Assessment of Population Structure and Genetic Diversity of Sudanese Native Chickens Using Microsatellite Markers

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Hasballa, Mohy eldein Adam Berima
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University of Khartoum
This study was conducted to evaluate the population structure and genetic diversity of six Sudanese native chicken populations collected from different areas. Three of the six populations were Large Beladi, collected from Zalingei (LBZ =16), Damazein (LBDa = 17) and the third (BAL = 48) was obtained from the European Collaborative Project on Chicken Biodiversity (AVIANDIV project) collected from Khartoum state. Two populations of Bare Neck were collected from Abu Naama (BNAb = 18), and El-Obeid (BNOb = 12) whereas the only Betwil population was collected from the Nuba Mountain (BT = 36). As reference populations, six purebred lines and six African populations from Malawi and Zimbabwe were selected for comparison with the native chicken of Sudan. A drop of blood samples from wing veins were collected into classic filter cards FTA and genomic DNA was extracted by phenol-chloroform method. DNA fragments produced by Polymerase Chain Reaction (PCR) amplification were visualized as bands on 8% polyacrylamide gel and investigated using 29 microsatellite markers. The study revealed that the total number of alleles across the populations was 201 with an average of 5.3 alleles per population. The mean number of alleles per locus was 6.93 ± 3.52 and ranging from three [(MCW103), (MCW098), (MCW248), (MCW165)] to 17 [(LEI234)]. XIII Moreover the results obtained from this study showed that all the 29 loci were polymorphic. The mean of the observed heterozygosity across all the 29 loci was 0.524, and ranging from 0.461 ± 0.023 for Large Beladi Zalingei (LBZ) to 0.578 ± 0.022 for Bare Neck El-Obeid (BNOb), while the mean of the expected heterozygosity was 0.552 and ranging from 0.507 ± 0.031 for LBZ to 0.581 ± 0.026 for BNOb. The total inbreeding coefficient (FIT) was 0.069±0.112 and almost fully explained by within population, while the inbreeding coefficient of subpopulations (FST) was 0.026±0.049 indicating the absence of clear sub-structuring of the Sudanese native chicken populations; whereas inbreeding coefficient (FIS) was 0.036±0.076. These three mentioned parameters comprised the fixation indices. The pairwise fixation coefficient value of subpopulations (FST ) with the smallest genetic distance was obtained for LBDa vs BNAb and the largest genetic distance was found for LBZ vs BNAb. Network tree was constructed from the MEK using Splitstree 4 software package. A Structure software program was used to cluster individuals to 2 ≤ k ≤7 assuming clusters to be examined. The solutions with the highest similarity coefficient (97 and 99 identical runs out of 100 run STRUCTURE ) were found at K =5 and K=6, in which Malawian, Zimbabwian, and purebred lines split out as independent clusters and the six Sudanese native chicken populations clustered into one population he results from this study led to a rejection of the hypothesis that Sudanese native chicken are sub-structured across breeds and agroecological zones. The results indicated the presence of high genetic diversity within the Sudanese native chicken populations and highlighted the uniqueness of these populations their being genetically distinct from other village chickens from similar African production systems and pure bred lines.
101 Pages
Native Chickens - Sudan; Genetic Diversity - Sudan;Poultry Production;Justification ; general objectives;Phenotypic characteristics of Sudanese native chickens;Molecular markers;;Study period