Synteny and candidate gene prediction using an anchored linkage map of Astyanax mexicanus

Authors

Joshua B. Gross, Department of Genetics, Harvard Medical SchoolFollow
Meredith E. Protas, Department of Genetics, Harvard Medical SchoolFollow
Melissa Conrad, Cave Biology Research Group, Department of Biology, New York UniversityFollow
Paul E. Scheid, Cave Biology Research Group, Department of Biology, New York University
Oriol Vidal, Cave Biology Research Group, Department of Biology, New York University
William R. Jeffery, Department of Biology, University of Maryland
Richard Borowsky, Cave Biology Research Group, Department of Biology, New York UniversityFollow
Clifford J. Tabin, Department of Genetics, Harvard Medical School

Document Type

Article

Source

Proceedings of the National Academy of Sciences of the United States of America

ISSN

1091-6490

Volume

105

Issue

51

First Page

20106

Last Page

20111

Publication Date

2008

Department

Natural Sciences and Mathematics

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.

Rights

Copyright © 2003 The Author(s)

PubMed ID

19104060

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-No Derivative Works 4.0 International License.