Polygenicity and Epistasis Underlie Fitness-Proximal Traits in the Caenorhabditis Elegans

Polygenicity and epistasis underlie fitness-proximal traits in the Caenorhabditis elegans multiparental experimental evolution (CeMEE) panel

Luke M. Noble, Ivo Chelo, Thiago Guzella, Bruno Afonso, David D. Riccardi, Patrick Ammerman, Adel Dayarian, Sara Carvalho, Anna Crist, Ania Pino-Querido, Boris Shraiman, Matthew V. Rockman, Henrique Teotónio

Genetic material

The CeMEE recombinant inbred lines will be distributed by the authors on request. Full RIL designations (sub-panel, population replicate) are listed in File S1 RIL_panel_ids.txt and sub-panel descriptions are in File S2 CeMEE_subpanels.txt.

Genotype data

Founder variant calls are in File S3 WS220.founder.bsqr.gtkHC.F.all.remapped.vcf. Reads aligned to the WS220 N2 reference genome are available for all founders and RILs from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under project accession PRJNA381203.

Filtered diallelic markers segregating in the founders and RILs are in File S4 (WS220_founders.txt) and File S5 (WS220_RIL_genotypes.txt), and interpolated genetic positions used for imputation of RIL genotypes are in File S7 WS220.clean.geneticMap.txt.

HPLC genotyping at a subset of SNPs for the A140 RILs, used to define appropriate filtering thresholds, are in File S21 Sequenom_genotypes.txt. Coordinates are based on the WS220 reference genome (0/1 for reference/alternate allele).

Founder haplotype reconstructions in the RILs are available from FigShare under DOI 10.6084/m9.figshare.5466574.v1.

Phenotype data

Raw fertility data with all metadata used for modeling are in File S9 worm_fertility_raw.txt. Standardized model coefficients used for QTL mapping in are File S10 fertility_coef.txt.

Raw size data with all metadata used for modeling are in File S11 worm_area_raw.txt.zip. Standardized model coefficients used for QTL mapping in are File S12 size_coef.txt.

All animal handling, phenotyping and statistical analysis is described in the Methods and Supplementary Methods sections.

Results

Single marker linear mixed model results (p-values and marker positions) for fertility and size are in File S14 fertility_size_lmm.txt, which were obtained using the genetic similarity matrices in File S15 (fertility_LDAK_GSM.txt) and File S16 (size_LDAK_GSM.txt).