Medaka Population Genome Structure and Demographic History Described via Genotyping-by-Sequencing
Medaka Population Genome Structure and Demographic History Described via Genotyping-by-Sequencing
复制标题
DOI：
10.1534/g3.118.200779
复制
发表时间：
2019-01-01
影响因子：
2.6
通讯作者：
Oota, Hiroki
中科院分区：
文献类型：
--
作者：
Katsumura, Takafumi;Oda, Shoji;Oota, Hiroki
青鳉是医学、遗传学、发育生物学和群体遗传学的模式生物。由100多个当地野生种群组成的实验室种群可用于这些领域的研究。因此，青鳉是一个潜在的优良的生物资源，用于筛选疾病风险和适应相关基因的全基因组关联研究。虽然在进行这种分析之前应该知道遗传种群结构，但尚未对野生青鳉种群的全基因组多样性进行全面研究。在这里，我们进行基因分型测序（GBS）的81和12青鳉捕获的生物资源和野生，分别。基于GBS数据，我们使用近似贝叶斯计算（ABC）框架评估了遗传群体结构并估计了人口统计学参数。全基因组的数据证实，当地人群之间有很大的差异，并支持我们以前提出的假设青鳉分散的线粒体基因组（mtDNA）数据的基础上。一个新的发现是，一个被认为是北方和南方日本人群体杂交的地方群体实际上是北方日本人群体的起源。因此，本文提出了第一个群体的基因组研究青鳉，揭示其群体结构和历史的基础上染色体遗传多样性。
Medaka is a model organism in medicine, genetics, developmental biology and population genetics. Lab stocks composed of more than 100 local wild populations are available for research in these fields. Thus, medaka represents a potentially excellent bioresource for screening disease-risk- and adaptation-related genes in genome-wide association studies. Although the genetic population structure should be known before performing such an analysis, a comprehensive study on the genome-wide diversity of wild medaka populations has not been performed. Here, we performed genotyping-by-sequencing (GBS) for 81 and 12 medakas captured from a bioresource and the wild, respectively. Based on the GBS data, we evaluated the genetic population structure and estimated the demographic parameters using an approximate Bayesian computation (ABC) framework. The genome-wide data confirmed that there were substantial differences between local populations and supported our previously proposed hypothesis on medaka dispersal based on mitochondrial genome (mtDNA) data. A new finding was that a local group that was thought to be a hybrid between the northern and the southern Japanese groups was actually an origin of the northern Japanese group. Thus, this paper presents the first population-genomic study of medaka and reveals its population structure and history based on chromosomal genetic diversity.