1. Genetics and Genomics
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Wild worm embryogenesis harbors ubiquitous polygenic modifier variation

  1. Annalise B Paaby  Is a corresponding author
  2. Amelia G White
  3. David D Riccardi
  4. Kristin C Gunsalus
  5. Fabio Piano
  6. Matthew V Rockman  Is a corresponding author
  1. New York University, United States
  2. New York University Abu Dhabi, United Arab Emirates
Research Article
Cite this article as: eLife 2015;4:e09178 doi: 10.7554/eLife.09178
3 figures, 4 tables, 2 data sets and 2 additional files

Figures

Experimental scheme and methods.

(A) Under ordinary conditions, wild-type Caenorhabditis elegans embryos hatch into larvae. (B) We targeted maternally-expressed genes by RNAi to induce embryonic lethality that varied in penetrance across strains. (C) L1 larvae in the parental generation were fed Escherichia coli expressing dsRNA against target genes, in 96-well plates in liquid media. 5 days later, wells were imaged to capture the penetrance of embryonic lethality in the next generation. (D, E) Raw images were evaluated using DevStaR (White et al., 2013), which identified objects as larvae (blue), dead embryos (green), or adults (red).

https://doi.org/10.7554/eLife.09178.003
Variability in embryonic lethality.

Each cell represents the embryonic hatching success for a strain and targeted gene, averaged from at least eight replicate wells. The rows and columns are ordered by average hatching, and boxplots illustrate hatching phenotypes for each strain (across all targeted genes) and for each gene (across all strains).

https://doi.org/10.7554/eLife.09178.004
Tests for gene-specific modifiers.

Introgression of part of chromosome II from strain N2 (yellow) into strain EG4348 (blue) rescues the N2 phenotype on lsy-22 (F = 12.15, DF = 2, p = 0.001) and pkc-3 (F = 55.87, DF = 2, p < 0.001); genome-wide analyses found associations between this region and hatching phenotypes for both lsy-22 and pkc-3.

https://doi.org/10.7554/eLife.09178.007
Figure 3—source data 1

This file provides source data for Figure 3, which reports hatching for three different strains targeted by RNAi against genes lsy-22 and pkc-3.

It provides counts of dead embryos (emb) or hatched larvae (larv) on individual agarose-media plates seeded with bacteria expressing dsRNA for the target genes. In the data file, the strain QG611 has the N2 genetic background.

https://doi.org/10.7554/eLife.09178.008

Tables

Table 1

Factorial analysis of deviance of lethality phenotypes for 55 wild-type strains in 29 perturbations of germline-expressed genes

https://doi.org/10.7554/eLife.09178.005
DFDevianceResid. DFResid. DevFp-value
NULL17,8552,201,873
Strain54338,61817,8011,863,255334.697<10−15
Targeted gene281,152,31017,773710,9452196.584<10−15
Adults per well135,31817,772675,6271885.113<10−15
Date1240617,771673,221128.416<10−15
Strain × gene1512349,41516,259323,80612.334<10−15
Strain × adults per well54671516,205317,0916.637<10−15
Gene × adults per well28735816,177309,73214.026<10−15
  1. The table rows report information associated with each term in our statistical model (see ‘Materials and methods’), which represent distinct sources for the variation we observed in embryonic lethality. All terms were highly significant, including the strain-by-gene interaction, which represents variation attributable to cryptic genetic modifiers that act gene-specifically. This term and the strain term, which represents variation attributable to informational modifiers affecting germline RNAi, explain similar amounts of variation, and together account for 31% of the total deviance.

Table 2

Genome heritability estimates for CGV phenotypes associated with 29 targeted genes

https://doi.org/10.7554/eLife.09178.006
Targeted geneHeritability estimatep-value
aph-10.67470.16
car-10.91490.02
cdc-370.73080.11
cdc-420.36390.29
emb-300.00000.46
fat-20.35480.32
lag-10.90750.01
lsy-220.12700.43
mel-260.82450.05
mel-280.84100.04
mel-320.00000.47
mex-30.00000.76
mom-20.74850.09
mom-50.00000.46
nmy-20.48410.26
par-10.78710.08
par-20.97190.01
par-30.00000.77
par-40.90320.07
par-50.66400.15
par-60.92580.01
pkc-30.81360.06
pos-10.73070.10
rfc-30.69580.13
rpn-90.87150.02
rpn-100.83970.05
skn-10.85990.03
skr-20.89610.02
sur-60.00000.47
Table 3

Factorial analysis of deviance of strain N2 lethality on targeted gene mom-2

https://doi.org/10.7554/eLife.09178.009
DfDevianceResid. DfResid. DevFPr (>F)
NULL2849191.7
Date11060.262838131.438.3972.0 × 10—09
Bacterial source2172.472817958.93.1230.04556
Table 4

Factorial analysis of deviance of strain N2 lethality phenotypes across 29 targeted genes

https://doi.org/10.7554/eLife.09178.010
DfDevianceResid. DfResid. DevFPr (>F)
NULL2254280,706
Silenced gene28221,081222659,624378.3275<2 × 10—16
Date16090222553,534291.8186<2 × 10—16
Adults per well1249222453,28511.92480.00056
Silenced gene × date285265219648,0209.0099<2 × 10−16
Silenced gene × adults per well282423216845,5974.14672.7 × 10—12

Data availability

The following data sets were generated
The following previously published data sets were used

Additional files

Supplementary file 1

This Excel file reports correlations for strain-by-gene interaction coefficients for each pairwise combination of targeted genes.

Above the diagonal are the estimated correlations; below the diagonal are the correlation p-values; in green are pairs of genes with interactions reported in the literature.

https://doi.org/10.7554/eLife.09178.011
Supplementary file 2

This extended table reports genome-wide SNPs associated with hatching phenotypes with p-values <0.0001 and <1.64 × 10−5 (*).

The LD column indicates clusters of SNPs in strong disequilibrium with each other (R2 > 0.90) across our test strains. A source data file has been deposited at Dryad under doi:10.5061/dryad.d5j06.

https://doi.org/10.7554/eLife.09178.012

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