A comprehensive expressed sequence tag linkage map for tiger salamander and Mexican axolotl: enabling gene mapping and comparative genomics in Ambystoma

Abstract

Expressed sequence tag (EST) markers were developed for Ambystoma tigrinum tigrinum (Eastern tiger salamander) and for A. mexicanum (Mexican axolotl) to generate the first comprehensive linkage map for these model amphibians. We identified 14 large linkage groups (125.5-836.7 cM) that presumably correspond to the 14 haploid chromosomes in the Ambystoma genome. The extent of genome coverage for these linkage groups is apparently high because the total map size (5251 cM) falls within the range of theoretical estimates and is consistent with independent empirical estimates. Unlike most vertebrate species, linkage map size in Ambystoma is not strongly correlated with chromosome arm number. Presumably, the large physical genome size ( approximately 30 Gbp) is a major determinant of map size in Ambystoma. To demonstrate the utility of this resource, we mapped the position of two historically significant A. mexicanum mutants, white and melanoid, and also met, a quantitative trait locus (QTL) that contributes to variation in metamorphic timing. This new collection of EST-based PCR markers will better enable the Ambystoma system by facilitating development of new molecular probes, and the linkage map will allow comparative studies of this important vertebrate group.

Figure 1.

(A) Plot of the distribution of the χ² statistic for 1:1 segregation of marker genotypes vs. standard χ² distributions for gene and EST-based markers. (B) Plot of the distribution of the χ² statistic for 1:1 segregation of marker genotypes vs. standard χ² distributions for anonymous markers (AFLPs and RAPDs). (C) Plot of χ² statistics for 1:1 segregation of marker genotypes vs. map position. The x-axis represents LG1–14 concatenated head to tail, and vertical bars demark boundaries between linkage groups.

Figure 2.

The tiger salamander linkage map (LG1–14).

Figure 2.

The tiger salamander linkage map (LG1–14).

Figure 3.

LRS plot for association between segregation of pigment phenotypes and marker genotypes in LG1 and LG14. Horizontal lines represent LRS thresholds for suggestive (37th percentile), significant (95th percentile), and highly significant (99.9th percentile) associations (Lander and Kruglyak 1995) estimated using MapMaker QTXb19.

Figure 4.

LRS plot for association between segregation of metamorphosis vs. paedomorphosis and marker genotypes in LG3 and LG4. Horizontal lines represent LRS thresholds for suggestive (37th percentile), significant (95th percentile), and highly significant (99.9th percentile) associations (Lander and Kruglyak 1995) estimated using MapMaker QTXb19.