title: Discovery and validation of gene-linked diagnostic SNP markers for assessing hybridization between Largemouth bass (Micropterus salmoides) and Florida bass (M. floridanus).
abstract: Efforts to improve recreational fisheries have included widespread stocking of Micropterus floridanus outside its native range of peninsular Florida. Hybridization of Florida bass (M. floridanus) with largemouth bass (Micropterus salmoides) has now dramatically expanded beyond a naturally occurring intergrade zone in the southeast U.S. In recent years, there has been growing interest in protecting the genetic integrity of native basses and assessing the impact and nature of M. salmoides/M. floridanus introgression from the standpoint of hatchery and sport-fishery managers, fish biologists, ecologists and evolutionary biologists. Here, we conducted RNA-seq-based sequencing of the transcriptomes of M. salmoides, M. floridanus and their F1 hybrid and identified a set of 3674 SNP markers with fixed-allelic differences from 2112 unique genes. We then developed a subset of 25 of these markers into a single diagnostic multiplex assay and validated its capacity for assessing integrity and hybridization in hatchery and wild populations of largemouth and Florida bass. The availability of this resource, high-quality transcriptomes and a large set of gene-linked SNPs, should greatly facilitate functional and population genomics studies in these key species and allow the identification of traits and processes under selection during introgressive hybridization.
authors.affiliation: School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
authors.forename: Chao
authors.initials: C
authors.lastname: Li
authors.forename: Spencer
authors.initials: S
authors.lastname: Gowan
authors.forename: Ammu
authors.initials: A
authors.lastname: Anil
authors.forename: Benjamin H
authors.initials: BH
authors.lastname: Beck
authors.forename: Wilawan
authors.initials: W
authors.lastname: Thongda
authors.forename: Huseyin
authors.initials: H
authors.lastname: Kucuktas
authors.forename: Ludmilla
authors.initials: L
authors.lastname: Kaltenboeck
authors.forename: Eric
authors.initials: E
authors.lastname: Peatman
mesh_terms: D000818:Animals; D001492:Bass / Q000145:classification* / Q000235:genetics*; D002678:Chimera; D060005:Genotyping Techniques / Q000379:methods*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D059467:Transcriptome
keywords: Micropterus; bass; hybridization; introgression; single nucleotide polymorphism