MIP-MAP: High-throughput mapping of Caenorhabditis elegans temperature-sensitive mutants via molecular inversion probes

Calvin A. Mok, Vinci Au, Owen A. Thompson, Mark L. Edgley, Louis Gevirtzman, John Yochem, Joshua Lowry, Nadin Memar, Matthew R. Wallenfang, Dominique Rasoloson, Bruce Bowerman, Ralf Schnabel, Geraldine Seydoux, Donald G. Moerman, Robert H. Waterston

Research output: Contribution to journalArticle

Abstract

Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans. Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C. elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS). To increase the repertoire of available mutants and to simplify identification of the causal change, we performed WGS on 173 temperature-sensitive (TS) lethal mutants and devised a novel mapping method. The mapping method uses molecular inversion probes (MIP-MAP) in a targeted sequencing approach to genetic mapping, and replaces the Hawaiian strain with a Million Mutation Project strain with high genomic and phenotypic similarity to the laboratory wild-type strain N2. We validated MIP-MAP on a subset of the TS mutants using a competitive selection approach to produce TS candidate mapping intervals with a mean size < 3 Mb. MIP-MAP successfully uses a non-Hawaiian mapping strain and multiplexed libraries are sequenced at a fraction of the cost of WGS mapping approaches. Our mapping results suggest that the collection of TS mutants contains a diverse library of TS alleles for genes essential to development and reproduction. MIP-MAP is a robust method to genetically map mutations in both viable and essential genes and should be adaptable to other organisms. It may also simplify tracking of individual genotypes within population mixtures.

Original languageEnglish (US)
Pages (from-to)447-463
Number of pages17
JournalGenetics
Volume207
Issue number2
DOIs
StatePublished - Oct 1 2017

Fingerprint

Molecular Probes
Caenorhabditis elegans
Temperature
Essential Genes
Libraries
Genome
High-Throughput Nucleotide Sequencing
Mutation
Chromosome Mapping
Mutagenesis
Population
Reproduction
Alleles
Genotype
Costs and Cost Analysis
Genes

Keywords

  • Caenorhabditis elegans
  • Genetic mapping
  • Massively multiplex sequencing
  • Molecular inversion probes
  • Temperature-sensitive mutations

ASJC Scopus subject areas

  • Genetics

Cite this

Mok, C. A., Au, V., Thompson, O. A., Edgley, M. L., Gevirtzman, L., Yochem, J., ... Waterston, R. H. (2017). MIP-MAP: High-throughput mapping of Caenorhabditis elegans temperature-sensitive mutants via molecular inversion probes. Genetics, 207(2), 447-463. https://doi.org/10.1534/genetics.117.300179

MIP-MAP : High-throughput mapping of Caenorhabditis elegans temperature-sensitive mutants via molecular inversion probes. / Mok, Calvin A.; Au, Vinci; Thompson, Owen A.; Edgley, Mark L.; Gevirtzman, Louis; Yochem, John; Lowry, Joshua; Memar, Nadin; Wallenfang, Matthew R.; Rasoloson, Dominique; Bowerman, Bruce; Schnabel, Ralf; Seydoux, Geraldine; Moerman, Donald G.; Waterston, Robert H.

In: Genetics, Vol. 207, No. 2, 01.10.2017, p. 447-463.

Research output: Contribution to journalArticle

Mok, CA, Au, V, Thompson, OA, Edgley, ML, Gevirtzman, L, Yochem, J, Lowry, J, Memar, N, Wallenfang, MR, Rasoloson, D, Bowerman, B, Schnabel, R, Seydoux, G, Moerman, DG & Waterston, RH 2017, 'MIP-MAP: High-throughput mapping of Caenorhabditis elegans temperature-sensitive mutants via molecular inversion probes', Genetics, vol. 207, no. 2, pp. 447-463. https://doi.org/10.1534/genetics.117.300179
Mok, Calvin A. ; Au, Vinci ; Thompson, Owen A. ; Edgley, Mark L. ; Gevirtzman, Louis ; Yochem, John ; Lowry, Joshua ; Memar, Nadin ; Wallenfang, Matthew R. ; Rasoloson, Dominique ; Bowerman, Bruce ; Schnabel, Ralf ; Seydoux, Geraldine ; Moerman, Donald G. ; Waterston, Robert H. / MIP-MAP : High-throughput mapping of Caenorhabditis elegans temperature-sensitive mutants via molecular inversion probes. In: Genetics. 2017 ; Vol. 207, No. 2. pp. 447-463.
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