Analyzing the genetic population structure using DNA marker and pedigree information in the artificially-reared population of an endangered animal species

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Since the current Japanese population of oriental stork originates from a small number of founders, understanding the genetic diversity between them is critical for the long-term protection and management of the population. The polymorphic DNA markers are essential tools for evaluating the genetic relatedness between the founders. To discover genome-wide DNA markers among five dominant founder genomes, we used a next-generation sequencer which produced sequences of over 10 Gb. We generated 185 million 101-bp reads and detected 74,552 putative single nucleotide polymorphisms (SNPs) by using bioinformatics. Out of them, 38,928 putative SNPs with the genotyping data in every founder were applied to the various analyses and the genetic relatedness between the founders were evaluated.