title: Next-generation mapping of Arabidopsis genes.
abstract: Next-generation genomic sequencing technologies have made it possible to directly map mutations responsible for phenotypes of interest via direct sequencing. However, most mapping strategies proposed to date require some prior genetic analysis, which can be very time-consuming even in genetically tractable organisms. Here we present a de novo method for rapidly and robustly mapping the physical location of EMS mutations by sequencing a small pooled F₂ population. This method, called Next Generation Mapping (NGM), uses a chastity statistic to quantify the relative contribution of the parental mutant and mapping lines to each SNP in the pooled F₂ population. It then uses this information to objectively localize the candidate mutation based on its exclusive segregation with the mutant parental line. A user-friendly, web-based tool for performing NGM analysis is available at http://bar.utoronto.ca/NGM. We used NGM to identify three genes involved in cell-wall biology in Arabidopsis thaliana, and, in a power analysis, demonstrate success in test mappings using as few as ten F₂ lines and a single channel of Illumina Genome Analyzer data. This strategy can easily be applied to other model organisms, and we expect that it will also have utility in crops and any other eukaryote with a completed genome sequence.
authors.affiliation: Centre for the Analysis of Genome Evolution and Function, University of Toronto, ON, Canada.
authors.forename: Ryan S
authors.initials: RS
authors.lastname: Austin
authors.forename: Danielle
authors.initials: D
authors.lastname: Vidaurre
authors.forename: George
authors.initials: G
authors.lastname: Stamatiou
authors.forename: Robert
authors.initials: R
authors.lastname: Breit
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Provart
authors.forename: Dario
authors.initials: D
authors.lastname: Bonetta
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Zhang
authors.forename: Pauline
authors.initials: P
authors.lastname: Fung
authors.forename: Yunchen
authors.initials: Y
authors.lastname: Gong
authors.forename: Pauline W
authors.initials: PW
authors.lastname: Wang
authors.forename: Peter
authors.initials: P
authors.lastname: McCourt
authors.forename: David S
authors.initials: DS
authors.lastname: Guttman
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics*; D001483:Base Sequence; D002473:Cell Wall / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D005020:Ethyl Methanesulfonate / Q000494:pharmacology*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020407:Internet; D009154:Mutation / Q000187:drug effects / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D036226:Seedlings / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D005020:Ethyl Methanesulfonate