eXtreme Array Mapping

Light-Response Quantitative Trait Loci Identified with Composite Interval and eXtreme Array Mapping in Arabidopsis thaliana

David J. Wolyn, Justin O. Borevitz, Olivier Loudet, Chris Schwartz, Julin Maloof, Joseph R. Ecker, Charles C. Berry and Joanne Chory

           based on the bulk segregant analysis of Single Feature Polymorphisms

Supplementary Data

Kas X Col improved genetic map with additional marker data

  This includes QTL data in this “kasqtl.zip” file

  Raw phenotypic measurements

  QTL cartographer map and cross file

              SRmap background marker file

  R scripts for epistasis and QTL effect estimation

And .cel files from ATH1 arrays in this “kascel.zip” file

  2 Col, 2 Kas, a short hypocotyl RIL pool

               and a tall RIL pool.

Setup files for ATH1,

  SFPcluster.R Extreme Array Mapping analysis scripts

              This will call SFPs and do clustering in R

                          with “affy” package from bioconductor

                          and “lcluster” windows, source

  readcel.R function to read .cel files

  bulk.kascol.csv SFP raw data

  selfings.R function to generate synthetic populations

  XAMloessSim.R eXtreme Array Mapping and simulation code for 8 genetic models

  XAMresult.R  Table out the results from the simulation code

Deletions in Kas predicted by clustering “Kas.del.csv”

SFPs in Kas predicted by tstat “kassfp.csv”