The maternal origin of indigenous domestic chicken from the Middle East, the north and the horn of Africa

BMC Genetics, Mar 2020

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). 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 South-Western region of Saudi Arabia and in Ethiopia. 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 maternal origin of indigenous domestic chicken from the Middle East, the north and the horn of Africa

Research article Open Access Published: 14 March 2020 The maternal origin of indigenous domestic chicken from the Middle East, the north and the horn of Africa Ahmed S. Al-Jumaili  ORCID: orcid.org/0000-0002-5613-76261,2, Selma Farah Boudali3, Adebabay Kebede4,5, Sahar A. Al-Bayatti6, Abdulamir A. Essa6, Abulgasim Ahbara1, Riyadh S. Aljumaah7, Raed M. Alatiyat8, Joram M. Mwacharo9, Gro Bjørnstad10, Arifa N. Naqvi11, Semir Bechir Suheil Gaouar12 & Olivier Hanotte1,5  BMC Genetics volume 21, Article number: 30 (2020) Cite this article 125 Accesses 1 Altmetric Metrics details Abstract 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 South-Western 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. Background Undoubtedly, village chickens are a valuable genetic resource for the countries around the world due to their adaptation to the local environment, including their higher resistance against endemic diseases. They supply high-quality protein and represent a major source of income to poor communities. Therefore, they contribute greatly to food security, poverty alleviation and management of natural resources [1]. The main production system of indigenous chicken is scavenging or semi-scavenging, which relies on a low level of inputs. This system makes up to 80% of the poultry stocks in the developing countries of Asia and Africa [2]. The Red junglefowl is the main ancestor of the domestic chicken [3]. Its natural habitat is the sub-humid and humid tropical areas in South and South-East Asia. In contrast to the wild ancestor, village chickens have adapted very effectively to a diversity of environments including the arid and semi-arid areas. They show extensive morphological diversity that may be connected to the adaptation to such hot and dry environments, including the naked-neck phenotype, small body size and frizzled plumage [4,5,6]. Recent genome studies have revealed candidate regions under positive selection which may be related to environmental adaptation in this species [7]. MtDNA analysis has been used intensively to unravel the history of domestic chickens [8]. Analysis of the mitochondrial DNA genome allows us to identify the wild ancestor(s) and the maternal lines that have contributed to a breed or population [9, 10]. Furthermore, such genetic marker can offer valuable information concerning the human-mediated dispersal of the species out of the domestication centres [10]. Finally, mtDNA characterisation of diversity may help the establishment of effective management practices and sustainable strategies for the conservation of diversity. This study aims to unravel the history and diversity of indigenous chicken from the Middle East, Northern and the Horn of Africa. It includes chicken from (i) Pakistan, a putative ancient centre of origin for domestic chicken in the northern part of the Indian subcontinent [11], (ii) Iraq, with its ancient Mesopotamian civilizations in contact with those of the Indus Valley, (iii) (...truncated)


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Ahmed S. Al-Jumaili, Selma Farah Boudali, Adebabay Kebede, Sahar A. Al-Bayatti, Abdulamir A. Essa, Abulgasim Ahbara, Riyadh S. Aljumaah, Raed M. Alatiyat, Joram M. Mwacharo, Gro Bjørnstad, Arifa N. Naqvi, Semir Bechir Suheil Gaouar, Olivier Hanotte. The maternal origin of indigenous domestic chicken from the Middle East, the north and the horn of Africa, BMC Genetics, 2020, pp. 1-16, Volume 21, Issue 1, DOI: 10.1186/s12863-020-0830-0