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

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.

Multi-trait evolution in a cave fish, Astyanax mexicanus.

When surface species colonize caves, a characteristic suite of traits eventually evolves over time, regardless of species. The genetic basis of the inevitable appearance of these very similar phenotypes was investigated through quantitative trait loci (QTL) mapping of 12 traits that differ significantly between the recently evolved (<1 Myr). Mexican cave tetra and its surface conspecific. The traits were a representative set, including eye size, pigment cell numbers, chemical sensitivity, body and skull morphology, standard length, and metabolism. We used both single- and multi-trait models for QTL mapping. QTL effects of these traits were significantly clustered in the genome. We mapped 13 regions in the genome with QTL effects on from three to nine traits. These clusters could be multigenic or could represent single locus with pleiotropic alleles. Given the relatively short time available to construct clusters from unlinked genes through genomic rearrangement, and the counterintuitive polarities of some of the substitution effects, we argue that at least some of the clusters must have a pleiotropic basis.