Development and application of diagnostic SNP marker resources for Northern (Micropterus salmoides salmoides) and Florida (Micropterus salmoides floridanus) largemouth bass.
Type of DegreeMaster's Thesis
Fisheries and Allied Aquacultures
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Efforts to improve recreational fisheries have included widespread stocking of Micropterus salmoides floridanus outside its native range of peninsular Florida. Hybridization of Florida bass (M. salmoides floridanus) with Northern largemouth bass (Micropterus salmoides 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.s. salmoides/M.s. floridanus introgression from the standpoint of hatchery and sport-fishery managers, fish biologists, ecologists and evolutionary biologists. Here, RNA-seq-based sequencing of the transcriptomes of M.s. salmoides, M.s floridanus and their F1 hybrid was conducted and a set of 3674 SNP markers with fixed-allelic differences from 2112 unique genes were identified. A subset of 61 of these markers were then developed into a set of diagnostic multiplex assays and their capacity for assessing integrity and hybridization in hatchery and wild populations of Northern largemouth and Florida bass was evaluated. Use of these markers for population comparisons and hybridization rate evaluations were demonstrated in populations spanning the state of Alabama. Geographic isolation by natural barriers (fall line and drainage basins) were found to lead to variation in introgression level, indicating limited effect of stocking efforts in some locations, while other populations appeared to have had successful introduction of FLMB alleles. iii An attempt was also made to use these markers to assess the effect of FLMB allele introgression on trophy bass populations in Lake Guntersville, AL. Correlation between genotype and size was observed in fish sampled from tournaments. The heavier fish had more FLMB influence and higher heterozygosity. Electrofishing surveys were also conducted to collect size at age data for the Lake Guntersville population and supplement the tournament samples. While growth differences were not apparent between genotype variants within this electrofishing sample, size and genotype differences were observed between fish caught by tournament anglers and fish caught by electrofishing surveys. Some individuals sampled from the tournament bass had higher observed weights than those found within the electrofishing sample. Also significantly higher mean FLMB allele frequency was observed in the tournament samples when compared to electrofishing samples. The availability of this resource, high-quality transcriptomes and a large set of gene-linked SNPs, should continue to greatly facilitate functional and population genomics studies in these key species and allow the identification of traits and processes under selection during introgressive hybridization, as well as facilitate more efficient genetic management of hatchery and stocking programs aimed at enhancing or conserving various populations of largemouth bass.