microsatellite Analyser, FSTAT, and Poptree2. 416 alleles with 18.99% rare and 81.01% fixed alleles were observed across populations. The mean number of alleles was 23.111 ± 0.43, mean effective number of alleles was 16.975 ± 0.75, the expected heterozygosity was 0.940 ± 0.00, observed heterozygosity was 0.396 ± 0.02, mean PIC value was 0.937, and mean gene flow rate was 10.874 ± 0.817. The mean FIS was 0.579 ± 0.037 and the global FST was 0.023 ± 0.002. Nei’s genetic distance revealed that Shika Brown and the Noiler chicken populations were related (0.6985). The combined exclusion probability (CPE) across markers and populations was 0.999 (excluding a parent) and CPF was 1.000 (excluding both parents). The PIC/marker values across populations were greater than the minimum value of 0.5. High FIS and low FST value indicated a high inbreeding level within and low degree of genetic differentiation among the chicken populations. In conclusion, the microsatellite markers used are highly polymorphic and suitable for parentage analysis, control inbreeding, and could be used as baseline genetic information in conservation programs

Polymorphism of IGF-1 Promoter and the UTR Regions of Nigerian Locally Adapted Chickens

Growth traits which are controlled by many genes are important economic traits in the poultry industry. The insulin-like growth factor gene (IGF-I) is a candidate gene for growth, body composition and metabolism, skeletal characteristics and growth of adipose tissue and fat deposition in chickens. The promoter and the untranslated region (UTR) of Insulin growth factor I gene was investigated to identify single nucleotide polymorphism, their genetic diversity and evolutionary relationship among six locally adapted strains of chicken in Nigerian. In this study, blood samples were collected and a specific primer pair was designed for amplifying a fragment of IGF-1 gene using polymerase chain reaction (PCR). The PCR products were sequenced while nucleotide sequences generated were edited and aligned using Mega v6.0 software. Nucleotide polymorphisms within each strain were detected using DNAsp v5 software. A total of eight SNPs were identified across the populations studied which were different already published SNPs associated with growth rate in chicken. Naked Neck chicken showed the highest genetic diversity from others with the highest number of polymorphic site, haplotype diversity and nucleotide diversity while the least were observed in Frizzle Feathered chicken. The phylogenic tree showed that small genetic differentiation exists among the chicken populations in this region. We reported the first genetic data from the promoter and the UTR regions of IGF-I gene in Nigerian native chickens and established baseline information regarding  variation in insulin growth factor I which should inform continued investigations into production potentials of these chickens and formulation of appropriate selection and breeding programs Keywords: SNPs, Genetic diversity, IGF-1, Chicke

Genetic Diversity and Population Structure of Nigerian Indigenous Chicken Populations Inferred from Microsatellite Markers

Knowledge of genetic diversity is a prerequisite for better utilization of any genetic resource. However, such information is insufficient for Nigerian indigenous chicken (NIC). Deoxyribonucleic acid (DNA) of NIC was extracted from FTA® paper and amplified with predefined microsatellite primer sets. A total of 180 chickens: northeast (NE; n=44), north[1]west (NW; n=25), north-central (NC; n=42) and southwest (SW; n=69) were genotyped along with 15 microsatellite markers to assess genetic diversity, demographic and population stratification. All microsatellites typed were found to be polymorphic (mean PIC = 0.53), and a total of 44 distinct alleles were detected. For all the loci, average inbreeding values (FIS) were ranged from -0.01 (NW chickens) to 0.17 (SW chickens), with an average value of 0.12, thus suggesting heterozygote excess. Most of the microsatellites deviated from Hardy[1]Weinberg equilibrium. SW and NC chickens related more closely having a genetic distance value of 0.02. The cluster analyses using STRUCTURE program indicated there were three primary populations, which provided evidence of extensive sharing of genetic variability, revealing varying levels of admixture among the studied population. The AMOVA analysis result indicated the proportion of genetic variation due to differences among populations and within populations was 5.46% and 96.56% respectively. Our results revealed multiple waves of introduction of diverse gene pools, and high panmixia has created and maintained a unique set of Gallus biodiversity in Nigeri

Haemoparasite Prevalence, Genetic Diversity of TLR2B Gene and Relationship with Haematological Parameters in Chicken

Haemoparasite constitute a major challenge in native chicken production in Africa. This study determines the genetic diversity and the effect of TLR2B gene polymorphism on haemoparasite and haematology of the chickens based on genotype and sex. 600 chickens of 25 weeks old consisting of Naked neck (NN), Normal feather (NF), and the Frizzle feather (FF) reared in battery cage-system were sampled for blood and analyzed for haematology, parasite occurrence and load, polymerase chain reaction, and gene sequencing. Polymorphisms were detected and their effect on haematology was determined. Results showed the occurrence of Plasmodium gallinacieum, Trypanosoma brucei, and Leucocytozoon schoutedeni with NF having the highest occurrence followed by NN and FF chicken genotype. There was a significant (P <0.05) effect of genotype and sex on haematology. Seven of the eight polymorphism detected were singleton and found only in NF while parsimonious 656GA was detected in all the chicken genotypes with no relationship with haematology and haemoparasite. NF had the highest nucleotide (0.00114) and haplotype diversity (0.584). The study revealed the occurrence of genetic variation in TLR2B gene, haematology, and haemoparasite in FUNAAB Alpha chickens which could provide baseline information in future breeding programmes of the chicken for the tropical environment

Application of non-linear models in description of growth of dual purpose FUNAAB Alpha chickens

Growth is explained mathematically by models that have parameters with biological interpretations. This study was conducted to compare five non-linear growth models (Gompertz, Brody, Logistics, Von Bertalanffy and Negative exponential) in order to describe growth in the three genotypes (normal feather, naked neck and frizzle feather) of the dual purpose FUNAAB Alpha chickens (n=332). Doesn’t Use Derivative iterative method of nonlinear procedure in SAS was used to estimate the model parameters. Computational difficultly, goodness of fit and residuals of the five models were also evaluated. Negative exponential model predicted the highest mature weight for the three genotypes while Logistics model predicted the highest coefficient of intensity of growth. The fitting of the five models presented no computational difficulty for normal feather chickens while Logistics failed to converge for male, naked neck and frizzle feather chickens. Based on goodness of fit (coefficient of determination, Bayesian information criterion, mean square error and residuals), Gompertz model was observed to have the best fit for normal feather and naked neck chickens while Brody model have the best fit for frizzle feather chickens and Von Bertalanffy for male chickens. From subjective approach (comparison of observed and predicted body weights), Logistics and Negative exponential models fitted well for normal feather than other models while Negative exponential model was the fittest among the models for naked neck and frizzle feather chickens and Gompertz for female chickens. It can be concluded that choice of appropriate model in description of growth depends on genotype and sex of dual purpose FUNAAB Alpha chickens

Genotypic differences in body weight and physiological response of local and exotic turkeys challenged with Salmonella typhimurium

To better understand susceptibility and/ or tolerance of locally adapted turkey to salmonellosis, we compared bodyweight, antibody titres and physiological traits based on genotype and sex of salmonella-infected turkeys. Three hundred poults from two genotypes (160 local and 140 exotic turkeys) were raised for twenty weeks. Bodyweight (BW), rectal temperature (RT), pulse rate (PR) and respiratory rate (RR) were measured weekly. Blood samples were collected from each turkey before and after inoculations at week 8 and 13 for serum antibody detection using enzyme-linked immunosorbent assay. Genotype had a significant (p 0.05) effect on all the parameters measured. Exotic turkey had higher weight than local while sexual dimorphism was in favour of toms despite challenge with Salmonella typhimurium. The RT was significantly higher (p 0.05) in exotic turkeys except at week 2, 6 and 8. In like manner, PR was higher (p 0.05) in exotic turkey except at week 4 (204.28±2.48 beats/minutes) and 8 (216.98±1.46 beats/minutes) where it was higher in local turkey. RR also followed the same trend while HSI was higher (p 0.05) in week 2 (1.53±0.06 breaths/minutes) and 14 (1.17±0.07 breaths/minutes) in exotic turkeys. Local turkeys had higher (p 0.05) antibodies against Salmonella organisms before and after inoculation while the hens of both genotypes had higher (p 0.05) antibody titres at the 7th day after inoculations. The present results seemed not to be convincing enough to suggest differences in tolerance/susceptibility to Salmonella infection and therefore the two genotypes may be equally adapted