dropsData: DROPS data sets

In statgenGWAS: Genome Wide Association Studies

DROPS data sets

Description

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.

Source

doi: 10.15454/IASSTN

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

statgenGWAS documentation built on Oct. 13, 2022, 5:05 p.m.