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Title: An integrated genetic linkage map and comparative genome analysis for the estuarine Atlantic killifish, Fundulus heteroclitus

Author
item WAITS, ERIC - Environmental Protection Agency (EPA)
item MARTINSON, JOHN - Environmental Protection Agency (EPA)
item RINER, BRIAN - Environmental Protection Agency (EPA)
item MORRIS, STEPHEN - Environmental Protection Agency (EPA)
item Proestou, Dina
item CHAMPLIN, DENISE - Environmental Protection Agency (EPA)
item NACCI, DIANE - Environmental Protection Agency (EPA)

Submitted to: Open Journal of Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/28/2016
Publication Date: 3/31/2016
Citation: Waits, E., Martinson, J., Riner, B., Morris, S., Proestou, D.A., Champlin, D., Nacci, D. 2016. An integrated genetic linkage map and comparative genome analysis for the estuarine Atlantic killifish, Fundulus heteroclitus. Open Journal of Genetics. 6:28-38.

Interpretive Summary: Examples of rapid contemporary evolution in the wild are rare among eukaryotic species. Multiple populations of the Atlantic killifish, Fundulus heteroclitus have recently adapted to highly toxic enviroments. In order to better understand the genetic mechanism(s) underlying this rapid evolutionary response, a suite of molecular tools are necessary. This manuscript describes the development of novel molecular markers and the construction of a genetic linkage map based on three independent genetic crosses of the Atlantic killifish. The map consists of 24 chromosomes containing 240 markers and will serve a critical role in future studies aimed at understanding evolved chemical tolerance in this species.

Technical Abstract: Background: Fundulus heteroclitus (Atlantic killifish), a non-migratory estuarine fish, exhibits high allelic and phenotypic diversity, partitioned among subpopulations that reside in disparate environmental conditions. An ideal candidate model organism for studying gene-environment reactions, the F. heteroclitus lacks the molecular tools necessary for linking genotype to phenotype. We report the contstruction of a first generation genetic linkage map of the F. heteroclitus genome and an analysis of shared synteny with two model fish species. Results: We identified hundreds of novel Simple Sequence Repeats (SSRs) which combined with existing SSRs and single nucleotide polymorphisms (SNPs) were used to construct a first generation genetic linkage map for F. heteroclitus. By integrating independent liknage maps from three F2-intercrosses, 24 linkage groups were identified consisting of 240 loci and spanning 2300 centiMorgans (cM) of recombinant genomic space. Comparisons between fish genomes support a high degree of shared synteny between the consensus F. heteroclitus linkage map and the medaka and (to a lesser extent) zebrafish physical genome assemblies. Conclusion: We developed a consensus genetic linkage map containing 24 linkage groups, consistent with the number of chromosomes reported for this species. This map will aid genome assembly, gene x environment linkage studies, and the identification of quantitative trait loci (QTL). Advanced knowledge of genome organization and content will promote F. heteroclitus as an important ecological genetic model to study evolution at the contemporary glacial scales.