Genetic diversity and structure of the Ryujin-jidori, a critically endangered native Japanese chicken breed, based on microsatellite DNA analysis

One of the breeds of native Japanese chickens is the Ryujin-Jidori (RJ) from Tanabe City (formerly Ryujin Village), Wakayama Prefecture, Japan. To estimate the genetic diversity of RJ, 29 microsatellite loci were analyzed with 68 RJ adult birds (all possible sires and dams) reared by five breeders (four and one breeders in Wakayama and Nara Prefectures, respectively) in April, 2012. Among the 29 loci, 14 to 20 loci were monomorphic depending on populations (breeders). Genetic diversity indices in RJ were also low in mean number of alleles (1.34 to 1.55) and expected heterozygosity (0.140 to 0.174). There was no reduction of genetic diversity in the RJ breed reared in Wakayama and Nara Prefectures in 2012, as compared with the RJ population in 2007 reported elsewhere. In the phylogenetic tree analysis, the birds from the Wakayama populations and Nara population were separated. The pairwise Fsub(ST) values and genetic structure analysis also supported the genetic uniqueness of the Nara population. Also, significant and positive Fsub(IS) value was estimated in the Nara population. The low genetic diversity and inbred condition observed in the RJ breed in 2012 indicated the necessity to promote the conservation of this breed immediately. For the conservation of the RJ breed, it might be better to maintain the Nara population and four Wakayama populations separately because of the significant Fsub(ST) value observed between them. However, integration of the Nara population to the Wakayama populations might become necessary in the near future because of the possibility that the Nara population can become extinct through inbred deficiency. The primary and immediate concern should be increasing the number of RJ individuals and avoiding inbreeding as far as possible with the cooperation of public institutions and private breeders.