title: Linkage Mapping and Comparative Genomics of Red Drum (Sciaenops ocellatus) Using Next-Generation Sequencing.
abstract: 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.
authors.affiliation: Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412 ch263@st-andrews.ac.uk.
authors.forename: Christopher M
authors.identifier: 0000-0003-0227-7225
authors.initials: CM
authors.lastname: Hollenbeck
authors.affiliation: Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412.
authors.forename: David S
authors.initials: DS
authors.lastname: Portnoy
authors.affiliation: Mote Marine Laboratory and Aquarium, Sarasota, Florida 34236.
authors.forename: Dana
authors.initials: D
authors.lastname: Wetzel
authors.affiliation: Mote Marine Laboratory and Aquarium, Sarasota, Florida 34236.
authors.forename: Tracy A
authors.initials: TA
authors.lastname: Sherwood
authors.affiliation: Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845.
authors.forename: Paul B
authors.initials: PB
authors.lastname: Samollow
authors.affiliation: Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412.
authors.forename: John R
authors.initials: JR
authors.lastname: Gold
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D010473:Perciformes / Q000235:genetics*; D026801:Synteny / Q000235:genetics*
keywords: RAD-seq; SNPs; genetic map; haplotypes; synteny