Genetic Structure and Diversity of Egyptian Native Chicken As Inferred from the Complete Mitochondrial DNA D-loop Sequence and Its Played Role on the Origin and Evolution of African Native Chickens

The genetic component and structure of Egyptian native chicken (ENC) are not well known. The aim of this study is to clarify the origin and evolution of African chickens through assessing the genetic diversity and structure of five ENC breeds using the mitochondrial D-loop sequences. Our result suggests there are genetic differentiation between the pure native breeds and the improved native breeds. In addition, we extensively analyzed the D-loop sequences from the ENC as well as the globally collected chicken (2,010 individuals in total). Our phylogenetic tree among the regional populations shows there are two distinct clades of African chickens. The first clade consists of North African (Egypt), Central African (Sudan and Cameroon), European, and West (and Central) Asian clade. The second consists of East African (Kenya, Malawi, and Zimbabwe) and Pacific chickens. It suggests the dual origins of African native chickens. The first group was probably originated from South Asia, and then migrated to West Asia, and finally arrived to Africa thorough Egypt. The second group migrated from Pacific to East Africa via Indian Ocean probably by Austronesian people. This dual origin hypothesis as well as estimated divergence times in this study is harmonious with the archaeological and historical evidences. Our migration analysis suggested there is limited gene flow within African continent. These findings obtained in this study are important for the better understanding of the diversity and uniqueness of African native chickens.

Key words: Egypt, genetic diversity, mtDNA, native chicken, origin