Genetic Diversity and Structure in the Sado Captive Population of the Japanese Crested Ibis

Urano, Kensuke; Tsubono, Kanako; Taniguchi, Yoshinori; Matsuda, Hideaki; Yamada, Takahisa; Sugiyama, Toshie; Homma, Kosuke; Kaneko, Yoshinori; Yamagishi, Satoshi; Iwaisaki, Hiroaki

doi:10.2108/zsj.30.432

Cited by 11 publications

(21 citation statements)

References 40 publications

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“…Whereas genetic management is critical for these projects, information on the genome sequence or polymorphic markers remains sparse. Currently available genetic markers include only 26 microsatellites [5–7]. …”

Section: Discussionmentioning

confidence: 99%

“…Moreover, deduced haplotype numbers on consensus sequences containing multiple putative SNP sites were 2–4 in most cases (Table 4). The allele numbers in several tens of STRs previously developed were 2-5 in Chinese population and 2 or 3 in Japanese population [5–7]. The only 2 haplotypes in mitochondria DNA control region were detected in Chinese wild and captive populations [21].…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide SNP and STR Discovery in the Japanese Crested Ibis and Genetic Diversity among Founders of the Japanese Population

et al. 2013

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The Japanese crested ibis is an internationally conserved, critically threatened bird. Captive-breeding programs have been established to conserve this species in Japan. Since the current Japanese population of crested ibis originates only from 5 founders donated by the Chinese government, understanding the genetic diversity between them is critical for an effective population management. To discover genome-wide single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) while obtaining genotype data of these polymorphic markers in each founder, reduced representation libraries were independently prepared from each of the founder genomes and sequenced on an Illumina HiSeq2000. This yielded 316 million 101-bp reads. Consensus sequences were created by clustering sequence reads, and then sequence reads from each founder were mapped to the consensus sequences, resulting in the detection of 52,512 putative SNPs and 162 putative STRs. The numbers of haplotypes and STR alleles and the investigation of genetic similarities suggested that the total genetic diversity between the founders was lower, although we could not identify a pair with closely related genome sequences. This study provided important insight into protocols for genetic management of the captive breeding population of Japanese crested ibis in Japan and towards the national project for reintroduction of captive-bred individuals into the wild. We proposed a simple, efficient, and cost-effective approach for simultaneous detection of genome-wide polymorphic markers and their genotypes for species currently lacking a reference genome sequence.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genome-Wide SNP and STR Discovery in the Japanese Crested Ibis and Genetic Diversity among Founders of the Japanese Population

et al. 2013

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“…Of the endangered bird species, genetic diversity has been estimated using microsatellite markers in the Japanese Crested Ibis (Urano et al, 2013;Tsubono et al, 2014), Japanese Crane (Hasegawa et al, 2000;Zou et al, 2010), Blakiston's Fish Owl (Omote et al, 2012), Golden Eagle (Dawnay et al, 2009), Common Murre (Ibarguchi et al, 2000;MorrisPocock et al, 2008), White-tailed Eagle (Molecular Ecology Resources Primer Development Consortium, 2012), Japanese wood pigeon (Ando et al, 2011), and the Ptarmigan (Bech et al, 2013). However, among these, research focusing on Japanese populations was conducted for only Onuma: Genetic Information of Nationally Endangered Species four species: Japanese Crested Ibis, Japanese Crane, Blakiston's Fish Owl, and the Japanese Wood Pigeon.…”

Section: Future Directionsmentioning

confidence: 99%

The Present Status of Available Genetic Information for Avian Species Distributing in Japan and on the List of “Nationally Endangered Species of Wild Fauna and Flora”

Onuma

2015

J. Poult. Sci.

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As of 2014, 89 species have been legally designated as "nationally endangered species of wild fauna and flora," including 37 avian species in Japan. To facilitate the breeding of endangered species and the maintenance of protected habitats, a program for the rehabilitation of natural habitats and maintenance of viable populations is being established by the Ministry of the Environment and other related ministries for 49 of the species on the above list. The programs have already been established for 15 such avian species, and are currently managed by zoos or local authorities. Maintaining genetic diversity is necessary to ensure the stable procreation of endangered species. A decline in breeding potential due to inbreeding can be prevented by careful maintenance of genetic diversity. In addition to the prevention of inbreeding depression, the maintenance of genetic diversity safeguards species' resistance to pathogens, as well as their capacity to cope with environmental change. This manuscript reports on the status of currently available genetic information for nationally endangered avian species in Japan, with a particular focus on the 15 species included in the conservation and propagation program. In the NCBI "Nucleotide" database, 315 entries were related to sequence information from the 15 endangered species. Mitochondrial DNA-related sequences constituted 238 (75.6%) of these entries. In the NCBI "Genome" database, genome sequence entries for three species were found. As is the case with mitochondrial DNA, microsatellite loci are very useful for endangered species conservation to evaluate genetic diversity. However, information about the endangered avian species' microsatellite makers is limited. This situation could have a considerable negative impact on captive breeding projects in particular. Hence, the development of microsatellite markers for these species is a priority.

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“…), and nine of these markers were polymorphic in the Japanese population (Urano et al . ). Microsatellite PCR primer pairs derived from one species are often found to amplify microsatellite loci in related species (Engel et al .…”

Section: Introductionmentioning

confidence: 97%

Identification of novel genetic markers and evaluation of genetic structure in a population of Japanese crested ibis

Tsubono

Taniguchi

Matsuda

et al. 2013

Animal Science Journal

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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.

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Genetic Diversity and Structure in the Sado Captive Population of the Japanese Crested Ibis

Cited by 11 publications

References 40 publications

Genome-Wide SNP and STR Discovery in the Japanese Crested Ibis and Genetic Diversity among Founders of the Japanese Population

Genome-Wide SNP and STR Discovery in the Japanese Crested Ibis and Genetic Diversity among Founders of the Japanese Population

The Present Status of Available Genetic Information for Avian Species Distributing in Japan and on the List of “Nationally Endangered Species of Wild Fauna and Flora”

Identification of novel genetic markers and evaluation of genetic structure in a population of Japanese crested ibis

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