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Unravelling the genetic history of any livestock species is central to understanding the origin, development and expansion of agricultural societies and economies. Domestic village chickens are widespread in Africa. Their close association with, and reliance on, humans for long-range dispersal makes the species an important biological marker in tracking cultural and trading contacts between human societies and civilizations across time. Archaezoological and linguistic evidence suggest a complex history of arrival and dispersion of the species on the continent, with mitochondrial DNA (mtDNA) D-loop analysis revealing the presence of five distinct haplogroups in East African village chickens. It supports the importance of the region in understanding the history of the species and indirectly of human interactions. Here, through a detailed analysis of 30 autosomal microsatellite markers genotyped in 657 village chickens from four East African countries (Kenya, Uganda, Ethiopia and Sudan), we identify three distinct autosomal gene pools (I, II and III). Gene pool I is predominantly found in Ethiopia and Sudan, while II and III occur in both Kenya and Uganda. A gradient of admixture for gene pools II and III between the Kenyan coast and Uganda's hinterland (P = 0.001) is observed, while gene pool I is clearly separated from the other two. We propose that these three gene pools represent genetic signatures of separate events in the history of the continent that relate to the arrival and dispersal of village chickens and humans across the region. Our results provide new insights on the history of chicken husbandry which has been shaped by terrestrial and maritime contacts between ancient and modern civilizations in Asia and East Africa., (© 2013 Blackwell Publishing Ltd.)

In this study, 30 microsatellite markers recommended by the International Society for Animal Genetics and the Food and Agriculture Organization were used to determine the extent of genetic differentiation and phylogenetic relationships among indigenous chicken populations sampled in Kenya, Uganda, Ethiopia and Sudan. Genetic differentiation (F(ST)) and chord genetic distances (D(C)) indicated that the indigenous chickens were genetically related but distinct from commercial broiler and egg layer lines. Genetic divergence among the indigenous chickens determined using the Mantel test was significantly influenced (P < 0.001) by geographic (reproductive) isolation. Genetic subdivisions were found between the Kenyan/Ugandan chicken populations and Ethiopian/Sudanese chicken populations. The Marsabit chicken population from northern Kenya was the most genetically distinct population within the Kenyan and Ugandan chicken cluster, thus warranting further investigation.