Developments in next-generation sequencing allow genotyping of thousands of genetic markers across hundreds of individuals in a cost-effective manner. Because of this, it is now possible to rapidly produce dense genetic linkage maps for nonmodel species. Here, we report a dense genetic linkage map for red drum, a marine fish species of considerable economic importance in the southeastern United States and elsewhere. We used a prior microsatellite-based linkage map as a framework and incorporated 1794 haplotyped contigs derived from high-throughput, reduced representation DNA sequencing to produce a linkage map containing 1794 haplotyped restriction-site associated DNA (RAD) contigs, 437 anonymous microsatellites, and 44 expressed sequence-tag-linked microsatellites (EST-SSRs). A total of 274 candidate genes, identified from transcripts from a preliminary hydrocarbon exposure study, were localized to specific chromosomes, using a shared synteny approach. The linkage map will be a useful resource for red drum commercial and restoration aquaculture, and for better understanding and managing populations of red drum in the wild.
Hollenbeck, C. M., Portnoy, D. S., Wetzel, D., Sherwood, T. A., Samollow, P. B., & Gold, J. R. (2017). Linkage mapping and comparative genomics of red drum (Sciaenops Ocellatus) using next-generation sequencing. G3: Genes, Genomes, Genetics, 7(3), 843–850. https://doi.org/10.1534/g3.116.036350