Identification of polymorphic microsatellite loci for the endangered Kagu (Rhynochetos jubatus) by high-throughput sequencing

We used 454 pyro-sequencing to establish microsatellite markers for the endangered Kagu (Rhynochetos jubatus), a bird endemic to New Caledonia. We screened 52,583 reads to identify 60 microsatellites candidates and established 12 polymorphic loci. The number of alleles per locus ranged from 2 to 15, the observed heterozygosity from 0.046 to 0.818, the expected heterozygosity from 0.046 to 0.906, and the polymorphic information content (PIC) from 0.043 to 0.875. Two loci showed significant deviation from the Hardy–Weinberg equilibrium, while we did not detect any linkage between loci. The panel of microsatellites identified and characterized in this study will be useful to assess the genetic constitution of wild Kagu populations, which is necessary for effective conservation and breeding strategies of captive birds.