A nematode-specific gene underlies bleomycin-response variation in Caenorhabditis elegans

Shannon C. Brady; Stefan Zdraljevic; Karol W. Bisaga; Robyn E. Tanny; Daniel E. Cook; Daehan Lee; Ye Wang; Erik C. Andersen

Using this package, read_data imported measurements from the BIOSORT and 157 remove_contamination was used to remove contaminated wells from analysis. The sumplate 158 function then calculated normalized measurements (norm.n --brood size normalized to number 159 of animals sorted, norm.EXT --EXT normalized by TOF measurements) and summary statistics 160 (mean, median, 10 th, 25 th , 75 th , 90 th percentile, interquartile range, covariance, and variance) of 161 each trait for the population of animals. A total of 26 HTA traits were measured. When strains 162 were phenotyped across multiple days, the regress(assay=TRUE) function was used to fit a 163 linear model with the phenotype as the dependent variable and assay as the independent variable 164 (phenotype ~ assay) to account for variation among assay days. Next, the prune_outliers() 165 function removed phenotypic values that were beyond two standard deviations of the mean 166 (unless at least 5% of the strains were outside this range in the case of RIAIL assays were called). The genotypic data and residual phenotypic data (after control-condition 207 regression) were merged into a cross object using the merge_pheno function with set = 2 to 208 include strains with a reduced allele-frequency skew on chromosome I. The fsearch function was 209 used to calculate logarithm of odds (LOD) scores for each marker and each trait as The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/565218 doi: bioRxiv preprint Two-factor genome scan: We performed a two-factor genome scan to identify potentially 241 epistatic loci that might contribute to traits of interest (either bleomycin responses or gene-242 expression levels). We used the scantwo function in the R qtl package to perform this analysis. 243