Date of Award
Doctor of Philosophy
Order Acipenseriformes (sturgeons and paddlefishes) is an ancient lineage of bony fishes (> 200 million years old) with most extant species at conservation risk. The pallid sturgeon, Scaphirhynchus albus, is a federally endangered species native to the Mississippi and Missouri River basins. Hybridization with sympatric shovelnose sturgeon, S. platorynchus, is one of several threats to pallid sturgeon. Current molecular markers cannot reliably distinguish among pure species and multigenerational backcrosses. This information is critical for implementation of management strategies to increase populations through natural reproduction and artificial propagation. Genotypes from a large panel of unlinked single-nucleotide polymorphisms (SNPs) may provide greater resolution of the two species; however, paralogous sequence variants (PSVs) within individuals resulting from an ancient whole genome duplication event confound SNP development. The aim of this dissertation was to produce unlinked disomic SNPs that would increases resolution between pallid sturgeon and shovelnose sturgeon. This was achieved by producing haploid gynogens, which contain only DNA from the maternal parent, and then producing a reference from these haploid gynogens. Sequence assembly based on haploids informed the presence of multi-locus contigs. More than 11,000 disomic SNP markers were produced that differentiate between the two species by mapping 120 individuals of either species onto the haploid reference. A linkage map, based on three haploid families, was able to resolve some paralogs and can be used to inform which discriminatory SNP markers are linked. Future research should convert the disomic markers derived in this study to an applied form, such as that achieved by genotyping-by-thousands.
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