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High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput microscopy data in the R environment. The package provides a logical workflow for the reading, analysis, and visualization of data generated using CellProfiler’s WormToolbox. We equipped easyXpress with powerful functions to customize the filtering of noise in data, specifically by identifying and removing objects that deviate from expected animal measurements. This flexibility in data filtering allows users to optimize their analysis pipeline to match their needs. In addition, easyXpress includes tools for generating detailed visualizations, allowing the user to interactively compare summary statistics across wells and plates with ease. Researchers studying C. elegans benefit from this streamlined and extensible package as it is complementary to CellProfiler and leverages the R environment to rapidly process and analyze large high-throughput imaging datasets.

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Hybrid male sterility (HMS) contributes to reproductive isolation commonly observed among house mouse (Mus musculus) subspecies, both in the wild and in laboratory crosses. Incompatibilities involving specific Prdm9 alleles and certain Chromosome (Chr) X genotypes are known determinants of fertility and HMS, and previous work in the field has demonstrated that genetic background modifies these two major loci. We constructed hybrids that have identical genotypes at Prdm9 and identical X chromosomes, but differ widely across the rest of the genome. In each case, we crossed female PWK/PhJ mice representative of the M. m. musculus subspecies to males from a classical inbred strain representative of M. m. domesticus: 129S1/SvImJ, A/J, C57BL/6J, or DBA/2J. We detected three distinct trajectories of fertility among the hybrids using breeding experiments. The PWK129S1 males were always infertile. PWKDBA2 males were fertile, despite their genotypes at the major HMS loci. We also observed age-dependent changes in fertility parameters across multiple genetic backgrounds. The PWKB6 and PWKAJ males were always infertile before 12 weeks and after 35 weeks. However, some PWKB6 and PWKAJ males were transiently fertile between 12 and 35 weeks. This observation could resolve previous contradictory reports about the fertility of PWKB6. Taken together, these results point to multiple segregating HMS modifier alleles, some of which have age-related modes of action. The ultimate identification of these alleles and their age-related mechanisms will advance understanding both of the genetic architecture of HMS and of how reproductive barriers are maintained between house mouse subspecies.

Quantitative genetics in C. elegans seeks to identify naturally segregating genetic variants that underlie complex traits. Genome-wide association studies (GWAS) scan the genome for individual genetic variants that are significantly correlated with phenotypic variation in a population, or quantitative trait loci (QTL). GWAS are a popular choice for quantitative genetic analyses because the QTL that are discovered segregate in natural populations. Despite numerous successful mapping experiments, the empirical performance of GWAS has not, to date, been formally evaluated in Caenorhabditis elegans. We developed an open-source GWAS pipeline called NemaScan and used a simulation-based approach to provide benchmarks of mapping performance in collections of wild C. elegans strains. Simulated trait heritability and complexity determined the spectrum of QTL detected by GWAS. Power to detect smaller-effect QTL increased with the number of strains sampled from the C. elegans Natural Diversity Resource (CeNDR). Population structure was a major driver of variation in mapping performance, with populations shaped by recent selection exhibiting significantly lower false discovery rates than populations composed of more divergent strains. We also recapitulated previous GWAS of experimentally validated quantitative trait variants. Our simulation-based evaluation of performance provides the community with critical context to pursue quantitative genetic studies using CeNDR to elucidate the genetic basis of complex traits in C. elegans natural populations.