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

利用 DNA 标记和谱系信息分析濒危动物人工饲养种群的遗传种群结构

• 批准号: 24658235
• 负责人: IWAISAKI Hiroaki
• 金额: $ 2.58万
• 依托单位: Kyoto University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Challenging Exploratory Research
• 财政年份: 2012
• 资助国家: 日本
• 起止时间: 2012-04-01 至 2014-03-31
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-24658235/
• 关键词: 絶滅危惧動物; コウノトリ; 人工飼育集団; 次世代シークエンサー; 一塩基多型; 血統情報; ゲノム関係行列; 遺伝的多様性

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.

由于目前的日本东方鹳人口源于少数创始人，因此了解它们之间的遗传多样性对于长期保护和人口管理至关重要。多态性DNA标记是评估创始人之间遗传相关性的重要工具。为了在五个主要的创建者基因组中发现全基因组DNA标记，我们使用了下一代序列器，该测序仪产生了超过10 GB的序列。我们通过使用生物信息学产生了1.85亿个101 bp读取并检测到74,552个假定的单核苷酸多态性（SNP）。在其中，对每个创始人的基因分型数据进行了38,928个推定的SNP，并将其应用于各种分析，并评估了创始人之间的遗传相关性。