Dissertation/Thesis Abstract

Using next-gen sequencing to assist a conservation hatchery: A SNP panel for the genetic management of endangered Delta Smelt
by Lew, Ryan, M.S., University of California, Davis, 2015, 124; 1590837
Abstract (Summary)

The federally threatened Delta Smelt has been cultured in a conservation hatchery since 2008 in response to significant declines in the wild. The refuge relies on accurate, efficacious, and repeatable molecular techniques to help maintain the population's overall genetic diversity and minimize inbreeding. We have created a panel of single nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management with microsatellites. Properly implemented, a SNP panel is a more powerful, repeatable, and higher-throughput method. Its use will streamline the management of the captive Delta Smelt population, which is performed in near real-time throughout the spawning season (February - May). For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn using restriction site associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single pair crosses at 2317 newly discovered loci with RAD-seq. We successfully mapped 1123 loci and identified 26 linkage groups. Fluidigm SNPtype genotyping assays were developed for 104 mapped loci selected for minor allele frequency (>20%), neutrality (Hardy-Weinberg equilibrium), and marker location. Candidates for the genotyping panel were evaluated on a 96x96 Integrated Fluidic Circuit and tested for marker accuracy and ability to accurately assign parentage. When applied in conjunction with mating records, we found that a panel of 24 independent SNPs successfully assigned 100% of tested offspring if all samples were genotyped at a minimum of 18 loci.

Indexing (document details)
Advisor: May, Bernie
Commitee: Miller, Michael R., Whitehead, Andrew R.
School: University of California, Davis
Department: Ecology
School Location: United States -- California
Source: MAI 54/05M(E), Masters Abstracts International
Source Type: DISSERTATION
Subjects: Ecology, Genetics, Aquatic sciences
Keywords: Conservation genetics, Endangered species, Parentage analysis, Pedigree-based managmeent, Restriction site associated DNA sequencing, Single nucleotide polymorphism
Publication Number: 1590837
ISBN: 9781321806656
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