RAD-seq, SNPs, genetic map, haplotypes, synteny
Digital Object Identifier (DOI)
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.
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Citation / Publisher Attribution
G3: Genes, Genomes, Genetics, v. 7, issue 3, p. 843-850
Scholar Commons Citation
Hollenbeck, Christopher M.; Portnoy, David S.; Wetzel, Dana; Sherwood, Tracy A.; Samollow, Paul B.; and Gold, John R., "Linkage Mapping and Comparative Genomics of Red Drum (Sciaenops ocellatus) Using Next-Generation Sequencing" (2017). C-IMAGE Publications. 51.