This dataset comes from the European Union project DROPS (DROught-tolerant
yielding PlantS). A panel of 256 maize hybrids was grown with two water
regimes (irrigated or rainfed), in seven fields in 2012 and 2013,
respectively, spread along a climatic transect from western to eastern
Europe, plus one site in Chile in 2013. This resulted in 28 experiments
defined as the combination of one year, one site and one water regime, with
two and three repetitions for rainfed and irrigated treatments, respectively.
A detailed environmental characterisation was carried out, with hourly
records of micrometeorological data and soil water status, and associated
with precise measurement of phenology. Grain yield and its components were
measured at the end of the experiment.
10 experiments have been selected from the full data set, two for each of
the five main environmental scenarios that were identified in the data. The
scenarios have been added to the data as well as a classification of the
genotypes in four genetic groups.
The main purpose of this dataset
consists in using the environmental characterization to quantify the genetic
variability of maize grain yield in response to the environmental drivers
for genotype-by-environment interaction. For instance, allelic effects at
QTLs identified over the field network are consistent within a scenario but
largely differ between scenarios.
The data is split in three separate data.frames.
- dropsMarkers
This data.frame contains the 50K genotyping matrix coded in allelic dose (012) filtered and imputed. Genotyping of 41,722 loci on 246 parental lines were obtained using 50K Illumina Infinium HD arrays (Ganal et al., 2011). Genotype were coded in allelic dose with 0 for the minor allele, 1 for the heterozygote, and 2 for the major allele. Genotype were filtered (MAF > 1%) and missing data imputed using Beagle v3.
A data.frame with 246 rows and 41723 columns.- Ind
name of the genotype
- SYMN83 to PZE-110111485
coded QTLs
- dropsMap
This data.frame contains the description of the 41,722 loci genotyped by 50K Illumina Infinium Array on the 246 lines.
A data.frame with 41722 rows and 5 columns.- SNP.names
name of the SNP
- Chromosome
number of the B73 reference genome V2
- Position
position on the B73 reference genome V2 in basepairs
- allele1
first original allele (A, T, G or C)
- allele2
second original allele (A, T, G or C)
- dropsPheno
This data.frame contains the genotypic means (Best Linear Unbiased Estimators, BLUEs), with one value per experiment (Location × year × water regime) per genotype.
A data.frame with 2460 rows and 19 columns.- Experiment
experiments ID described by the three first letters of the city’s name followed by the year of experiment and the water regime with W for watered and R for rain-fed.
- parent1
identifier of donor dent line
- Code_ID, Variety_ID, Accession_ID
identifier of the genotype
- geno.panel
project in which the genetic material was generated
- grain.yield
genotypic mean for yield adjusted at 15% grain moisture, in ton per hectare (t ha^-1)
- grain.number
genotypic mean for number of grain per square meter
- grain.weight
genotypic mean for individual grain weight in milligram (mg)
- anthesis
genotypic mean for male flowering (pollen shed), in thermal time cumulated since emergence (d_20°C)
- silking
genotypic mean for female flowering (silking emergence), in thermal time cumulated since emergence (d_20°C)
- plant.height
genotypic mean for plant height, from ground level to the base of the flag leaf (highest) leaf in centimeter (cm)
- tassel.height
genotypic mean for plant height including tassel, from ground level to the highest point of the tassel in centimeter (cm)
- ear.height
genotypic mean for ear insertion height, from ground level to ligule of the highest ear leaf in centimeter (cm)
- year
year in which the experiment was performed
- loc
location where the experiment was performed, a three letter abbreviation
- scenarioWater
water scenario for the experiment, well watered (WW) or water deficit (WD)
- scenarioTemp
temperature scenario for the experiment, Cool, Hot or Hot(Day)
- scenarioFull
the full scenario for the experiment, a combination of scenarioWater and scenarioTemp
- geneticGroup
the genetic group to which the genotype belongs
Note
From the source data, the experiments from 2011 have been removed since these do not contain all genotypes. Also the experiment Gra13W has been removed.
References
Millet, E. J., Pommier, C., et al. (2019). A multi-site experiment in a network of European fields for assessing the maize yield response to environmental scenarios - Data set. doi:10.15454/IASSTN
Ganal MW, et al. (2011) A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome. PLoS ONE 6(12): e28334. doi:10.1371/journal.pone.0028334