Large-scale pooled selection enables mapping of modifiers of RNAi gene knockdown effects in C. elegans
- 1University of California, Los Angeles
Abstract
Genetic interactions contribute to phenotypic variation, yet most studies characterize them in a small number of reference backgrounds rather than across natural populations. Studying genetic interactions in Caenorhabditis elegans is facilitated by RNAi by feeding, which enables gene-specific knockdowns across many genetic backgrounds without the need to construct individual mutant lines. However, individually screening hundreds of isolates across many RNAi conditions is laborious. Here, we developed a pooled platform that uses whole-genome sequencing to quantify the fitness of hundreds of genetically distinct C. elegans strains competing in a single flask. We leveraged this platform to evaluate RNAi responses in a pooled population of RNAi-sensitive C. elegans strains and identified two classes of QTL that influence RNAi responses. The first class influences responses to knockdowns of specific genes and is exemplified by a QTL that is specific to knockdown of mig-6. The second class influences general RNAi-response across multiple knockdowns. One QTL in this class localized to the right arm of chromosome III and was detected by both GWA and xQTL mapping, which suggests that a common large-effect variant underlies this QTL. We identified a T96K missense change in the dsRNA receptor SID-2 as the underlying causal variant. The 96K allele resides in the extracellular domain of SID-2 and confers increased RNAi sensitivity relative to the 96T allele. We hypothesize that the 96K allele enables greater uptake of ingested lumenal dsRNA through higher-affinity binding to the dsRNA phosphate backbone. The platform we developed enables systematic mapping of genetic interactions across natural populations at a previously impractical scale.
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BibTeX
@misc{zdraljevic2026largescale,
title = {{Large-scale pooled selection enables mapping of modifiers of RNAi gene knockdown effects in C. elegans}},
author = {S. Zdraljevic and A. Lee and L. Walter-McNeill and H. Marquez and A. K. Webster and R. Chitrakar and J. Blount and L. R. Baugh and J. S. Bloom and L. Kruglyak},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.08.757717},
url = {https://www.biorxiv.org/content/10.64898/2026.10.08.757717v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Large-scale pooled selection enables mapping of modifiers of RNAi gene knockdown effects in C. elegans
AU - S. Zdraljevic
AU - A. Lee
AU - L. Walter-McNeill
AU - H. Marquez
AU - A. K. Webster
AU - R. Chitrakar
AU - J. Blount
AU - L. R. Baugh
AU - J. S. Bloom
AU - L. Kruglyak
PY - 2026
DA - 2026/10/08
PB - bioRxiv
DO - 10.64898/2026.10.08.757717
UR - https://www.biorxiv.org/content/10.64898/2026.10.08.757717v1
AB - Genetic interactions contribute to phenotypic variation, yet most studies characterize them in a small number of reference backgrounds rather than across natural populations. Studying genetic interactions in Caenorhabditis elegans is facilitated by RNAi by feeding, which enables gene-specific knockdowns across many genetic backgrounds without the need to construct individual mutant lines. However, individually screening hundreds of isolates across many RNAi conditions is laborious. Here, we developed a pooled platform that uses whole-genome sequencing to quantify the fitness of hundreds of genetically distinct C. elegans strains competing in a single flask. We leveraged this platform to evaluate RNAi responses in a pooled population of RNAi-sensitive C. elegans strains and identified two classes of QTL that influence RNAi responses. The first class influences responses to knockdowns of specific genes and is exemplified by a QTL that is specific to knockdown of mig-6. The second class influences general RNAi-response across multiple knockdowns. One QTL in this class localized to the right arm of chromosome III and was detected by both GWA and xQTL mapping, which suggests that a common large-effect variant underlies this QTL. We identified a T96K missense change in the dsRNA receptor SID-2 as the underlying causal variant. The 96K allele resides in the extracellular domain of SID-2 and confers increased RNAi sensitivity relative to the 96T allele. We hypothesize that the 96K allele enables greater uptake of ingested lumenal dsRNA through higher-affinity binding to the dsRNA phosphate backbone. The platform we developed enables systematic mapping of genetic interactions across natural populations at a previously impractical scale.
ER -