ABSTRACT
This thesis observed evolutionary relationships, compare the effectiveness of mitochondrial DNA (cytochrome oxidase b gene) among some species of poultry, 30 birds per breeds or species (Rhode Island Red, Rhode Island White, Shikabrown, Francolins, Guinea Fowls and Japanese Quails) using mitochondrial DNA`s cytochrome b oxidase gene and chicken microsatellite markers. It has also evaluated some quantitative trait loci (QTL) affecting egg quality traits on chromosome 1 to 5 of 205 Shikabrown F2 crossed using 25 microsatellites markers. In the mitochondrial analysis, a total of 83 haplotypes were identified from 414 polymorphic sites. Rhode Island White (RHIW) had the highest haplotypes 26, while Rhode Island Red (RHIR) had the least haplotype number 3. The highest number of transition was observed in Japanese quails (JPQ) 78. RHIW had the highest mismatch observed mean value 18.94. The value of Tajima`s D and Fu`s Fswere negative in all the species. The probability sum of squared difference P(Sim. SSD Obs. SSD), and probability Harpending`s raggedness index P(Sim.r Obs.r) 0.92, 0.33, 0.40, 0.68 and 0.79, 0.76, 1.00, 0.42 were not significant in RHIW, RHIR, Shikabrown (SHBR) and Guinea Fowl (GFW), but significant 0.001, 0.05 and 0.0.03, 0.05 in JPQ and Francolins (FRN). Phylogenetic tree and Median network analysis grouped RHIW, RHIR, SHBR, and GFW together. Analysis of molecular variance (AMOVA) showed that among population maternal genetic variance was 58.23%, while within population maternal genetic variance was 41.77%. Fixation index (FST) among population was 0.58. SHBR had the highest mean number of alleles (MNA) 5.37±0.43, and mean number of effective alleles (MNEA) 3.1±0.29 in the microsatellite analysis, the mean number of alleles in the whole population was 4.67±0.20, while the mean number of effective allele in the whole population was 2.70±0.0.13.The mean Shannon information index (I) across the populations was 1.1±0.04. The mean observed heterozygosity (Ho) across population was 0.58±0.03, while the mean expected heterozygosity across population (He) was 0.5±0.02. AMOVA indicated that 20% of variation was among population, 78% of variation was among individuals and 2% was within individuals.QTLs affecting, shell thickness, yolk length, egg weight, yolk weight, albumen weight, shell weight and albumen length were identified on these chromosomes. The effect of genotype on some of these traits were additive while others were dominant. Two QTLs located on chromosome 2 (shell thickness and shell weight), and three QTLs located on chromosome 3 (albumen weight, yolk weight and egg weight) showed pleiotropic effect, correlations between these QTLs were positive, negative and significant.It was concluded that all the species studied showed genetic variation at cytochrome b gene. Variation within microsatellite was only observed in the chicken breeds. Chicken microsatellite markers amplified the Japanese Quails, Guinea Fowl and Francolins DNA poorly. Chromosome 1 to 5 contain genes affecting egg quality traits. Mitochondrial DNA is highly recommended in studies involving species because less problem of genome amplification was encountered, while due to the problem of amplifying other species genome using microsatellites they are recommended for analysis within the chicken species only. Further analysis should be carried out using higher density markers to fine-tune positions of markers linked with these loci controlling egg quality.
