The C. elegans genome is compact, measuring just over 100MB. With approximately 20,000 predicted genes, this eukaryotic genome can generate a complex organism with a highly-predictable and well-defined cell lineage. Despite the depth of knowledge regarding this organism, the function of nearly half of its genes remains unclear. Although there are many forward and reverse genetic techniques available, all of them require culturing each strain individually. To improve the ability to phenotypically characterize genetic variants, we sought to develop a method to assay many variants in parallel. [AR1] The Million Mutation Project (MMP) yielded a library of 2007 mutagenized strains and 40 wild isolates with fully sequenced genomes encompassing in toto more than 1.4M single nucleotide variants. We hypothesized that a number of these mutations could impact organismal fitness across a wide range of environmental conditions. Based on genomic data, we designed a series of molecular inversion probes (MIPs) that targeted strain-specific variants. We naively pooled sets of 40-60 MMP strains or wild isolates and cultured these for four to ten generations under conditions that varied by food source or temperature. Using the phenotype of population fitness, we analysed overall population composition at multiple timepoints via sequencing (phenoMIPs). Our analysis of phenoMIP libraries, generated population growth phenotypes allowing us to assign strains into one of multiple fitness categories. From this data, we mapped several slow-growth mutants to specific loci via MIP-MAP. We further observed strain-specific alterations to population fitness that were dependent upon culture conditions. Amongst the wild isolate strains, we also tested for RNAi-specific intra-strain growth differences to identify potential genetic interactions. In particular we identified a suppression of lethality on
emb-27 RNAi by the wild isolate ED3052 and mapped this to the left arm of LGIII. By phenoMIPs, we examined 202 MMP strains grown across 8 pooling experiments. Our data suggests that amongst the MMP mutant strains, there may be as many as 77% of strains with reduced fitness [AR2] phenotypes on one of three common bacterial food sources. We believe that phenoMIPs is a robust, cost-efficient methodology for identifying differential fitness phenotypes that could further elucidate the function of the many unexplored genes and regulatory regions within the C. elegans genome.