Open Access Anim Biosci Vol. 34, No. 6:941-948 June 2021 https://doi.org/10.5713/ajas.19.0932 pISSN 2765-0189 eISSN 2765-0235 Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens Sayed A.-M. Osman1,2, Masahide Nishibori1, and Takahiro Yonezawa3,* * Corresponding Author: Takahiro Yonezawa Objective: In Japan, approximately 50 breeds of indigenous domestic chicken, called Tel: +81-462-70-6572, E-mail: [email protected] Japanese native chickens (JNCs), have been developed. JNCs gradually became established based on three major original groups, “Jidori”, “Shoukoku”, and “Shamo”. Tosa-Jidori is 1 Laboratory of Animal Genetics, Department a breed of Jidori, and archival records as well as its morphologically primitive characters of Animal Life Science, Graduate School of Integrated Sciences for Life, Hiroshima suggest an ancient origin. Although Jidori is thought to have been introduced from East University, Hiroshima 739-8528, Japan Asia, a previous study based on mitochondrial D-loop sequences demonstrated that Tosa- 2 Department of Genetics, Faculty of Jidori belongs to haplogroup D, which is abundant in Southeast Asia but rare in other Agriculture, Minia University, El Minia, Eg- 61517, Egypt regions, and a Southeast Asian origin for Tosa-Jidori was therefore suggested. The relatively 3 Faculty of Agriculture, Tokyo University of small size of the D-loop region offers limited resolution in comparison with mitogenome Agriculture, Atsugi, Kanagawa 243-0034, phylogeny. This study was conducted to determine the phylogenetic position of the Japan Tosa-Jidori breed based on complete mitochondrial D-loop and mitogenome sequences, ORCID and to clarify its evolutionary relationships, possible maternal origin and routes of intro- Sayed A.-M. Osman duction into Japan. https://orcid.org/0000-0001-6925-9414 Methods: Maximum likelihood and parsimony trees were based on 133 chickens and Masahide Nishibori https://orcid.org/0000-0002-8378-4490 consisted of 86 mitogenome sequences as well as 47 D-loop sequences. Takahiro Yonezawa Results: This is the first report of the complete mitogenome not only for the Tosa-Jidori https://orcid.org/0000-0002-0012-1887 breed, but also for a member of one of the three major original groups of JNCs. Our Submitted Dec 4, 2019; Revised Feb 20, 2020; phylogenetic analysis based on D-loop and mitogenome sequences suggests that Tosa- Accepted Apr 9, 2020 Jidori individuals characterized in this study belong to the haplogroup D as well as the sub-haplogroup E1. Conclusion: The sub-haplogroup E1 is relatively common in East Asia, and so although the Southeast Asian origin hypothesis cannot be rejected, East Asia is another possible origin of Tosa-Jidori. This study highlights the complicated origin and breeding history of Tosa-Jidori and other JNC breeds. Keywords: D-loop; Jidori; Mitogenome; Phylogeny; Chicken; Gallus gallus INTRODUCTION Given the unique geographical location of Japan in the East Asian peripheral region, with water surrounding it on all sides, Japanese native chicken (JNC) breeds of Gallus gallus have been profoundly influenced by continental breeds, but at the same time, they have developed indigenously. There are approximately 50 breeds of JNCs [1]. Until 1867, most of them were developed for their special plumage, crowing and cockfighting, while subse- quently, from the end of the 19th century to the early stages of the 20th century, some new breeds were created to produce eggs and/or meat. Most of today’s JNC breeds were established from members of three major original groups or breeds: “Jidori”, “Shoukoku”, and “Shamo” [2]. Jidori does not specify a breed, but is a generic name used for various local primitive chickens whose ancestors are thought to have been introduced to Japan in the Yayoi period (300 BC through 300 AD) via Korea. The Copyright © 2021 by Animal Bioscience This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, www.animbiosci.org and reproduction in any medium, provided the original work is properly cited. 941 Osman et al (2021) Anim Biosci 34:941-948 Jidori group includes the three well-known breeds Tosa-Jidori, Although Tosa-Jidori is one of the oldest and most impor- Gifu-Jidori, and Mie-Jidori. Shoukoku is a breed originating tant breeds of JNCs, its origin is still unclear. Understanding in China that has developed as an aesthetic breed, which was the source of Tosa-Jidori will thus shed more light on the or- introduced to Japan in the Heian period (794 through 1192 igin and routes of introduction of JNC breeds. The aim of AD). Shoukoku and its derivative breeds such as Onaga-dori this study was therefore to determine the phylogenetic posi- and Toutenkou constitute the Shoukoku group. Shamo is tion of Tosa-Jidori, based on complete mitochondrial D-loop thought to have been derived from a Malay-type chicken and mitogenome sequences, and to clarify its phylogenetic from Thailand during the early 17th century (Edo period). relationships, possible maternal origin and routes of intro- The Shamo group comprises seven breeds, namely Oh-Shamo, duction into Japan. Ko-Shamo, Yamato-Shamo (Yamato Gunkei), Yakido, Kin- pa, Nankin-Shamo, and Echigo-Nankin-Shamo. However, MATERIALS AND METHODS the details of how these groups reached Japan are obscure [3-6]. Sample collection and DNA isolation Population genetic analysis of JNC breeds has been largely Because the taxonomic characters within Gallus are based carried out by Oka et al [6]. However, their study was based on male morphological features, DNA was extracted from on mitochondrial DNA D-loop sequence only, and they used peripheral blood of one male from each of six different strains limited numbers of global chicken samples other than JNC. (910, 921, 911, 922, 51, and Tsuchimoto) of the Tosa-Jidori Most studies of chicken mitochondrial DNA have also relied breed kept at Kochi Prefectural Livestock Experiment Station on D-loop sequencing [7-12]. The small size (about 1,230 (KPLES), using the phenol/chloroform method as described bp) of the D-loop limits the resolution of the maternal phy- by Green and Sambrook [15]. These blood samples were logeny. Moreover, the mutation rate in this region is higher collected by author (M.N.) and staff of the KPLES under the than that in the coding region, which can blur the structure ethics guidelines of the KPLES and Hiroshima University. of the matrilineal genealogy [13]. Recently, fine-grained anal- The sequenced birds are parent stocks with no kin relation- yses have used the mitogenome to reconstruct the history of ships among individuals. Blood samples were collected from chicken domestication [13,14]. These updated phylogenies the brachial vein, using heparinized syringes. The samples provide new insights into the origins and history of domes- were transferred to ice and then kept frozen at –40°C for later tication. Miao et al [13] noted some discordances between analysis. D-loop and complete mitogenome sequence data. Several sequences which previously fell into haplogroup D, based on Amplification and sequencing D-loop data, were assigned to haplogroups Y and C based We determined the complete sequence of the mitochondrial on mitogenome data. Moreover, a sequence that was previ- D-loop region for one individual from each strain (910, 921, ously classified as a basal branch in haplogroup C was redefined 911, 922, 51, and Tsuchimoto), following the procedure de- as belonging to the new haplogroup X based on mitogenome scribed by Osman et al [10], and the individual from strain data. Also, Huang et al [14] found that some lineages of red 921 was chosen for determination of the complete mitochon- junglefowl from Thailand, previously assigned to haplogroup drial genome sequence. C* based on D-loop sequences, were re-clustered as a new Subsequently, the complete mitogenome sequence was haplogroup V based on their mitogenomes. These lineages determined by the following procedures. Mitochondrial of red junglefowl were situated at the basal branch of hap- DNA fragments were specifically amplified using a KOD-FX logroups C and D, which were defined according to Miao kit (KOD-FX polymerase, Toyobo, Osaka, Japan) with puri- et al [13]. To achieve the highest possible level of molecular fied DNA as a template and LA-PCR primer sets, following resolution, complete mitogenome sequences are necessary the procedure described in previous studies [16,17]. Two [13]. primer sets were used for LA-PCR: the first primer set for Tosa-Jidori is a small type of Jidori that was already in 16S ribosomal RNA (16S rRNA) was as follows: LA16SF, Kochi Prefecture by the end of the Edo period (1603 through 5′-CCTACGTGATCTGAGTTCAGACCGGAGCAATC 1867) [2]. Tosa-Jidori together with 16 other JNC breeds are CAG-3′; and LA16SR, 5′-TGCACCATTAGGTTGTCCT designated as “natural national monuments” by the Japa- GATCCAACATCGAGGT-3′. This set was designed to amplify nese Government [3]. Oka et al [6] reported previously that a fragment of about 16 kilobase pairs (kb) from downstream Tosa-Jidori belonged to haplogroup D, which is abundant in of 16S rRNA to upstream of 16S rRNA, spanning the cyto- Southeast Asia but rare in other regions. Therefore, they con- chrome b (Cytb) gene. The second primer set for the Cytb cluded that Tosa-Jidori is of Southeast Asian origin, although, gene was as follows: LACytbF, 5′-TACACGAATCAGGCT as noted above, their study was based on the mitochondrial CAAACAACCCCCTAGGCATC-3′; and LACytbR: 5′-AG D-loop region only. ATACAGATGAAGAAGAATGAGGCGCCGTTTGCG-3′. 942 www.animbiosci.org Osman et al (2021) Anim Biosci 34:941-948 This primer set was also designed to amplify a fragment of collected from NCBI) as well as 47 D-loop sequences (five about 16 kb from downstream of Cytb to upstream of Cytb, Tosa-Jidori individuals determined in this study and 42 spanning 16S rRNA.