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 (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. T HE tiger salamander (Ambystoma tigrinum) species complex consists of several closely related and phenotypically diverse taxa that range from central Mexico to southern Canada (Shaffer and McKnight 1996). The complex as a whole is an important, naturalistic model system because taxa are characterized by extensive interspecific and intraspecific variation for a number of ecologically important traits, including expression of metamorphic vs.

Rapid spread of invasive genes into a threatened native species

“…2). These three markers (E6E11, E12C11, and E23C6) are unlinked and map to linkage groups 11, 14, and 4, respectively, in the Ambystoma mexicanum x tigrinum linkage map (32). It is possible that these three exceptional markers are not diagnostic and we are mistakenly attributing a natural pattern of variation to introgression.…”

“…Markers were developed (8) by sequencing mapped EST markers sampled at ≈50 cM intervals based on ref. 32. Candidate single nucleotide differences were identified in a panel of four California Tiger Salamanders (from Jepson Prairie, well outside the introgression zone) and four Barred Tiger Salamanders.…”

Variation in genomic recombination rates among animal taxa and the case of social insects

“…Care was taken to cover the full range of genomic recombination densities for these taxa. For example, for the vertebrates, we chose the animals with both the highest and the lowest recombination densities known today, the chicken Gallus domesticus and the tiger salamander Ambystoma tigrinum (Smith et al, 2005), respectively as well as recent examples from the literature.…”

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

“…Because gene-associated markers are conserved through a wide evolutionary spectrum of species, they have become the most desirable type of marker for comparative mapping (Martin et al 2005;Moretzsohn et al 2005;Smith et al 2005;Snelling et al 2005;Casasoli et al 2006;Kim et al 2006;Sasazaki et al 2006;Sawera et al 2006). We have previously reported the identification of a large number of ESTassociated microsatellites and SNPs (He et al 2003;Serapion et al 2004a;Wang et al 2008).…”