Medaka Population Genome Structure and Demographic History Described via Genotyping-by-Sequencing

• Published in: G3 : genes - genomes - genetics Vol. 9; no. 1; pp. 217 - 228
• Main Authors: Katsumura, Takafumi, Oda, Shoji, Mitani, Hiroshi, Oota, Hiroki
• Format: Journal Article
• Language: English
• Published: United States Genetics Society of America 01.01.2019; Oxford University Press
• Subjects: Animals; bioresource; demography; DNA, Mitochondrial - genetics; freshwater fish; Genetics, Population; Genome - genetics; Genome-Wide Association Study; Genotype; Genotyping Techniques; Investigations; local population; Metagenomics - methods; Oryzias - genetics; RAD-seq; Sequence Analysis, DNA; local population; RAD-seq; bioresource; demography; freshwater fish
• ISSN: 2160-1836; 2160-1836
• DOI: 10.1534/g3.118.200779

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.