animals Article Geographic Origin and Genetic Characteristics of Japanese Indigenous Chickens Inferred from Mitochondrial D-Loop Region and Microsatellite DNA Markers Ayano Hata 1, Atsushi Takenouchi 2,3, Keiji Kinoshita 4, Momomi Hirokawa 5, Takeshi Igawa 3,6 , Mitsuo Nunome 4,* , Takayuki Suzuki 1,4,* and Masaoki Tsudzuki 2,3,* 1 Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
[email protected] 2 Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan;
[email protected] 3 Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan;
[email protected] 4 Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
[email protected] 5 Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
[email protected] 6 Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan * Correspondence:
[email protected] (M.N.);
[email protected] (T.S.);
[email protected] (M.T.) Received: 21 October 2020; Accepted: 3 November 2020; Published: 9 November 2020 Simple Summary: Chickens have long lived with humans as companion animals for religious, ornamental, food production, or entertainment purposes. Chickens cannot fly or move long distances by themselves, and their introduction history is closely related to the history of human migration and trade.