Intellectual merit: DNA damage is important and costly enough that organisms devote scores of genes to its repair, but little is known about how individuals in natural populations vary in their underlying mutation rates, or in their ability to repair those mutations. Furthermore, little is understood about the identity of the genetic determinants of this variation, and whether these genes differ from those found in studies on laboratory organisms. This gap in knowledge seriously limits the ability to understand the mechanisms that maintain genome integrity, and to understand natural variation in mutation-dependent phenomena such as senescence. The long-term goal of this project is to understand the genetic and environmental factors that affect genome stability in nature. The central hypothesis of this project is that individuals vary in somatic mutation rate, and that this variation is caused by differences in gene sequences and gene expression. To test the central hypothesis, this project examines variation in somatic mutation rate in 40 inbred lines of Drosophila melanogaster derived from a natural population in North Carolina. Genome-wide expression and sequence data are available for these lines. The study is made possible by the recent creation of a transgenic model to measure somatic mutation rates in vivo in the fruit fly with a lacZ reporter gene. Aim 1 will involve experiments to test the hypothesis that genetic variation exists for somatic mutation rate by placing a lacZ reporter gene into the 40 inbred lines and measuring line-, sex- and tissue-specific variation for somatic mutation. This hypothesis is strongly supported by preliminary data showing heritable variation for somatic mutation rate. In Aim 2, genetic and regulatory factors associated with somatic mutation rate will be investigated. Genome-wide association studies of single nucleotide polymorphisms will be used to identify genes associated with somatic mutation rate. Expression data will be analyzed to search for networks of co-regulated genes whose expression levels correlate with somatic mutation rate. Aim 3 will determine whether genotypes with naturally high somatic mutation rate show relatively large increases in mutation frequency when exposed to paraquat, a herbicide that has been shown previously to increase the frequency of mutations in Drosophila. This project uses a creative combination of quantitative genetics, molecular genetics, and high-throughput genomics. In its focus on natural genetic variation, this work is expected to lead to the discovery of new genes that influence evolutionarily relevant variation in somatic mutation rates and to create a novel paradigm for understanding the genetic basis of somatic mutation rate. This new framework should provide better understanding of the evolution of genome stability and genome structure.
Broader impacts: This proposal provides the first direct study of natural variation for somatic mutation rate, and should lead to the identification of novel genes associated with somatic mutation rate. All novel strains developed and all expression data collected during the course of this project will be made freely available to the research community. The project will provide continued hands-on research training for high school and undergraduate students, including students from underrepresented populations. Trainees will be given the opportunity to publish scientific articles and to attend national scientific meetings with the investigator.