Background: Indigenous domestic chicken represents a major source of protein for agricultural communities around the world. In the Middle East and Africa, they are adapted to hot dry and semi-dry areas, in contrast to their wild ancestor, the Red junglefowl, which lives in humid and sub-humid tropical areas. Indigenous populations are declining following increased demand for poultry meat and eggs, favouring the more productive exotic commercial breeds. In this paper, using the D-loop of mitochondrial DNA as a maternally inherited genetic marker, we address the question of the origin and dispersal routes of domestic chicken of the Middle East (Iraq and Saudi Arabia), the northern part of the African continent (Algeria and Libya) and the Horn of Africa (Ethiopia). Results: The analysis of the mtDNA D-loop of 706 chicken samples from Iraq (n = 107), Saudi Arabia (n = 185), Algeria (n = 88), Libya (n = 23), Ethiopia (n = 211) and Pakistan (n = 92) show the presence of five haplogroups (A, B, C, D and E), suggesting more than one maternal origin for the studied populations. Haplogroup E, which occurred in 625 samples, was the most frequent in all countries. This haplogroup most likely originates from the Indian subcontinent and probably migrated following a terrestrial route to these different countries. Haplotypes belonging to haplogroup D were present in all countries except Algeria and Libya, it is likely a legacy of the Indian Ocean maritime trading network. Haplogroup A was present in all countries and may be of commercial origin. Haplogroup B was found only in Ethiopia. Haplogroup C was only detected in the SouthWestern region of Saudi Arabia and in Ethiopia. Conclusion: The results support a major influence of the Indian subcontinent on the maternal diversity of the today's chicken populations examined here. Most of the diversity occurs within rather than between populations. This lack of phylogeographic signal agrees with both ancient and more recent trading networks having shaped the modern-day diversity of indigenous chicken across populations and countries.

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The improved tropically adapted chicken breeds (iTABs) are low-input-high-output chickens suitable for smallholder poultry (SHP). Six iTABs (Fulani, FUNAAB Alpha, Kuroiler, Noiler, Sasso and Shika Brown) were introduced, and were raised under semi-intensive management system and tested under the African Chicken Genetic Gains project in Nigeria. The objective of this study was to evaluate the genetic diversity of these iTABs tested in Imo State Nigeria using mitochondrial DNA (mtDNA), Blood samples were collected from 77 chickens belonging to these six populations of iTABs in the ratio (12:12:14:13:13:13), for Noiler, FUNAAB Alpha, Shika Brown, Kuroiler, Sasso and Fulani chickens, respectively. Genomic DNA was extracted from seventy-seven birds randomly selected from the six iTABs. A 450-bp mtDNA D-loop region was sequenced.  The highest (H=5) and the lowest (H=2) number of haplotypes were found within Noiler, and Shika Brown/Fulani, respectively. Among the six populations, haplotype and nucleotide diversity was 0.558±0.063 and 0.0064±0.0013, respectively. A total of 8 haplotypes were identified from 15 polymorphic sites. These haplotypes clustered into three clades with 87.89% of the total maternal genetic variations occurring within population. Fulani and Shika Brown had the least (0.000) genetic distance. Tajima’s D was negative among populations and within Noiler, Kuroiler, Sasso and Fulani populations but was only statistically significant within the Noiler population. Diversity indices of this study revealed that mtDNA polymorphism was on the average both within populations and among populations. The results indicate the existence of two distinct maternal lineages from Southeast Asia, south central and Southeast China evenly distributed among the iTABs. The average genetic diversity observed within population can be utilized for the long-term genetic improvement and stabilization of the breeds.