title: Identification of novel genetic markers and evaluation of genetic structure in a population of Japanese crested ibis.
abstract: Japanese population of the Japanese crested ibis Nipponia nippon was founded by five individuals gifted from the People's Republic of China. In order to exactly evaluate genetic structure, we first performed development of novel genetic makers using 89 microsatellite primer pairs of related species for cross-amplification. Of these, only three primer pairs were useful for the genetic markers. Additionally, we sequenced allelic PCR products of these three markers together with 10 markers previously identified. Most markers showed typical microsatellite repeat units, but two markers were not simple microsatellites. Moreover, over half of the markers did not have the same repeat units as those of the original species. These results suggested that development of novel genetic markers in this population by cross-amplification is not efficient, partly because of low genetic diversity. Furthermore, the cluster analysis by STRUCTURE program using 17 markers showed that the five founders were divided into two clusters. However, the genetic relationships among the founders indicated by the clustering seemed to be questionable, because the analysis relied largely on a small number of triallelic markers, in spite of the addition of the three useful markers. Therefore, more efficient methods for identifying large numbers of single nucleotide polymorphisms are desirable.
authors: Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors: Kanako
authors: K
authors: Tsubono
authors: Yukio
authors: Y
authors: Taniguchi
authors: Hirokazu
authors: H
authors: Matsuda
authors: Takahisa
authors: T
authors: Yamada
authors: Toshie
authors: T
authors: Sugiyama
authors: Kosuke
authors: K
authors: Homma
authors: Yoshinori
authors: Y
authors: Kaneko
authors: Satoshi
authors: S
authors: Yamagishi
authors: Hiroaki
authors: H
authors: Iwaisaki
mesh_terms: D000818:Animals; D001483:Base Sequence; D001717:Birds / Q000235:genetics*; D016000:Cluster Analysis; D056727:Endangered Species; D053476:Extinction, Biological; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D007564:Japan; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers
keywords: Nipponia nippon; cross-amplification; genetic diversity; microsatellite