ArticleG3 (Bethesda, Md.)2014
Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish.
Article in G3 (Bethesda, Md.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 69 citations in OpenAlex.
- Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes.Genome research · 2026Article
- Discovery and characterization of gene-by-environment and epistatic genetic effects in a vertebrate model.Cell genomics · 2026Article
- Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes.bioRxiv : the preprint server for biology · 2025Article
- Natural genetic variation quantitatively regulates heart rate and dimension.Nature communications · 2025Article
- A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics.Molecular biology and evolution · 2024Article
- Characterizing medaka visual features using a high-throughput optomotor response assay.PloS one · 2024Article
- Stability in gene expression and body-plan development leads to evolutionary conservation.EvoDevo · 2023Article
- Individual identification of inbred medaka based on characteristic melanophore spot patterns on the head.Scientific reports · 2023Article
- Comparison of anxiety-like and social behaviour in medaka and zebrafish.Scientific reports · 2022Article
- Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.Genome biology · 2022Article
- The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.Genome biology · 2022Article
- Conserved and diverged asymmetric gene expression in the brain of teleosts.Frontiers in cell and developmental biology · 2022Article
- Population genetic characteristics of Hainan medaka with whole-genome resequencing.Frontiers in genetics · 2022Article
- Strain-Specific Liver Metabolite Profiles in Medaka.Metabolites · 2021Article
- Whole-genome resequencing of Japanese whiting (Zoological research · 2021Article
- The chemical defensome of five model teleost fish.Scientific reports · 2021Article
- Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes.Nature communications · 2021Article
- A fish is not a mouse: understanding differences in background genetics is critical for reproducibility.Lab animal · 2021Review
- Unidirectional response to bidirectional selection on body size. I. Phenotypic, life-history, and endocrine responses.Ecology and evolution · 2020Article
Corrections and comments
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Authors and funding
13 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Oryzias latipes (medaka) has been established as a vertebrate genetic model for more than a century and recently has been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate medaka genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Here we characterize the genomes of wild medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near-isogenic panel of wild lines. The population is free of significant detrimental population structure and has advantageous linkage disequilibrium properties suitable for the establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition, high-throughput genome sequencing of these medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese medaka existed as a larger older population that went through a relatively recent bottleneck approximately 10,000 years ago. In addition, we detect patterns of recent positive selection in the Southern population. These data indicate that the genetic structure of the Kiyosu medaka samples is suitable for the establishment of a vertebrate near-isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at http://www.ebi.ac.uk/birney-srv/medaka-ref-panel.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.