Population structure and genetic diversity of Sudanese native chickens

Abstract

The objectives of this study were to analyze genetic diversity and population structure of Sudanese native chicken breeds involved in a conservation program. Five Sudanese native chicken breeds were compared with populations studied previously, which included six purebred lines, six African populations and one Sudanese chicken population. Twenty-nine (29) microsatellite markers were genotyped individually in these five populations. Expected and observed heterozygosity, mean number of alleles per locus and inbreeding coefficient were calculated. A model based cluster analysis was carried out and a Neighbor net was constructed based on marker estimated kinships. Two hundred and one alleles were detected in all populations, with a mean number of 6.93 ± 3.52 alleles per locus. The mean observed and expected heterozygosity across 29 loci was 0.524 and 0.552, respectively. Total inbreeding coefficient (F_IT) was 0.069±0.112, while differentiation of subpopulations (F_ST 0.026±0.049) was low indicating the absence of clear sub-structuring of the Sudanese native chicken populations. The inbreeding coefficient (F_IS) was 0.036±0.076. STRUCTURE software was used to cluster individuals to 2 ≤ k ≤ 7 assumed clusters. Solutions with the highest similarity coefficient were found at K=5 and K=6, in which Malawian, Zimbabwean, and purebred lines split from Sudanese gene pool. The six Sudanese native chicken populations formed one heterogeneous cluster. We concluded that Sudanese native chickens are highly diverse, and are genetically separated from Malawian, Zimbabwean chickens and six purebred lines. Our study reveals the absence of population sub-structuring of the Sudanese indigenous chicken populations.

Key words: Genetic diversity, microsatellites, population structure, Sudanese native chickens.