Electronic Thesis and Dissertation Repository

Thesis Format

Monograph

Degree

Master of Science

Program

Biology

Supervisor

Hill, Kathleen A.

Abstract

In the study of genetic diversity in non-model species there is a notable lack of the low-cost, high resolution tools that are readily available for model organisms. Genotyping microarray technology for model organisms is well-developed, affordable, and potentially adaptable for cross-species hybridization. The Mouse Diversity Genotyping Array (MDGA), a single nucleotide polymorphism (SNP) genotyping tool designed for M. musculus, was tested as a tool to survey genomic diversity of wild species for inter-order, inter-family, inter-genus, and intra-genus comparisons. Application of the MDGA cross-species provides genetic distance information that reflects known taxonomic relationships reported previously between non-model species, but there is an underestimation of genetic diversity for non-Mus samples. The number and types of samples included in sets genotyped together must be considered in cross-species hybridization. The number of loci with heterozygous genotypes mapped to published genome sequences indicates potential for cross-species MDGA utility.

Summary for Lay Audience

There is a need for a tool that can assay DNA sequence differences in species that are understudied and for which there is little or no DNA sequence information available. One method of analyzing differences in DNA sequences in species with well-understood genomes is through a genotyping microarray, a technology with demonstrated utility cross-species. This tool is capable of examining the DNA sequence information at hundreds of thousands of sites across the genomes of well-studied organisms in a single assay. The Mouse Diversity Genotyping Array (MDGA) is a tool that was designed to examine known differences at 493,290 sites across the genome of the house mouse, Mus musculus. Given that the MDGA was designed for the house mouse, and that closely-related organisms share genetic similarity, the MDGA was tested for utility in identifying genome variation in other wild (feral) mice and rodents. The MDGA was tested on 44 DNA samples from inbred laboratory mice and wild species that last shared a common ancestor millions of years ago. Variation identified from more distantly-related species that were not of the same genus as the laboratory house mouse was an underestimate of the true amount of variation present in the genome of wild species. The utility of the MDGA for use with DNA from wild species is best suited to mice from the same genus as the house mouse. Identifying changes in genetic variation within populations of wild rodents can help researchers understand the links between specific genome changes and the ability to adapt to pressures in the environment, as well as better understand the evolution of rodents. The MDGA is a cost-effective tool for rapidly identifying genetic variation in wild rodent species until the cost of sequencing the genomes of understudied species is reduced.

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