ArabMAGIC

Data from Gnan et al. (2014) 19-way Arabidopsis MAGIC

Source

Data from Gnan et al. (2014), on seed size and number in the 19-way Arabidopsis MAGIC lines of Kover et al. (2009).

The raw data were included as supplements: the genotypes in File S1 and the phenotypes in File S2.

There is genotype data (at a total of 1260 markers on 5 chromosomes) on 703 MAGIC lines. 677 of the lines have phenotype data, for 8 phenotypes.

We don't have a genetic map of the markers, but we do have a physical map, in two forms: positions in the "TAIR8 build" were present in the Gnan et al. (2014) data (though just for 1024 markers), and positions in the "TAIR9 build" are from http://mtweb.cs.ucl.ac.uk (for 1251 markers).

For related data, see http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/magic.html and the supplementary material from Kover et al. (2009).

File conversion

• R/convert_data.R for converting the data to R/qtl2 format.

• Makefile to automate and document the data conversions.

• I also make use of a Python script, xlsx2csv.py; the Makefile includes instructions for downloading and using it.

Files

• arabmagic_tair8.json - the JSON control file, pointing to the TAIR8 physical map
• arabmagic_tair9.json - the JSON control file, pointing to the TAIR9 physical map
• arabmagic_foundergeno.csv - the founder genotype data
• arabmagic_geno.csv - the MAGIC genotype data
• arabmagic_pheno.csv - the MAGIC phenotype data
• arabmagic_pmap_tair8.csv - physical map of the markers with TAIR8 build
• arabmagic_pmap_tair9.csv - physical map of the markers with TAIR9 build
• arabmagic_tair8.zip - all of the data zipped into one file, with the TAIR8 physical map
• arabmagic_tair9.zip - all of the data zipped into one file, with the TAIR9 physical map

File format

See the R/qtl2 input file format.

Citations

• Gnan S, Priest A, Kover PX (2014) The genetic basis of natural variation in seed size and seed number and their trade-off using Arabidopsis thaliana MAGIC lines. Genetics 198:1751-1758. doi:10.1534/genetics.114.170746

• Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R (2009) A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genetics 5:e1000551. doi:10.1371/journal.pgen.1000551

Use with R/qtl2

Load these data into R directly from the web as follows (for the TAIR9 version of the physical map; replace 9 with 8 for the TAIR8 version):

library(qtl2)
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/main/ArabMAGIC/arabmagic_tair9.zip")
arab <- read_cross2(file)