Individuals within a population vary across a broad range of traits, including many that are influenced by multiple genetic factors as well as the environment. Complex traits that are medically relevant include susceptibilities to many common diseases, such as cancer, along with sensitivity to drugs, such as chemotherapeutics. However, the identification and validation of genetic loci underlying complex traits in humans is difficult. Caenorhabditis elegans is a tractable model that can be used to identify the genetic factors that cause variation in complex traits by pairing high-throughput phenotypic assays with a broad range of genetic tools.
Like humans, strains of C. elegans, vary in sensitivity to the chemotherapeutic drug bleomycin. The laboratory strain, N2, is sensitive to the drug whereas a genetically diverged strain, CB4856, is more resistant. We examined bleomycin sensitivity in a panel of 350 whole-genome sequenced recombinant inbred advanced intercross lines (RIAILs) generated from a cross between the N2 and CB4856 parents. Recombinant strains exhibited variation in bleomycin sensitivity as determined by changes in growth rate, offspring production, and feeding rate. Approximately 1,600 markers across the genome were used to correlate genotype with phenotype. Linkage analysis identified a quantitative trait locus (QTL) on chromosome V with a 162-kb confidence interval that is strongly correlated with bleomycin sensitivity. Within this interval, we identified five candidate genes — three genes with nonsynonymous variants and two genes with varied gene expression between N2 and CB4856.
I have developed a multi-pronged approach to identify any and all causative variants that contribute to bleomycin sensitivity. This approach involves experimental and computational methods, including building nearly isogenic lines (NILs) to empirically narrow the interval and determine the effect of the chromosome V QTL on bleomycin sensitivity as well as creating CRISPR-generated knock-out alleles of each candidate gene in both genetic backgrounds. Ultimately, I aim to identify the gene(s) within the 162-kb QTL on chromosome V in which variation explains differential sensitivity to bleomycin, thus improving our understanding of variation in human response to this chemotherapeutic.