Model organisms provide the opportunity to experimentally test the correlations between genes and disease-related processes because of the high-level of conservation and the ease of manipulation. However, most model organism research is based on a single wild-type strain background with little connection to natural variation, which is like studying a single person to make conclusions about the entire human species. C. elegans is isolated worldwide and has genetic variation comparable to that of humans. Therefore, C. elegans provides the opportunity to identify the genes that vary among individuals and the molecular mechanisms for how genetic variation causes phenotypic differences.

High-throughput approaches to understand conserved drug responses

To map sensitivities to drugs, we use high-throughput assays to rapidly phenotype a collection of over 800 worldwide natural C. elegans isolates (for association mapping) or a panel of nearly 1200 recombinant inbred lines between the Bristol (N2) and Hawaii (CB4856) strains (for linkage mapping). High-throughput assays measure fecundity, growth rates, and pharyngeal pumping rates. Each trait allows us to determine different effects on the physiology of the animals. Growth rates and fecundity assay chronic exposures to compounds or stresses. By contrast, pharyngeal pumping measures the more acute response of the pharyngeal muscles and neurons to compounds or stresses. We use the COPAS Biosort system from Union Biometrica, along with other robotics to prepare and score assays. Our high-throughput phenotyping platform assays 30 conditions in 96 independent strains per week. These assays strictly control bacterial food, humidity, and temperature, eliminating much of the assay-to-assay variation and behavioral differences caused by standard agar plate assays. These high-throughput assays give us the ability to identify natural variants or induced mutations at unprecedented speeds and with increased statistical power. Currently, we are measuring responses to diverse chemotherapeutics used on the human population, to anthelmintics used on parasitic nematode populations, and to diverse toxins (pesticides and heavy metals) in which we do not know the genetic targets.

Genetic causes of resistance to anthelmintic compounds

Using high-throughput assays that measure organismal fitness (offspring production, growth rate) and behaviors (feeding rate and paralysis), we are investigating how three clade V nematode species, Caenorhabditis briggsae, Caenorhabditis elegans, and Caenorhabditis tropicalis vary in responses to anthelmintic (anti-nematode) compounds. Our goal is to identify resistance mechanisms conserved with parasitic roundworms to better treat infected people in developing countries. Our recent focus is on the genetic variants that mediate avermectin and benzimidazole resistance across natural populations. For avermectin, we have identified at least five other loci that control resistance in natural populations beyond variation in the glutamate-gated chloride channel gene, glc-1. For benzimidazoles, we found a new genomic locus involved in resistance and also high levels of natural heterogeneity in the benzimidazole target ben-1. We are collaborating with parasite research groups to validate our Caenorhabditis findings in tractable parasitic helminths.

Genetic causes of differential susceptibility to chemotherapeutic compounds

Patients that receive the same dose of a particular chemotherapeutic compound have differential susceptibilities to these drugs both in treatment efficacy and side effects. We use the model nematode Caenorhabditis elegans to identify conserved mechanisms of differential susceptibility to these compounds. Over the past five years, we generated data for animal responses to diverse chemotherapeutics using high-throughput assays that measure fecundity, growth rates, and pharyngeal pumping rates. We use the COPAS BIOSORT system from Union Biometrica, along with other robotics to prepare and score assays.

Species-wide and genome-wide variant discovery, genome assembly, and annotation

Because of the efforts of a number of highly dedicated scientists and citizen volunteers, we have amassed a large collection of more than 800 C. elegans strains from throughout the world. These strains represent nearly all known isolation locations where we have found this species. Our goals are to use this large strain collection to identify functional variation for a large number of traits and to understand more about the population genetic forces shaping the genome.

To this end, we deep sequenced all of these strains using the Illumina HiSeq platform (minimum 50x depth of coverage). This large sequence data set allows us to not only identify single nucleotide variants but to dig deeper into other classes of genetic variation, including insertion/deletions, transposon insertions, genomic rearrangements, microsatellite repeats, and copy number variants. We hope that these additional classes of variation will contribute to our understanding of how genetic variation contributes to phenotypic variation and genome evolution.

Sequence-based traits and genome evolution

Our resequencing studies of C. elegans have enabled us to identify sequence variants across the species. However, short-read sequence data enables for the exploration of sequence-based traits. Examples include but are not limited to telomere length, codon bias, rDNA copy number, and cell mitochondrial content.

Investigating sequence-based traits enables us to identify factors directly involved in the maintenance, stability, and regulation of genomes. Additionally, we can learn about long-term processes that contribute broadly to differences in genomic content among individuals.