Fine mapping with MAGIC Recombinant Inbred Lines in Arabidopsis thaliana

This page contains online resources for a population of recombinant inbred lines of the model plant Arabidopsis thaliana. The lines, termed MAGIC (for Multiparent Advanced Generation InterCross) are descended from 19 accessions of A. thaliana. The seeds for the lines are available from the Stock Centre.

• Browse Genome Scans via the GSCANDB database.
• Genotypes for 1260 SNPS (text files, arranged so each row is one line or accessions, each column is one SNP). Note that this data has been cleaned of heterozygotes and any low-quality SNP calls. Missing genotypes are coded as "NA".
  • 19 founders of the MAGIC lines
  • 527 MAGIC RILS
• SNP information
  • Genome locations of 1260 SNPs used for genotyping
• Phenotype Data (averaged over replicates)
  • Manchester University Phenotypes (days from bolting to flowering, days to bolt, days to germination, total height of plant in cm, leaves at day 28 given days to germinate)
  • New York University Phenotypes (DaysToFlower.LongDay RosetteLeafNumber.LongDay DaysToFlower.ShortDay RosetteLeafNumber.ShortDay)
• R code to analyse the data
  • The R happy package (used as the basis for the analysis).
  • William Valdar's bagphenotype programme used to perform the QTL searches (fixed effects and mixed effects models).
  • Caroline Durrant's code for Hierachical Bayes analysis
  • Additional code specific to the analysis of the data.
  • The Genotypes reformatted for the HAPPY package
• A paper describing the lines
  • PDF of the paper
  • Supplemental Tables