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.

Hybridization and Genetic Structure in Phenotypic Spotted Bass in Texas

“…More extensive sampling from these populations and the surrounding drainages could clarify the extent of hybridization, the presence of a potential hybrid zone, and possibly resolve additional population structure. Numerous genetic resources have been developed to allow for discrimination among Micropterus species (Philipp et al 1983;Lutz-Carrillo et al 2008;Seyoum et al 2013;Li et al 2014;Gowan 2015;Tringali et al 2015), but these sister species (Guadalupe Bass and Spotted Bass) have remained difficult to reliably distinguish (Kassler et al 2002;Ray et al 2015). Here, we confirmed the utility of two nuclear and one mitochondrial taxa-specific fixed SNPs that should aid in discriminating between these congeners.…”

“…; Li et al. ; Gowan ; Tringali et al. ), but these sister species (Guadalupe Bass and Spotted Bass) have remained difficult to reliably distinguish (Kassler et al.…”

SNP panel development for genetic management of wild and domesticated white bass (Morone chrysops)

“…Toward this end, we utilized a genotyping‐by‐sequencing (GBS) approach for bulk SNP sequencing and screening, followed by SNP validation and panel creation using MassARRAY technology (Li et al . ; Thongda et al . ; Zhao et al .…”

genotypeR: An integrated r package for single nucleotide polymorphism genotype marker design and data analysis

“…Both Golden Gate and Sequenom genotyping platforms offer a cost effective alternative to GBS when addressing problems not requiring many markers (Perkel, ). For example ancestry informative markers can be designed from few high coverage NGS samples to screen many individuals assigning ancestry or admixture status (Li, Gown, et al., ; Li, Waldbieser, et al., ). In addition, genotyping can be used to map phenotypes to chromosomal locations with quantitative trait loci (QTL) analysis (Erickson, Fenster, Stenoien, & Price, ), and to study recombination rate variation with linkage analysis (Stevison, Hoehn, & Noor, ; Stevison & Noor, ).…”

“…In addition, SNP genotyping can facilitate non‐model organism conservation when whole genome re‐sequencing is cost prohibitive. Recently, genotyping was used to investigate natural/artificial introgression between Blue Catfish and bass populations (Li, Gown, et al., ; Li, Waldbieser, et al., ). Similarly, SNP genotyping correctly identified fathers in cooperative breeding bird populations cheaper and more often than microsatellites (Weinman, Solomon, & Rubenstein, ).…”