Genetic differentiation of six improved tropically adapted chicken breeds in Imo State Nigeria using mitichondrial DNA
| dc.contributor.author | Okani-Onyejiaka, Mirian Chikodi | |
| dc.date.accessioned | 2025-12-05T13:25:58Z | |
| dc.date.available | 2025-12-05T13:25:58Z | |
| dc.date.issued | 2020-09 | |
| dc.description | This thesis is for the award of Master of Science (MSc.) in Animal Breeding and Genetics | |
| dc.description.abstract | This study investigated the genetic differentiation (degree of divergence) of six Improved Tropically Adapted Chicken Breeds (iTABs), raised under semi-intensive management system in Imo State. Blood samples were collected from 77 chickens belonging to these six populations of iTABs in the ratio (12:12:14:13:13:13), for Noiler, FUNAAB-Alpha, Shika Brown, Kuroiler, Sasso and Fulani chickens, respectively. Genomic DNA was extracted from the blood samples in the same ratio for the same populations, respectively. A 592-bp of mtDNA D-loop region was amplified followed by partial sequencing of the mtDNA D-loop region. A 315 bp long sequence fragment was subsequently realized and used for the various analysis using different softwares. Results showed that 14 haplotypes were identified from 62 polymorphic sites. The highest (H=10) and the lowest (H=5) number of haplotypes were found within FUNAAB-Alpha, and Shika Brown/Noiler, respectively. The haplotype diversity (Hd) and nucleotide diversity (Pi) within population ranged from 0.731 (Sasso) - 0.970 (FUNAAB Alpha), and 0.383 (Sasso) – 0.471 (FUNAAB Alpha), respectively while the Hd and Pi among population were 0.796±0.025 and 0.386±0.013, respectively. The phylogenetic analysis grouped the iTABs into three main clades out of the seven clades identified in Asian domestic chicken with 97.39 % of the total maternal genetic variations occurring within population. Sasso and Shika Brown had the least (0.385) genetic distance. The analysis of mutation type associated with SNP revealed a total of 157 SNPs in the six breeds. There was an abundance of non-synonymous transition mutations within and across the breeds‟ except in Shika brown that have higher abundance of synonymous transition mutations. There was a moderate to high genetic differentiation between the six populations of iTABs as revealed by Arlequin 3.5.1.3 software, but significant value was observed only between Sasso and FUNAAB-Alpha (0.517). Tajima‟s D and Fu‟s F statistics were positive both within and among populations but was only statistically significant among the populations. Significant Fu‟s F was observed within the population of Noiler, Shika Brown, Kuroiler, and Fulani. Diversity indices of this study revealed that mtDNA polymorphism was high within populations and low among populations. All the breeds shared a common ancestry with Sasso while Shika Brown was more closely related. The iTABs originated from three distinct maternal lineages from Southeast Asia, Indian subcontinent and Southwest China. Results of the mutation analysis gives an indication that there is a conservation substitution in which case the alteration of the observed SNPs are less likely to have any severe effect on the protein structure and function. Therefore, it is recommended that the findings of this study could be utilized for the long term genetic improvement and stabilization of the breeds. | |
| dc.identifier.citation | Okani-Onyejiaka, M. C. (2020). Genetic differentiation of six improved tropically adapted chicken breeds in Imo State Nigeria using mitichondrial DNA (Unpublished Masters' Thesis). Federal University of Technology, Owerri, Nigeria | |
| dc.identifier.uri | https://repository.futo.edu.ng/handle/20.500.14562/2338 | |
| dc.language.iso | en | |
| dc.publisher | Federal University of Technology, Owerri | |
| dc.rights | Attribution-NonCommercial-ShareAlike 4.0 International | en |
| dc.rights.uri | http://creativecommons.org/licenses/by-nc-sa/4.0/ | |
| dc.subject | Smallholder poultry | |
| dc.subject | mtDNA | |
| dc.subject | genetic differentiation | |
| dc.subject | polymorphism | |
| dc.subject | phylogenetics | |
| dc.subject | geneflow | |
| dc.subject | Department of Animal Science | |
| dc.title | Genetic differentiation of six improved tropically adapted chicken breeds in Imo State Nigeria using mitichondrial DNA | |
| dc.type | Master’s Thesis |