Genetic Diversity, Runs of Homozygosity, and Selection Signatures in Native Japanese Chickens: Insights from Single-Nucleotide Polymorphisms

Understanding genetic diversity, runs of homozygosity (ROH), and selection signatures is critical for the conservation and breeding management of native Japanese chickens. In this study, genetic diversity, ROH, and selection signatures in 11 populations of seven native Japanese breeds and three foreign breeds with different genetic and behavioral backgrounds were investigated using 11,493 SNPs identified through restriction-site-associated DNA sequencing. The Oh-Shamo (OSM), an aggressive cockfighting breed, exhibited the highest genetic diversity. Six native Japanese breeds, Ingie (IG), Ryujin-Jidori (RYU), Tosa-Jidori (TJI), Tosa-Kukin (TKU), Nagoya (NAG), and Ukkokei (UK), showed intermediate levels of genetic diversity and ROH. Population analyses grouped the 11 populations into four distinct clusters: (1) five populations comprising three foreign breeds (the Fayoumi inbred line, closed-colony G line of White Leghorn, commercial T line of WL, and White Plymouth Rock) and the IG Japanese breed; (2) OSM and two old Jidori breeds (RYU and TJI); (3) TKU and UK; and (4) the meat-type Nagoya breed. ROH and Fst analyses identified seven SNPs on chromosomes 13, 17, 20, 24, and 26, five of which were candidate genetic variants for fear-related behavior. These findings provide insights into genetic diversity and conserved genomic segments valuable for breeding and conservation in Japanese chicken breeds.