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

由于目前日本东方鹳种群起源于少数创始者，了解它们之间的遗传多样性对于种群的长期保护和管理至关重要。多态性DNA标记是评价建立者之间遗传关系的重要工具。为了在五个主要的创始者基因组中发现全基因组DNA标记，我们使用了下一代测序仪，该测序仪产生了超过10 Gb的序列。我们通过生物信息学产生了1.85亿个101-bp的读段，并检测了74，552个推定的单核苷酸多态性（SNP）。其中，38，928个推定的SNP与每个创始人的基因分型数据被应用于各种分析，并评估创始人之间的遗传相关性。

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.