Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens

Abstract

14 15 ORCID 16 Sayed A.-M. Osman: https://orcid.org/0000-0001-6925-9414 ABSTRACT 27 Objective: In Japan, approximately 50 breeds of indigenous domestic chicken, called Japanese native 28 chickens (JNCs), have been developed. JNCs gradually became established based on three major 29 original groups, "Jidori", "Shoukoku" and "Shamo". Tosa-Jidori is a breed of Jidori, and archival 30 records as well as its morphologically primitive characters suggest an ancient origin. Although Jidori 31 is thought to have been introduced from East Asia, a previous study based on mitochondrial D-loop s 32 equences demonstrated that Tosa-Jidori belongs to haplogroup D, which is abundant in Southeast Asia 33 but rare in other regions, and a Southeast Asian origin for Tosa-Jidori was therefore suggested. The 34 relatively small size of the D-loop region offers limited resolution in comparison with mitogenome 35 phylogeny. This study was conducted to determine the phylogenetic position of the Tosa-Jidori breed 36 based on complete mitochondrial D-loop and mitogenome sequences, and to clarify its 37 evolutionary relationships, possible maternal origin and routes of introduction into Japan.38 Methods: Maximum parsimony trees were based on 133 chickens, and consisted of 86 mitogenome 39 sequences as well as 47 D-loop sequences.40Results: This is the first report of the complete mitogenome not only for the Tosa-Jidori breed, but 41 also for a member of one of the three major original groups of JNCs. Our phylogenetic analysis based 42 on D-loop and mitogenome sequences suggests that Tosa-Jidori individuals characterized in this study 43 belong to the haplogroup D as well as the sub-haplogroup E1. 44 Conclusion: \The sub-haplogroup E1 is relatively common in East Asia, and so although the 45 Southeast Asian origin hypothesis cannot be rejected, East Asia is another possible origin of Tosa-46 Jidori. This study highlights the complicated origin and breeding history of Tosa-Jidori and other JNC 47 breeds.48 49 A c c e p t e d A r t i c l e 53 Given the unique geographical location of Japan in the East Asian peripheral region, with 54 water surrounding it on all sides, Japanese native chicken (JNC) breeds of Gallus gallus have been 55 profoundly influenced by continental breeds, but at the same time, they have developed indigenously. 56 There are approximately 50 breeds of Japanese native chickens [1]. Until 1867, most of them were 57 developed for their special plumage, crowing and cockfighting, while subsequently, from the end of 58 the 19th century to the early stages of the 20th century, some new breeds were created to produce eggs 59 and/or meat. 60 Most of today's JNC breeds were established from members of three major original groups or 61 breeds: "Jidori", "Shoukoku", and "Shamo" [2]. Jidori does not specify a breed, but is a generic name 62 used for various local primitive chickens whose ancestors are thought to have been introduced to 63 Japan in the Yayoi period (300 BC-300 AD) via Korea. The Jidori group includes the three well-64 kn...

Genetic diversity among two native Indian chicken populations using cytochrome c oxidase subunit I and cytochrome b DNA barcodes

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