Microsatellites are defined as simple sequence repeats (SSRs) with a repeats length of up to 13 bases, whereas longer repeats give rise to minisatellites (Gibson G & Muse SV 2009). These repetitive DNA sequences are randomly distributed throughout eukaryotic genomes. They are usually highly polymorphic and exhibit a large number of alleles. The high degree of polymorphism and the codominant mode of inheritance make them extremely informative and suitable for analysis of gene flow and for characterization of the mating system in many plant species. Differences in the number of repeats at microsatellite loci are commonly recognized by differences in sizes of the amplified fragments (Tautz D. 1989, Weber JL & May PE. 1989). Microsatellite markers have been widely used to
Quercus phillyraeoides A. Gray is an evergreen oak and typical member of the lucidophyllus forests on the Pacific and the East China Sea coasts, and especially abundant around the Seto Inland Sea, which is known to have one of the lowest precipitation rates in Japan throughout the year. These oaks commonly grow on sunny, dry, windy hills near the coast and can grow to a height of 15 m, but typically reach 3 to 5 m. Its leaves are small and thick with shallow sinuses on the edge. They grow along the ocean coast from Boso Peninsula at their northern limit to the southwest. The southernmost (and westernmost) population in the Japanese Archipelago is seen in Okinawa-jima, the main island of Ryukyu Islands. Except for some of the populations maintained as production forests of famous white charcoal, or Bincho-tan, such as in Wakayama Prefecture, many of these forests are isolated and occur in small patches often threatened with extinction. The easternmost populations in Chiba and Kanagawa prefectures and are assigned to critically endangered and endangered species. The species is also assigned as near threatened in Nagasaki Prefecture and Miyazaki Prefecture, and vulnerable in Okinawa Prefecture. To know the genetic variation, genetic differentiation and genetic structure are the first step for planning the conservation of the species.