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Population Selection and Sequencing of Caenorhabditis elegans Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance.

Publication ,  Journal Article
Webster, AK; Hung, A; Moore, BT; Guzman, R; Jordan, JM; Kaplan, REW; Hibshman, JD; Tanny, RE; Cook, DE; Andersen, E; Baugh, LR
Published in: G3 (Bethesda, Md.)
October 2019

To understand the genetic basis of complex traits, it is important to be able to efficiently phenotype many genetically distinct individuals. In the nematode Caenorhabditis elegans, individuals have been isolated from diverse populations around the globe and whole-genome sequenced. As a result, hundreds of wild strains with known genome sequences can be used for genome-wide association studies (GWAS). However, phenotypic analysis of these strains can be laborious, particularly for quantitative traits requiring multiple measurements per strain. Starvation resistance is likely a fitness-proximal trait for nematodes, and it is related to metabolic disease risk in humans. However, natural variation in C. elegans starvation resistance has not been systematically characterized, and precise measurement of the trait is time-intensive. Here, we developed a population-selection-and-sequencing-based approach to phenotype starvation resistance in a pool of 96 wild strains. We used restriction site-associated DNA sequencing (RAD-seq) to infer the frequency of each strain among survivors in a mixed culture over time during starvation. We used manual starvation survival assays to validate the trait data, confirming that strains that increased in frequency over time are starvation-resistant relative to strains that decreased in frequency. Further, we found that variation in starvation resistance is significantly associated with variation at a region on chromosome III. Using a near-isogenic line (NIL), we showed the importance of this genomic interval for starvation resistance. This study demonstrates the feasibility of using population selection and sequencing in an animal model for phenotypic analysis of quantitative traits, documents natural variation of starvation resistance in C. elegans, and identifies a genomic region that contributes to such variation.

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Published In

G3 (Bethesda, Md.)

DOI

EISSN

2160-1836

ISSN

2160-1836

Publication Date

October 2019

Volume

9

Issue

10

Start / End Page

3477 / 3488

Related Subject Headings

  • Starvation
  • Selection, Genetic
  • Quantitative Trait, Heritable
  • Phenotype
  • Genome-Wide Association Study
  • Chromosomes
  • Chromosome Mapping
  • Caenorhabditis elegans
  • Animals
  • Adaptation, Biological
 

Citation

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Webster, A. K., Hung, A., Moore, B. T., Guzman, R., Jordan, J. M., Kaplan, R. E. W., … Baugh, L. R. (2019). Population Selection and Sequencing of Caenorhabditis elegans Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance. G3 (Bethesda, Md.), 9(10), 3477–3488. https://doi.org/10.1534/g3.119.400617
Webster, Amy K., Anthony Hung, Brad T. Moore, Ryan Guzman, James M. Jordan, Rebecca E. W. Kaplan, Jonathan D. Hibshman, et al. “Population Selection and Sequencing of Caenorhabditis elegans Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance.G3 (Bethesda, Md.) 9, no. 10 (October 2019): 3477–88. https://doi.org/10.1534/g3.119.400617.
Webster AK, Hung A, Moore BT, Guzman R, Jordan JM, Kaplan REW, et al. Population Selection and Sequencing of Caenorhabditis elegans Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance. G3 (Bethesda, Md). 2019 Oct;9(10):3477–88.
Webster, Amy K., et al. “Population Selection and Sequencing of Caenorhabditis elegans Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance.G3 (Bethesda, Md.), vol. 9, no. 10, Oct. 2019, pp. 3477–88. Epmc, doi:10.1534/g3.119.400617.
Webster AK, Hung A, Moore BT, Guzman R, Jordan JM, Kaplan REW, Hibshman JD, Tanny RE, Cook DE, Andersen E, Baugh LR. Population Selection and Sequencing of Caenorhabditis elegans Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance. G3 (Bethesda, Md). 2019 Oct;9(10):3477–3488.

Published In

G3 (Bethesda, Md.)

DOI

EISSN

2160-1836

ISSN

2160-1836

Publication Date

October 2019

Volume

9

Issue

10

Start / End Page

3477 / 3488

Related Subject Headings

  • Starvation
  • Selection, Genetic
  • Quantitative Trait, Heritable
  • Phenotype
  • Genome-Wide Association Study
  • Chromosomes
  • Chromosome Mapping
  • Caenorhabditis elegans
  • Animals
  • Adaptation, Biological