ESTIMATION OF GENETIC RELATIONSHIPS AMONG SOME POULTRY SPECIES USING CYTOCHROME b GENE AND MICROSATELLITE MARKERS
ESTIMATION OF GENETIC RELATIONSHIPS AMONG SOME POULTRY SPECIES USING CYTOCHROME b GENE AND MICROSATELLITE MARKERS
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Date
2015-11
Authors
GALADIMA, Mohammed Awwal
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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.
Description
A THESIS SUBMITTED TO THE SCHOOL OF POSTGRADUATE STUDIES,
AHMADU BELLO UNIVERSITY, ZARIA.IN PARTIAL FULFILLMENT OF THE
REQUIREMENTS FOR THE AWARD OF DOCTOR OF PHILOSOPHY IN ANIMAL
SCIENCE.
DEPARTMENT OF ANIMAL SCEINCE,
FACULTY OF AGRICULTURE,
AHMADU BELLO UNIVERSITY, ZARIA,
NIGERIA
Keywords
ESTIMATION,, GENETIC RELATIONSHIPS,, POULTRY SPECIES,, CYTOCHROME b GENE,, MICROSATELLITE MARKERS,