The broad objective of the proposed research is the genetic dissection of a large number of complex and quantitative traits in the nematode worm and model organism C. elegans, with a focus on two classes of traits with relevance to human health: responses to pathogens and drugs. Success in understanding the genetic basis of phenotypic variation in a metazoan will provide critical guidance for the design of genotype-phenotype studies in humans and other organisms of medical, biological, and agricultural interest. The methods and resources developed will be broadly applicable to other phenotypes in C. elegans. The results will improve our understanding of the genes and pathways involved in susceptibility to pathogens, and in the mechanisms of action, resistance, and off-target effects of chemotherapeutics, anthelmintics, pesticides, and other compounds. Specifically, we will develop high-throughput quantitative phenotyping assays for these traits and apply them to genetic resources developed during the previous project period: a large set of high-resolution advanced intercross recombinant inbred lines from a cross between Bristol and Hawaii isolates, and a diverse collection of wild isolates extensively characterized for sequence variation. We will also apply these assays to new genetic resources that we will develop as part of the proposed research: we will build and genotype mapping populations from a maximally diverse subset of wild isolates. We will also develop new approaches for rapid identification of quantitative trait loci for any starting set of parent strains. We expect these efforts to produce:(i) a set of well-characterized diverse wild isolates and a broadly useful multiparent mapping population that will be shared with the C. elegans research community;(ii) new mapping methods applicable to C. elegans and other species;and (iii) a large set of loci for further investigation. We then propose to identify the genes and polymorphisms that underlie these loci, and to investigate the genetic architectures of the traits, including the population frequencies of the relevant alleles. We will confirm candidate genes and regions by using RNAi and transgenics to knock down or express genes in the appropriate strains. We will measure the frequencies of the identified alleles in the full diverse collection of wild isolates, and answer questions about rare vs. common alleles, additivity vs. dominance, and the role of genetic interactions. We expect to elucidate key principles of genetic architecture that will guide study design in C. elegans and other species. The pathways C. elegans uses to respond to biotic and abiotic stresses are conserved in humans and involved in a variety of diseases, including cancer and diabetes. Thus, we will leverage the power of the worm to better understand human biology.

Public Health Relevance

Genetic factors underlie susceptibility to virtually every human disease, and much of current biomedical research is based on the expectation that identifying these factors is a crucial step in improving diagnosis, prevention, and treatment. Identification i difficult because the genetic basis of common disorders is complex, with disease susceptibility influenced by multiple genes. The proposed research will improve our understanding of genetic complexity and provide critical guidance for studies of the genetic basis of common human diseases. The proposed research will also provide insights into the genetic basis of two classes of traits with immediate health relevance-responses to pathogens and to drugs.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
2R01HG004321-04A1
Application #
8295375
Study Section
Genetic Variation and Evolution Study Section (GVE)
Program Officer
Brooks, Lisa
Project Start
2007-08-16
Project End
2015-05-31
Budget Start
2012-08-18
Budget End
2013-05-31
Support Year
4
Fiscal Year
2012
Total Cost
$336,000
Indirect Cost
$124,810
Name
Princeton University
Department
None
Type
Organized Research Units
DUNS #
002484665
City
Princeton
State
NJ
Country
United States
Zip Code
08544
Andersen, Erik C; Bloom, Joshua S; Gerke, Justin P et al. (2014) A variant in the neuropeptide receptor npr-1 is a major determinant of Caenorhabditis elegans growth and physiology. PLoS Genet 10:e1004156
Andersen, Erik C; Gerke, Justin P; Shapiro, Joshua A et al. (2012) Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity. Nat Genet 44:285-90
Seidel, Hannah S; Ailion, Michael; Li, Jialing et al. (2011) A novel sperm-delivered toxin causes late-stage embryo lethality and transmission ratio distortion in C. elegans. PLoS Biol 9:e1001115
Rockman, Matthew V; Skrovanek, Sonja S; Kruglyak, Leonid (2010) Selection at linked sites shapes heritable phenotypic variation in C. elegans. Science 330:372-6
Ehrenreich, I M; Gerke, J P; Kruglyak, L (2009) Genetic dissection of complex traits in yeast: insights from studies of gene expression and other phenotypes in the BYxRM cross. Cold Spring Harb Symp Quant Biol 74:145-53
Reddy, Kirthi C; Andersen, Erik C; Kruglyak, Leonid et al. (2009) A polymorphism in npr-1 is a behavioral determinant of pathogen susceptibility in C. elegans. Science 323:382-4
Rockman, Matthew V; Kruglyak, Leonid (2009) Recombinational landscape and population genomics of Caenorhabditis elegans. PLoS Genet 5:e1000419
McGrath, Patrick T; Rockman, Matthew V; Zimmer, Manuel et al. (2009) Quantitative mapping of a digenic behavioral trait implicates globin variation in C. elegans sensory behaviors. Neuron 61:692-9
Seidel, Hannah S; Rockman, Matthew V; Kruglyak, Leonid (2008) Widespread genetic incompatibility in C. elegans maintained by balancing selection. Science 319:589-94
Palopoli, Michael F; Rockman, Matthew V; TinMaung, Aye et al. (2008) Molecular basis of the copulatory plug polymorphism in Caenorhabditis elegans. Nature 454:1019-22

Showing the most recent 10 out of 12 publications