Resistance to Germline RNA Interference in a Caenorhabditis elegans Wild Isolate Exhibits Complexity and Nonadditivity

Resolving the genetic complexity of heritable phenotypic variation is fundamental to understanding the mechanisms of evolution and the etiology of human disease. Trait variation among isolates from genetically efficient model organisms offers the opportunity to dissect genetic architectures and identify the molecular mechanisms of causation. Here we present a genetic analysis of loss of sensitivity to gene knockdown via exogenous RNA interference in the germline of a wild isolate of the roundworm Caenorhabditis elegans. We find that the loss of RNA interference sensitivity in the wild isolate CB4856 is recessive to the sensitivity of the lab strain N2. A cross of the strains produced F2 with intermediate sensitivities, and the segregation of the trait among F2s strongly deviated from a single locus recessive allele expectation. Linkage analysis in recombinant inbred lines derived from CB4856 and N2 identified a single significant locus on chromosome I that includes the argonaute gene ppw-1. The alleles for ppw-1 were unable to explain the sensitivity of 18 (12.1%) of the recombinant inbred lines. Complementation tests and F2 segregation analysis of these recombinant inbred lines revealed cases of complex epistatic suppression and enhancement of the effects of ppw-1. We conclude that the variation in RNA interference sensitivity between CB4856 and N2 likely involves the nonadditive interactions of eight or more genes in addition to ppw-1.