MaizeMAGIC

Data on Maize MAGIC lines

This is data on a set of maize MAGIC lines. Largely 8 founders, but a ninth founder was introduced for some lines due to incompatibility between a pair of founders.

Source

Dell'Acqua et al. (2015) Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays. Genome Biol. 16:167 doi:10.1186/s13059-015-0716-z

The raw data are available as supplemental tables and at Figshare:

• Founders genotypes (with replicates) https://doi.org/10.6084/m9.figshare.1437453; direct download https://ndownloader.figshare.com/files/2096751

• MAGIC lines' genotypes https://doi.org/10.6084/m9.figshare.1437449; direct download https://ndownloader.figshare.com/files/2096747

• Founders sequence-based genotypes (imputed) https://doi.org/10.6084/m9.figshare.1425350; direct download https://ndownloader.figshare.com/files/2081430

• Table S1: details of maize founder lines

• Table S2: MM population breeding design

• Table S3: genetic map

• Table S6: phenotypes (pollen shed, PS; plant height PH, ear height EH, transformed grain yield GYrad)

Files

The following files comprise the data reformatted for R/qtl2. We're treating the data as a recombinant inbred lines with nine founders. For the founder genotypes, we combined the array-based data (which had a lot of missing or heterozygous calls for the 9th founder, CML91) with the sequence-based imputed genotypes.

• maize_magic.json, the control file (JSON format)
• maize_magic_geno.csv, genotype data for the MAGIC lines
• maize_magic_foundergeno.csv, genotype data for the 9 founder lines
• maize_magic_gmap.csv, genetic map
• maize_magic_pmap.csv, physical map
• maize_magic_crossinfo.csv, cross information (number of generations followed by values indicating the relative contributions of the nine founders)
• maize_magic_pheno.csv, phenotype data
• maize_magic_phenocovar.csv, phenotype covariates, with just descriptions of the phenotype

The data are also available as a zip file, maize_magic.zip.

File format

See the R/qtl2 input file format.

Citation

Dell’Acqua M, et al. (2015) Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays. Genome Biol. 16:167 doi:10.1186/s13059-015-0716-z

Use with R/qtl2

Load these data into R directly from the web as follows:

library(qtl2)
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/main/MaizeMAGIC/maize_magic.zip")
mm <- read_cross2(file)