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

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.

Fig. 1.

Schematic diagram of the relative positions of anchored genomic sequences of Astyanax LGI 1–12 to chromosomes in Danio. Astyanax LGI 1 is anchored to Danio chromosomes 5, 20, 24, 3 and 13; LGI 2 is anchored to Danio chromosomes 15, 2, 20; LGI 3 is anchored to Danio chromosomes 9 and 17; LGI 4 is anchored to Danio chromosomes 6 and 3; LGI 5 is anchored to Danio chromosomes 13, 1, 5; LGI 6 is anchored to Danio chromosomes 14, 25, 4; LGI 7 is anchored to Danio chromosomes 4, 14, 25; LGI 8 anchors exclusively to Danio chromosome 1; LGI 9 is anchored to Danio chromosomes 8 and 5; LGI 10 is anchored to Danio chromosomes 12 and 5; Astyanax LGI 11 anchors exclusively to Danio chromosome 18; and LGI 12 is anchored to Danio chromosomes 22 and 8. Markers are color-coded, denoting their relative positions in each integrated Astyanax linkage group. In each image, chromosomes in Danio are shown with the highest number of hits first (blue), second highest number of hits (green), third highest (orange), fourth highest (purple) and fifth highest (brown). The largest predicted distance (Mb) spanned by respective anchored genomic markers in the Danio genome depicted within each color-coded region (white box). Note: schematic diagrams of chromosomes and linkage groups are not drawn to scale. Markers are indicated at their relative positions along each chromosome or linkage group.

Fig. 2.

Schematic diagram of the relative positions of anchored genomic sequences of Astyanax LGI 13–24 and 26 to chromosomes in Danio. Astyanax LGI 13 is anchored to Danio chromosomes 16, 24, 6; LGI 14 anchors exclusively to Danio chromosome 2; LGI 15 is anchored to Danio chromosomes 21, 2, 24; LGI 16 anchors exclusively to Danio chromosomes 12; LGI 17 is anchored to Danio chromosomes 7, 9, 10, 21; LGI 18 is anchored exclusively to Danio chromosomes 10; (C) LGI 19 is anchored to Danio chromosomes 19 and 3; LGI 20 is anchored to Danio chromosomes 5 and 22; LGI 21 anchors exclusively to Danio chromosomes 1; LGI 22 is anchored to Danio chromosomes 7 and 2; (C) LGI 23 anchors exclusively to Danio chromosomes 17; LGI 24 anchors exclusively to Danio chromosome 7; and LGI 26 is anchored to Danio chromosomes 23 and 7. Markers are color-coded, denoting their relative positions in each integrated Astyanax linkage group. In each panel, chromosomes in Danio are shown with the highest number of hits first (blue), second highest number of hits (green), third highest (orange) and fourth highest (purple). The largest predicted distance (Mb) spanned by respective anchored genomic markers in the Danio genome depicted within each color-coded region (white box). Note: schematic diagrams of chromosomes and linkage groups are not drawn to scale. Markers are indicated at their relative positions along each chromosome or linkage group.