ArticleG3 (Bethesda, Md.)2014
A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology.
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 23 papers.
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Who cites it
23 citing papers in PubMed, 37 citations in OpenAlex.
- Disruption of carotenoid metabolism in cavefish via loss of beta-carotene oxygenase 2a.Current biology : CB · 2026Article
- Quantitative trait loci concentrate in specific regions of the Mexican cavefish genome and reveal key candidate genes for cave-associated evolution.The Journal of heredity · 2025Article
- Extraordinary model systems for regeneration.Development (Cambridge, England) · 2024Article
- The spatiotemporal and genetic architecture of extraoral taste buds in Astyanax cavefish.Communications biology · 2024Article
- Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals, and origin of novel traits.BMC ecology and evolution · 2021Article
- A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution.Nature communications · 2021Article
- An Asymmetric Genetic Signal Associated with Mechanosensory Expansion in Cave-Adapted Fish.Symmetry · 2020Article
- Stable transgenesis in Astyanax mexicanus using the Tol2 transposase system.Developmental dynamics : an official publication of the American Association of Anatomists · 2019Article
- An Adult Brain Atlas Reveals Broad Neuroanatomical Changes in Independently Evolved Populations of Mexican Cavefish.Frontiers in neuroanatomy · 2019Article
- High-Density Genetic Map Construction and QTL Mapping of Leaf and Needling Traits inFrontiers in plant science · 2019Article
- Heart Regeneration in the Mexican Cavefish.Cell reports · 2018Article
- Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Construction of a high-density genetic map: genotyping by sequencing (GBS) to map purple seed coat color (Hereditas · 2018Article
- Article
- Evolution and conservation of Characidium sex chromosomes.Heredity · 2017Article
- A High-Density Genetic Linkage Map and QTL Fine Mapping for Body Weight in Crucian Carp (G3 (Bethesda, Md.) · 2017Article
- Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing.Scientific reports · 2017Article
- Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum.Scientific reports · 2017Article
- Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass.Scientific reports · 2016Article
- The rise of Astyanax cavefish.Developmental dynamics : an official publication of the American Association of Anatomists · 2015Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The Mexican tetra, Astyanax mexicanus, is a unique model system consisting of cave-adapted and surface-dwelling morphotypes that diverged >1 million years (My) ago. This remarkable natural experiment has enabled powerful genetic analyses of cave adaptation. Here, we describe the application of next-generation sequencing technology to the creation of a high-density linkage map. Our map comprises more than 2200 markers populating 25 linkage groups constructed from genotypic data generated from a single genotyping-by-sequencing project. We leveraged emergent genomic and transcriptomic resources to anchor hundreds of anonymous Astyanax markers to the genome of the zebrafish (Danio rerio), the most closely related model organism to our study species. This facilitated the identification of 784 distinct connections between our linkage map and the Danio rerio genome, highlighting several regions of conserved genomic architecture between the two species despite ~150 My of divergence. Using a Mendelian cave-associated trait as a proof-of-principle, we successfully recovered the genomic position of the albinism locus near the gene Oca2. Further, our map successfully informed the positions of unplaced Astyanax genomic scaffolds within particular linkage groups. This ability to identify the relative location, orientation, and linear order of unaligned genomic scaffolds will facilitate ongoing efforts to improve on the current early draft and assemble future versions of the Astyanax physical genome. Moreover, this improved linkage map will enable higher-resolution genetic analyses and catalyze the discovery of the genetic basis for cave-associated phenotypes.
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Registered trials
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.