Large-scale survey of mitochondrial D-loop of the red-crowned crane Grus japonensis in Hokkaido, Japan by convenient genotyping method.

The Red-crowned Crane, Grus japonensis, is an endangered species of crane that has two separate breeding populations, one in the Amur River basin (continental population) and the other in eastern or northern Hokkaido, Japan (island population). So far, only two haplotypes (Gj1 and Gj2) have been identified in the mitochondrial D-loop in island population, whereas seven haplotypes have been found in continental population (Gj3-Gj9). We developed a rapid and inexpensive method of extensive genotyping of D-loop haplotypes in Red-crowned Cranes, based on amplification refractory mutation system (ARMS) PCR assay. Two hundred and three cranes in eastern Hokkaido were studied with this method and supplemental DNA sequencing. Only two haplotypes, Gj1 and Gj2, were confirmed in eastern Hokkaido with Gj2 as a major haplotype. Additionally, only Gj2 was identified in twelve feathers from both sexes found in northern Hokkaido. These results suggest scarce genetic diversity in island population of Red-crowned Cranes in Hokkaido, Japan.