CBA: QEIB: Estimation and Interpretation of Allele Frequencies: Novel Theoretical Analyses and High-Throughput Quantitation by DNA Pooling

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Simple sequence repeats (SSRs) are repetitive sequences of DNA that have been found throughout the genome. SSRs are studied in diverse scientific settings in many kinds of organisms. Relative to the standard approach of individual genotyping, protocols using SSR DNA pooled from multiple individuals have the potential to improve laboratory efficiency (in terms of time and money) for many kinds of population genetic studies. This study investigates laboratory methods for estimating SSR allele frequencies using pooled striped bass DNA to determine optimal protocols. A complementary set of mathematical analyses will investigate the estimation of associations among alleles, the assessment of genetic structure among subpopulations, alternative stochastic models for genetic drift, and the spatial rate of spread of novel, advantageous genes into structured populations.Allele frequency estimation by DNA pooling has the potential to facilitate a wide variety of genetic investigations, including applications in disease mapping, forensic science, virology, and microbial ecology. Moreover, striped bass is economically important in the fishing and aquaculture industries, and the mathematical analyses will facilitate population genetic studies concerning the management of this and other species whose populations are of conservation and/or economic importance. Finally, this research is interdisciplinary, involving investigators with experience in statistics and genetics, physiology and biotechnology, and population ecology and genetics, and the expectation is that the senior personnel and their students, as well as their science, will benefit from the interaction.