Origin and genetic diversity of Egyptian native chickens based on complete sequence of mitochondrial DNA D-loop region

Abstract

Domestic chickens (Gallus gallus) play a significant role, ranging from food and entertainment to religion and ornamentation. However, the details on their domestication process are still controversial, especially the origin and evolution of African chickens. Egypt is thought to be important place for this event because of its geographic location as well as its long history of civilization. However, the genetic component and structure of Egyptian native chicken (ENC) have not been studied so far. The aim of this study is to clarify the origin and evolution of African chickens through assessing the genetic diversities and structure of five ENC breeds using the mitochondrial D-loop sequences. Our results suggest there is genetic differentiation between the pure native breeds and the improved native breeds. The latter breeds were established by the hybridization of the pure native and the exotic breeds. The pure native breeds were estimated to be established about 800 years ago. Subsequently, we extensively analyzed the D-loop sequences from the ENC as well as the globally collected chickens (2,010 individuals in total). Our phylogenetic tree among the regional populations shows African chickens can be separated to two distinct clades. The first clade consists of North African (Egypt), Central African (Sudan and Cameroon), European, and West (and Central) Asian chickens. The second clade 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 suggests there is limited gene flow within African continent. These obtained findings are important for the better understanding of the diversity and uniqueness of African native chickens.

Phylogenetic Studies on Red Junglefowl (<i>Gallus gallus</i>) and Native Chicken (<i>Gallus gallus domesticus</i>) in Samar Island, Philippines using the Mitochondrial DNA D-Loop Region

“…MtDNA diversity indices of Samar Red jungle fowl and native chicken populations and the number of haplotypes (SPW1-5 and SPN1-17) 5 17 5 1.00±0.20 0.0050±0.0016 1 1 1 1 1 Native CWS 9 20 6 0.91±0.08 0.0061±0.0011 1 3 1 1 1 2 chickens LES 13 20 8 0.91±0.06 0.0047±0.0007 2 1 2 1 1 4 1 1 SES 3 13 3 1.00±0.18 0.0054±0.0024 1 1 1 BWS 18 21 8 0.86±0.06 0.0055±0.0005 3 1 1 1 1 6 1 4 Overall 43 27 17 0.92±0.02 0.0056±0.0004 3 1 2 1 1 5 1 2 3 1 1 7 1 1 9 1 3 N -number of sequences; S -number of polymorphic (segregating) sites; Ht -number of haplotypes; Hd -haplotype diversity; π -nucleotide diversity; CWS, LES, LNS, SES and BWS -refers to the abbreviations in Table 1 Fig (Miao et al, 2013). Moreover, haplogroup E was distributed with high frequency in domestic chickens around South Asia, West Asia, Europe, South America, Africa, and among commercial breeds (Mwacharo et al, 2011, Miao et al, 2013, Osman et al, 2016, while the maternal lineages of commercial lines consisted of the three most common haplogroups A, B, and E1 (Miao et al, 2013).…”

Genetic Diversity of Crested and Non Crested Dandarawi Egyptian Native Chicken Based on Microsatellite Markers

“…Even though genetic analyses can reveal the extent of biodiversity in chicken breeds (Dorji et al, 2012), additional data on exact environmental adaptability and efficient performance is needed to adequately evaluate each breed for breeding and conservation programs. (Osman et al, 2016).…”

MitochondrialDNAD‐loop haplogroup contributions to the genetic diversity of East European domestic chickens from Russia

“…; Osman et al . ). The East European Plain with its famous communication waterways from the Varangians to the Greeks and to the Arabs thought to be important for chicken dispersal to Central and Northern Europe through Russia directly from Central Asia and China (West & Zhou ; Crawford ).…”

“…Chicken was domesticated nearly 8000 years ago in South and South-East Asia. During the next 5000 years, domestic chickens expanded through Western Asia to Northern Africa, Southern and Western Europe and by the 4th-2nd century before Christ (BC) they were kept by inhabitants of Greek, German, Belgium and English settlements (West & Zhou 1989;Flink et al 2014;Osman et al 2016). The East European Plain with its famous communication waterways from the Varangians to the Greeks and to the Arabs thought to be important for chicken dispersal to Central and Northern Europe through Russia directly from Central Asia and China (West & Zhou 1989;Crawford 1995).…”