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Title: Genome-Wide SNP and STR Discovery in the Japanese Crested Ibis and Genetic Diversity among Founders of the Japanese Population.
Authors: Taniguchi, Yukio  kyouindb  KAKEN_id  orcid https://orcid.org/0000-0001-7065-8447 (unconfirmed)
Matsuda, Hirokazu  kyouindb  KAKEN_id
Yamada, Takahisa
Sugiyama, Toshie
Homma, Kosuke
Kaneko, Yoshinori
Yamagishi, Satoshi
Iwaisaki, Hiroaki  KAKEN_id
Author's alias: 谷口, 幸雄
Issue Date: 21-Aug-2013
Publisher: Public Library of Science
Journal title: PloS one
Volume: 8
Issue: 8
Thesis number: e72781
Abstract: 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.
Rights: © 2013 Taniguchi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
URI: http://hdl.handle.net/2433/178739
DOI(Published Version): 10.1371/journal.pone.0072781
PubMed ID: 23991150
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