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C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy.

Doitsidou, M; Poole, RJ; Sarin, S; Bigelow, H; Hobert, O; (2010) C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy. PLOS One , 5 (11) , Article e15435. 10.1371/journal.pone.0015435. Green open access

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Abstract

Whole-genome sequencing (WGS) is becoming a fast and cost-effective method to pinpoint molecular lesions in mutagenized genetic model systems, such as Caenorhabditis elegans. As mutagenized strains contain a significant mutational load, it is often still necessary to map mutations to a chromosomal interval to elucidate which of the WGS-identified sequence variants is the phenotype-causing one. We describe here our experience in setting up and testing a simple strategy that incorporates a rapid SNP-based mapping step into the WGS procedure. In this strategy, a mutant retrieved from a genetic screen is crossed with a polymorphic C. elegans strain, individual F2 progeny from this cross is selected for the mutant phenotype, the progeny of these F2 animals are pooled and then whole-genome-sequenced. The density of polymorphic SNP markers is decreased in the region of the phenotype-causing sequence variant and therefore enables its identification in the WGS data. As a proof of principle, we use this strategy to identify the molecular lesion in a mutant strain that produces an excess of dopaminergic neurons. We find that the molecular lesion resides in the Pax-6/Eyeless ortholog vab-3. The strategy described here will further reduce the time between mutant isolation and identification of the molecular lesion.

Type: Article
Title: C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy.
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1371/journal.pone.0015435
Publisher version: http://dx.doi.org/10.1371/journal.pone.0015435
Language: English
Additional information: © 2010 Doitsidou et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This work was funded by the Howard Hughes Medical Institute and the National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Keywords: Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Chromosome Mapping, Female, Genetic Association Studies, Genome, Helminth, Genome-Wide Association Study, Genotype, Male, Mutation, Paired Box Transcription Factors, Phenotype, Polymorphism, Single Nucleotide, RNA Interference, Reproducibility of Results, Sequence Analysis, DNA, Software
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Cell and Developmental Biology
URI: https://discovery.ucl.ac.uk/id/eprint/1369024
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