Mapping mutations in plant genomes with the user-friendly web application CandiSNP

Etherington, Graham J, Monaghan, Jacqueline, Zipfel, Cyril and MacLean, Dan (2014) Mapping mutations in plant genomes with the user-friendly web application CandiSNP. Plant Methods, 10 (1). p. 41. ISSN 1746-4811

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BACKGROUND: Analysis of mutants isolated from forward-genetic screens has revealed key components of several plant signalling pathways. Mapping mutations by position, either using classical methods or whole genome high-throughput sequencing (HTS), largely relies on the analysis of genome-wide polymorphisms in F2 recombinant populations. Combining bulk segregant analysis with HTS has accelerated the identification of causative mutations and has been widely adopted in many research programmes. A major advantage of HTS is the ability to perform bulk segregant analysis after back-crossing to the parental line rather than out-crossing to a polymorphic ecotype, which reduces genetic complexity and avoids issues with phenotype penetrance in different ecotypes. Plotting the positions of homozygous polymorphisms in a mutant genome identifies areas of low recombination and is an effective way to detect molecular linkage to a phenotype of interest. RESULTS: We describe the use of single nucleotide polymorphism (SNP) density plots as a mapping strategy to identify and refine chromosomal positions of causative mutations from screened plant populations. We developed a web application called CandiSNP that generates density plots from user-provided SNP data obtained from HTS. Candidate causative mutations, defined as SNPs causing non-synonymous changes in annotated coding regions are highlighted on the plots and listed in a table. We use data generated from a recent mutant screen in the model plant Arabidopsis thaliana as proof-of-concept for the validity of our tool. CONCLUSIONS: CandiSNP is a user-friendly application that will aid in novel discoveries from forward-genetic mutant screens. It is particularly useful for analysing HTS data from bulked back-crossed mutants, which contain fewer polymorphisms than data generated from out-crosses. The web-application is freely available online at

Item Type: Article
Uncontrolled Keywords: high-throughput sequencing,single nucleotide polymorphisms,forward-genetics,mapping ,web application
Faculty \ School: Faculty of Science > School of Biological Sciences
UEA Research Groups: Faculty of Science > Research Groups > Plant Sciences
Depositing User: Pure Connector
Date Deposited: 08 Mar 2016 16:00
Last Modified: 21 Oct 2022 04:33
DOI: 10.1186/s13007-014-0041-7

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