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”