title: Mapping mutations in plant genomes with the user-friendly web application CandiSNP.
abstract: 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 http://candisnp.tsl.ac.uk.
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK.|The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH UK.
authors.forename: Graham J
authors.initials: GJ
authors.lastname: Etherington
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Monaghan
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK.
authors.forename: Cyril
authors.initials: C
authors.lastname: Zipfel
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK.
authors.forename: Dan
authors.initials: D
authors.lastname: MacLean
keywords: Forward-genetics; High-throughput sequencing; Mapping; Single nucleotide polymorphisms; Web application