Using population selection and sequencing to characterize natural variation of starvation resistance in Caenorhabditis elegans

Abstract

Starvation resistance is important to disease and fitness, but the genetic basis of its natural variation is unknown. Uncovering the genetic basis of complex, quantitative traits such as starvation resistance is technically challenging. We developed a synthetic-population (re)sequencing approach using molecular inversion probes (MIP-seq) to measure relative fitness during and after larval starvation in C. elegans. We applied this competitive assay to 100 genetically diverse, sequenced, wild strains, revealing natural variation in starvation resistance. We confirmed that the most starvation-resistant strains survive and recover from starvation better than the most starvation-sensitive strains using standard assays. We performed genome-wide association (GWA) with the MIP-seq trait data and identified three quantitative trait loci (QTL) for starvation resistance, and we created near isogenic lines (NILs) to validate the effect of these QTL on the trait. These QTL contain numerous candidate genes including several members of the Insulin/EGF Receptor-L Domain (irld) family. We used genome editing to show that four different irld genes have modest effects on starvation resistance. Natural variants of irld-39 and irld-52 affect starvation resistance, and increased resistance of the irld-39; irld-52 double mutant depends on daf-16/FoxO. DAF-16/FoxO is a widely conserved transcriptional effector of insulin/IGF signaling (IIS), and these results suggest that IRLD proteins modify IIS, though they may act through other mechanisms as well. This work demonstrates efficacy of using MIP-seq to dissect a complex trait and it suggests that irld genes are natural modifiers of starvation resistance in C. elegans.

High-throughput phenotyping of infection by diverse microsporidia species reveals a wild C. elegans strain with opposing resistance and susceptibility traits

“…To synchronize infections, we treated adult populations with a sodium hydroxide and sodium hypochlorite mixture (known as bleach synchronizing) and allowed the recovered embryos to hatch in the absence of food. The process of bleach synchronizing animals for microsporidia infection has been shown to have similar levels of infection between bleached versus laid embryos, and short-term starvation is reported to have minimal impact on wild isolates [ 19 , 20 , 40 ]. We pooled equal numbers of synchronized first larval stage (L1) wild isolates and a laboratory reference-derived strain (VC20019) into a single population.…”

“…Although studying phenotypic variation in wild isolates is a powerful approach, measuring each strain individually is time consuming and laborious. To circumvent this issue, strategies have been developed to perform multiplex competitive fitness assays under selective conditions such as starvation stress or different bacterial diets [38][39][40]. Several sequencing-based approaches, termed either PhenoMIP or MIP-seq, determine the identity of these individual strains by using molecular inversion probes (MIPs) to enrich for their unique genomic signatures [39,40].…”

Structure-specific variation in per- and polyfluoroalkyl substances toxicity among genetically diverseCaenorhabditis elegansstrains

“…Within these two PFAS as well as the short-chain PFCAs, PFPeA and PFBA, and the long-chain PFCA, PFNA, the strain DL238 was the most resistant to each exposure. DL238 is also resistant to starvation, which suggests that this strain harbors genetic variants that support stress resistance more generally (Webster et al 2022). On the contrary, CB4856 is the most sensitive strain to respond to PFOS, PFNA, and PFOA, which suggests that this strain contains variants which contribute to sensitivity to exposure.…”

The C. elegans truncated insulin receptor DAF-2B regulates survival of L1 arrested larvae

“…elegans [ 33 ]. Moreover, genetic deletion of two of these genes was sufficient to extend L1 starvation survival [ 33 ]. Thus, it is tempting to speculate that these two IRLD proteins are acting to sequester antagonist ILPs and could form part of a larger family of ILP binding proteins.…”