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Webster AK, Chitrakar R, Powell M, Chen J, Fisher K, Tanny RE, Stevens L, Evans K, Wei A, Antoshechkin I, Andersen EC, Baugh LR. Using population selection and sequencing to characterize natural variation of starvation resistance in C. elegans. eLife 2022; 11:80204. [PMID: 35727141 PMCID: PMC9262388 DOI: 10.7554/elife.80204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Amy K Webster
- Department of Biology, Duke University, Durham, United States
| | - Rojin Chitrakar
- Department of Biology, Duke University, Durham, United States
| | - Maya Powell
- Department of Biology, Duke University, Durham, United States
| | - Jingxian Chen
- Department of Biology, Duke University, Durham, United States
| | - Kinsey Fisher
- Department of Biology, Duke University, Durham, United States
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Kathryn Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Angela Wei
- Department of Biology, Duke University, Durham, United States
| | - Igor Antoshechkin
- Division of Biology, California Institute of Technology, Pasadena, United States
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, United States
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