Table 1.
List of breeds of Japanese indigenous chickens and indigenous chickens overseas examined in this study.
| Category | Breeds | Breed ID | No. of Individuals | Source of Samples † | D-Loop | Microsatellite |
|---|---|---|---|---|---|---|
| Japanese indigenous chicken | Aidu-Jidori | AJI | 3 | FPLES | 3 | 3 |
| Chabo | CHB | 64 | Fukushima1-3, Kanagawa1-3, Mie1, Hiroshima1-3, Yamaguchi, IPLES, AZES, Shimane1-2 | 64 | 25 | |
| Chahn | CHN | 24 | Okinawa, Osaka | 21 | 24 | |
| EchigoNankin | ENK | 1 | Hiroshima University | 1 | 1 | |
| Gifu-Jidori | GJI | 13 | IPLES, GPLRI, Hiroshima University, Fukuoka1 | 9 | 13 | |
| Hinai | HNI | 39 | Fukushima4, APLES, TUA, Yamaguchi, AZES, Hiroshima University | 30 | 39 | |
| Iwate-Jidori | IJI | 5 | IPAHES | 4 | 5 | |
| Jitokko | JTK | 37 | Hiroshima1-2, Hiroshima University, Osaka, Miyazaki, Kagoshima, Yamaguchi | 15 | 37 | |
| Kawachi-Yakko | KWC | 16 | Osaka, Mie2-3, TUA, Hiroshima2, IPLES | 16 | 11 | |
| Kinpa | KNP | 4 | Fukushima4 | 4 | 4 | |
| Koeyoshi | KYS | 16 | Osaka, Aomori, TUA, Yamaguchi | 15 | 11 | |
| Ko-Shamo | KSM | 20 | Hiroshima university | 19 | 20 | |
| Kumamoto | KMM | 20 | KLES | 13 | 20 | |
| Kureko-dori | KRK | 23 | Kumamoto | 22 | 19 | |
| Kurokashiwa | KKS | 25 | Hyogo1, Hiroshima1, Mie3, YPLES, Shimane1-5 | 14 | 25 | |
| Mie-Jidori | MJI | 10 | Mie2-4, Hiroshima2 | 6 | 10 | |
| Minohiki-dori | MNH | 29 | IPLES, Shizuoka1 | 29 | 26 | |
| Nagoya | NGY | 22 | Hiroshima Univerisity | 20 | 20 | |
| Ohiki | OHK | 31 | Kochi, Shimane1-2, Kochi1-2 | 26 | 31 | |
| Oh-Shamo | OSM | 59 | Fukushima1, KPLES, Hiroshima University, Kagoshima2, Ehime | 59 | 53 | |
| Onaga-dori | ONG | 39 | Kochi3-9 | 29 | 11 | |
| Ryujin-Jidori | RJI | 9 | Wakayama1-4, Nara1 | 9 | 9 | |
| Sadohige-Jidori | SJI | 10 | Hiroshima University | 7 | 10 | |
| Satsuma-dori | STM | 23 | Osaka, Nara2, TUA, Yamaguchi, Hiroshima2 | 18 | 23 | |
| Shokoku | SHK | 33 | Osaka, Hyogo2, Hiroshima University, Mie2-5, Hiroshima2, TUA, Yamaguchi | 25 | 21 | |
| Tokudi-Jidori | TKJ | 6 | Yamaguchi | 6 | 6 | |
| Tomaru | TMR | 14 | Shizuoka2, TUA, NAHES, IPLES | 14 | 8 | |
| Tosa-Jidori | TSJ | 35 | Osaka, Fukushima4, Kochi1-2, Kochi10-11, KPLES | 16 | 35 | |
| Tosa-Kukin | TSK | 1 | Osaka | 1 | 1 | |
| Totenko | TTK | 51 | Kochi12, Osaka, Fukushima5, Mie3, Mie5, Hiroshima1-2, Ymaguchi, Kochi10 | 36 | 51 | |
| Ukokkei | UKK | 29 | Aichi1, Fukushima4, Hiroshima1-2, Mie3, IPLES, AZES, MLRD, APLRC | 29 | 25 | |
| Uzurao | UZR | 16 | Kochi1-2, Kochi13-14 | 16 | 11 | |
| Yakido | YKD | 3 | Mie4, Fukushima4 | 3 | 1 | |
| Yamato Gunkei | YMG | 2 | Yamaguchi | 2 | 0 | |
| Cochin | CCN | 20 | Fukushima6 | 18 | 20 | |
| Ingie | ING | 20 | Fukuoka2, Hiroshima University, Yamaguchi | 19 | 20 | |
| Rhoad Island Red | RIR | 20 | Aichi2 | 16 | 20 | |
| Barred Plymouth Rock | BPR | 20 | Hiroshima University | 15 | 20 | |
| Indigenous chicken overseas | Araucana | ARC | 20 | Aichi2 | 20 | 20 |
| Black Minorca | BMN | 20 | Nagoya university, Fukushima7 | 5 | 20 | |
| Brahma | BRM | 20 | Hiroshima University | 18 | 20 | |
| Lite Saussex | LSX | 20 | Aichi2 | 14 | 20 | |
| Belgian Mille Fleur bantam | MIL | 2 | Hiroshima University | 0 | 2 | |
| White Leghorn-LA | WLL | 20 | Aichi1 | 0 | 20 | |
| White Leghorn-MK | WLM | 20 | Aichi, Fukushima4, Hiroshima1-2, Mie1, IPLES, AZES, MLRD | 0 | 20 | |
| Wild ancestor | Red junglefowl | RJF | 20 | Nagoya university | 0 | 20 |
| Total | 955 | 726 | 831 |
† FPLES: Fukushima Prefectural Livestock Experimental Station, IPLES: Ibaraki Prefectural Livestock Experiment Station, AZES: Aomori Zootechnical Experiment Station, GPLRI: Gifu Prefectural livestock research institute, APLES: Akita Prefectural Livestock Experiment Station, TUA: Tokyo University of Agriculture, IPAHES: Iwate Prefectural Animal Husbandry Experiment Station, KLES: Kumamoto Livestock Experiment Station, YPLES: Yamaguchi Prefectural Livestock Experiment Station, KPLES: Kochi Prefectural Livestock Experiment Station, NAHES: Niigata Animal Husbandry Experiment Station, MLRD: Mie Livestock Research Division. Prefecture followed by number indicates each chicken fancier.