Genetic Linkage Map and Comparative Genome Analysis for the Atlantic Killifish (<i>Fundulus heteroclitus</i>)

Abstract

Genetic linkage maps are valuable tools in evolutionary biology; however, their availability for wild populations is extremely limited. Fundulus heteroclitus (Atlantic killifish) is a non-migratory estuarine fish that exhibits high allelic and phenotypic diversity partitioned among subpopulations that reside in disparate environmental conditions. An ideal candidate model organism for studying gene-environment interactions, the molecular toolbox for F. heteroclitus is limited. We identified hundreds of novel microsatellites which, when combined with existing microsatellites and single nucleotide polymorphisms (SNPs), were used to construct the first genetic linkage map for this species. By integrating independent linkage maps from three genetic crosses, we developed a consensus map containing 24 linkage groups, consistent with the number of chromosomes reported for this species. These linkage groups span 2300 centimorgans (cM) of recombinant genomic space, intermediate in size relative to the current linkage maps for the teleosts, medaka and zebrafish. Comparisons between fish genomes support a high degree of synteny between the consensus F. heteroclitus linkage map and the medaka and (to a lesser extent) zebrafish physical genome assemblies.

Genetic basis for rapidly evolved tolerance in the wild: adaptation to toxic pollutants by an estuarine fish species

“…Genotyping was conducted using microsatellite and single nucleotide polymorphism (SNP) markers, identified as polymorphic in the parental (P) generation in each cross, selected from the dense panel of genetic markers used to create the first genetic map for this species (Waits et al . ). Statistical analysis identified highly significant phenotype‐to‐genotype associations, characterized as logarithm of odds of linkage (LOD) scores, which measure the strength of evidence for the presence of a QTL (Van Ooijen ).…”

“…QTL were annotated using recently developed killifish genomic resources, including gene models for F. heteroclitus (https://my.mdibl.org/display/FGP/Home; NSF DEB‐1120512) and the first killifish genetic map (Waits et al . ). In addition, orthology and conserved syntenic relationships between fish species provided further support for the identification of putative tolerance genes.…”

“…) and interpreted QTL using newly published gene models (National Science Foundation, DEB‐1120512) and genetic map for F. heteroclitus (Waits et al . ) (see details below and in SI). There are relatively few QTL analyses of ecologically valuable traits in marine fishes, with exception of several studies to identify the basis for repeated evolution concurrent with transition to freshwater habitats among three‐spine stickleback populations (review Nielsen et al .…”

“…contributed significantly to design and implementation of data analysis and interpretation and contributed to the writing of the manuscript; he is the lead author of companion study: Waits et al . ().…”

A high-density genetic linkage map for Chinese perch (Siniperca chuatsi) using genotyping-by-sequencing (GBS)

“…Segregation distortion is a phenomenon that genotype frequencies at a locus deviate from their Mendelian expectations [35], and it is considered to be a feature of genetic maps in many species, such as red drum [6], Atlantic Killifish [36], bighead carp [37], and Nile tilapia [38]. Many studies have already reported that inclusion of distorted markers in map construction has slight impact on the accuracy for determining maker orders and map length [39,40].For better understanding the distribution pattern of segregation distortion between the two sexes in S. chuatsi, all the distorted markers were retained and used to reconstruct the sex-specific maps.…”