ArticleProceedings of the National Academy of Sciences of the United States of America2008
Synteny and candidate gene prediction using an anchored linkage map of Astyanax mexicanus.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Evolution of a central dopamine circuit underlies adaptation of a light-evoked sensorimotor response in the blind cavefish.Science advances · 2026Article
- Evolution of a central dopamine circuit underlies adaptation of light-evoked sensorimotor response in the blind cavefish,bioRxiv : the preprint server for biology · 2024Article
- Immunogenetic losses co-occurred with seahorse male pregnancy and mutation in tlx1 accompanied functional asplenia.Nature communications · 2022Article
- Article
- Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World's Largest Cavefish Diversification (Cyprinidae,Frontiers in microbiology · 2022Article
- Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals, and origin of novel traits.BMC ecology and evolution · 2021Article
- Construction of a High-Density Genetic Linkage Map and QTL Mapping for Growth-Related Traits in Takifugu bimaculatus.Marine biotechnology (New York, N.Y.) · 2020Article
- Stable transgenesis in Astyanax mexicanus using the Tol2 transposase system.Developmental dynamics : an official publication of the American Association of Anatomists · 2019Article
- Effects of temperature and water turbulence on vertebral number and body shape in Astyanax mexicanus (Teleostei: Characidae).PloS one · 2019Article
- Article
- A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication.G3 (Bethesda, Md.) · 2018Article
- Embryonic origin and genetic basis of cave associated phenotypes in the isopod crustacean Asellus aquaticus.Scientific reports · 2018Article
- Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish (Royal Society open science · 2018Article
- Using Linkage Maps as a Tool To Determine Patterns of Chromosome Synteny in the GenusG3 (Bethesda, Md.) · 2017Article
- Lens apoptosis in the Astyanax blind cavefish is not triggered by its small size or defects in morphogenesis.PloS one · 2017Article
- Two - three loci control scleral ossicle formation via epistasis in the cavefish Astyanax mexicanus.PloS one · 2017Article
- The rise of Astyanax cavefish.Developmental dynamics : an official publication of the American Association of Anatomists · 2015Article
- Distinct genetic architecture underlies the emergence of sleep loss and prey-seeking behavior in the Mexican cavefish.BMC biology · 2015Article
- A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology.G3 (Bethesda, Md.) · 2014Article
- The cavefish genome reveals candidate genes for eye loss.Nature communications · 2014Article
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8 authors.
Funding
Abstract
The blind Mexican cave tetra, Astyanax mexicanus, is a unique model system for the study of parallelism and the evolution of cave-adapted traits. Understanding the genetic basis for these traits has recently become feasible thanks to production of a genome-wide linkage map and quantitative trait association analyses. The selection of suitable candidate genes controlling quantitative traits remains challenging, however, in the absence of a physical genome. Here, we describe the integration of multiple linkage maps generated in four separate crosses between surface, cave, and hybrid forms of A. mexicanus. We performed exhaustive BLAST analyses of genomic markers populating this integrated map against sequenced genomes of numerous taxa, ranging from yeast to amniotes. We found the largest number of identified sequences (228), with the most expect (E) values <10(-5) (95), in the zebrafish Danio rerio. The most significant hits were assembled into an "anchored" linkage map with Danio, revealing numerous regions of conserved synteny, many of which are shared across critical regions of identified quantitative trait loci (QTL). Using this anchored map, we predicted the positions of 21 test genes on the integrated linkage map and verified that 18 of these are found in locations homologous to their chromosomal positions in D. rerio. The anchored map allowed the identification of four candidate genes for QTL relating to rib number and eye size. The map we have generated will greatly accelerate the production of viable lists of additional candidate genes involved in the development and evolution of cave-specific traits in A. mexicanus.
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