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A multi-site experiment in a network of European fields for assessing the maize yield response to environmental scenarios
A multi-site experiment in a network of European fields for assessing the maize yield response to environmental scenarios
Version 2.0
Millet, Emilie J.; Pommier, Cyril; Buy, Mélanie; Nagel, Axel; Kruijer, Willem; Welz-Bolduan, Therese; Lopez, Jeremy; Richard, Cécile; Racz, Ferenc; Tanzi, Franco; Spitkot, Tamas; Canè, Maria-Angela; Negro, Sandra S.; Coupel-Ledru, Aude; Nicolas, Stéphane D.; Palaffre, Carine; Bauland, Cyril; Praud, Sébastien; Ranc, Nicolas; Presterl, Thomas; Bedo, Zoltan; Tuberosa, Roberto; Usadel, Björn; Charcosset, Alain; van Eeuwijk, Fred A.; Draye, Xavier; Tardieu, François; Welcker, Claude, 2019, "A multi-site experiment in a network of European fields for assessing the maize yield response to environmental scenarios", https://doi.org/10.15454/IASSTN, Portail Data INRAE, V2, UNF:6:zF9w0A2f+MHeW7maeeXJWA== [fileUNF]
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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 29 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. The main purpose of this dataset consists in using the environmental characterisation 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.
Subject Climate; Plant Breeding and Plant Products
Keyword Phenotyping, Envirotyping, Genotype-by-environment interaction, Multi-environment, Zea mays
Related Publication Genome-Wide Analysis of Yield in Europe: Allelic Effects Vary with Drought and Heat Scenarios. 2016. Emilie J. Millet, Claude Welcker, Willem Kruijer, Sandra Negro, Aude Coupel-Ledru, Stéphane D. Nicolas, Jacques Laborde, Cyril Bauland, Sebastien Praud, Nicolas Ranc, Thomas Presterl, Roberto Tuberosa, Zoltan Bedo, Xavier Draye, Björn Usadel, Alain Charcosset, Fred Van Eeuwijk & François Tardieu. 2016. Plant Physiology, 172 (2) 749-764 doi: 10.1104/pp.16.00621
Link to data https://urgi.versailles.inra.fr/ephesis/ephesis/viewer.do#dataResults/trialSetIds=42
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8-Info_Maize_variety.tab
Tabular Data - 25.4 KB - Mar 27, 2019 - 77 Downloads
13 Variables, 256 Observations - UNF:6:CvjCsNsZylZz3bYvvbrilA==
This file contains the description of the genotypes. Briefly, all studied hybrids result from a F1 cross between the donor dent lines (parent 1) and one flint tester (parent 2, UH007 from University of Hohenheim). (Negro et al. 2018, https://doi.org/10.1101/476598). The file contains 13 columns: «Variety_ID», «Accession_ID, «accession_holding»: Two accession identifiers (“_H” stands for “hybrids”) and the holding institution. «parent1», «parent1_synonym», «parent1_holding»: Donor dent lines with their identifiers, possible synonyms and the holding institution. «parent2», «parent2_holding»: Tester flint parent with its holding institution. «Code_ID»: code/lot number. «Panel_246»: Is this hybrid included in the 246 panel? Can be “yes” or “no”. «genetic_group»: Four genetic groups were identified using the ADMIXTURE software, namely “Iodent”, “Lancaster”, “Stiff Stalk” and diverse dent lines that do not belong to the former three heterotic groups (“Other”). «holding», «Holding name»: Identifiers of the holing institutions.
7b-InfoSNP_50K_41722.tab
Tabular Data - 1.4 MB - Mar 27, 2019 - 86 Downloads
5 Variables, 41722 Observations - UNF:6:qX8c1+AJ/hlLdQM3pbL9bw==
This file contains the description of the 41,722 loci («SNP.names») genotyped by 50K Illumina Infinium Array on the 246 lines: position on B73 reference genome V2 («Chromosome», «Position»), original allele A, T, G, C («allele1», «allele2»).
7a-Genotyping_50K_41722.tab
Tabular Data - 19.6 MB - Mar 27, 2019 - 115 Downloads
41723 Variables, 246 Observations - UNF:6:RvLByT0PadG58Qsb6vxctQ==
This file contains the 50K genotyping Matrix tabulated 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. Inbred parental lines in lines (first column «Ind») and loci in columns. Description of loci can be found in «7b-InfoSNP_50K_41722.csv».
6-Plant_Ref_Geno_level-1.tab
Tabular Data - 80.4 KB - Nov 5, 2019 - 45 Downloads
27 Variables, 830 Observations - UNF:6:UMvI/mrx9OP74h15xrl0yQ==
This file contains plant traits measured at the plant level (10 plants per plot) for the reference genotype only (B73_H). It contains 27 columns: «Site», «year», «Experiment»: experiments ID with location («Site») and year («year») of experiment. In «Experiment», experiments are 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. «treatment»: targeted water regime. «Idplot»: plot identifier (when available) «replicate», «block»: experimental design factors. «Code_ID», «Accession_ID»: two genotype ID where «Code_ID» is a project code of each genotype, «Accession_ID» is the project name of the hybrid. «Plant»: plant number (10 plants where sampled per plot). «TnbL»: total number of leaves. «L8-L15»: length of leaf 8 to leaf 15. «W8-W15»: width of leaf 8 to leaf 15.
5-Leaf_Stages_Plot_level.tab
Tabular Data - 16.4 KB - Mar 27, 2019 - 102 Downloads
8 Variables, 306 Observations - UNF:6:ZrshAc+27bhVJwDcveem1w==
This file contains the number of leaves scored at several dates at the plant level (10 plants per plot) for the reference genotype only (B73_H). Values are provided averaged per plot. It contains 8 columns: «Site», «year», «Experiment»: experiments ID with location («Site») and year («year»). In «Experiment», experiments are 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. «treatment»: targeted water regime. «Rep»: experimental replicate. «Date»: calendar date in the crop cycle. «NbL»: number of ligulated leaves. «NbV»: number of visible leaves.
4-Genotypic_variables.tab
Tabular Data - 29.2 KB - Mar 27, 2019 - 89 Downloads
13 Variables, 246 Observations - UNF:6:M2FS4P1d0irrFERDPuRsiA==
This file contains the genotypic variables used for grain yield dissection and prediction. It contains 13 columns: «parent1», «Code_ID», «Variety_ID», «Accession_ID»: four genotype ID described in file «8-Info_Maize_variety». «genetic.group»: is the affiliation to one of the four genetic groups identified in the diversity panel. «genotypic.main»: main genotypic effect on grain number (from the factorial regression). «beta.Tnight.Flo»: sensitivity of grain number to night temperature around flowering time (from the factorial regression, in grains m-2 °C-1). «beta.Ri.Early»: sensitivity of grain number to intercepted radiation in vegetative period (from the factorial regression, in grains MJ-1). «beta.Psi.Flo»: sensitivity of grain number to soil water potential around flowering time (from the factorial regression, in grains m-2 MPa-1). «leaf.em.rate»: leaf emission rate from the Phenoarch platform (leaf d20°C-1). «nbFF»: final number of leaves. «silking.pot»: silking date average in well-watered experiments (d20°C). «GW.geno»: genotypic mean grain weight (mg).
3-Indices_GenoEnv_level.tab
Tabular Data - 1.1 MB - Mar 27, 2019 - 95 Downloads
16 Variables, 6150 Observations - UNF:6:kJtQpQTdt2QwE1cefrVilw==
This file contains the environmental indices. An environmental index is calculated as the average or the sum of one environmental variable over a genotype-specific phenological phase. The environmental variables used to calculate these indices can be found in the file «1-Env_variables_daily». It contains five columns of identification of experiments and genotypes, same as in file «2b-GrainYield_components_BLUEs_level». It also contains 11 columns with the environment-specific indices per genotype: «Tnight.Early»: night temperature averaged between the floral transition and the silk initiation for each genotype in each environment. «Tnight.Flo»: night temperature averaged between the silk initiation and the end of grain abortion for each genotype in each environment. «Tnight.Fill»: night temperature averaged between the end of grain abortion and the physiological maturity of the grain for each genotype in each environment. «Ri.Early»: intercepted radiation cumulated between the floral transition and the silk initiation for each genotype in each environment. «Ri.Flo»: intercepted radiation cumulated between the silk initiation and the end of grain abortion for each genotype in each environment. «Ri.Fill»: intercepted radiation cumulated between the end of grain abortion and the physiological maturity of the grain for each genotype in each environment. «Psi.Flo»: soil water potential averaged between the silk initiation and the end of grain abortion for each genotype in each environment. The soil water potential used here was the median between 30 and 60cm depth. «Psi.Fill»: soil water potential averaged between the end of grain abortion and the physiological maturity of the grain for each genotype in each environment. «Tmax.Early»: maximum temperature averaged between the floral transition and the silk initiation for each genotype in each environment. «Tmax.Flo»: maximum temperature averaged between the silk initiation and the end of grain abortion for each genotype in each environment. «Tmax.Fill»: maximum temperature averaged between the end of grain abortion and the physiological maturity of the grain for each genotype in each environment.
2b-GrainYield_components_BLUEs_level.tab
Tabular Data - 1.2 MB - Mar 27, 2019 - 111 Downloads
14 Variables, 7390 Observations - UNF:6:RvroACo7JrvAJnOGz2autg==
This file contains the genotypic means (Best Linear Unbiased Estimation, BLUEs), with one value per experiment (Location × year × water regime) per genotype. It contains 6 columns of identification of experiments and genotypes: «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», «Code_ID», «Variety_ID», «Accession_ID»: four genotype ID described in file «8-Info_Maize_variety». «geno.panel»: project in which the genetic material was generated. It also contains eight columns with the genotypic means for eight traits: «grain.yield»: yield adjusted at 15% grain moisture, in ton per hectare (t ha-1). «grain.number»: number of grain per square meter. «grain.weight»: individual grain weight (mg). «anthesis»: male flowering (pollen shed), in thermal time cumulated since emergence (d20°C). «silking»: female flowering (silking emergence), in thermal time cumulated since emergence (d20°C). «plant.height»: plant height, from ground level to the base of the flag leaf (highest) leaf (cm). «tassel.height»: plant height including tassel, from ground level to the highest point of the tassel (cm). «ear.height»: ear insertion height, from ground level to ligule of the highest ear leaf (cm).
2a-GrainYield_components_Plot_level-1.tab
Tabular Data - 3.1 MB - Nov 5, 2019 - 71 Downloads
21 Variables, 19358 Observations - UNF:6:phDn6BYQMmku8afU5s3U0A==
This file contains the raw phenotypic data per experiment (Location × year × water regime): one value per individual plot and outliers have been removed. It contains 12 columns for identifying the experiment, the genotypes and metadata: «Site», «year», «Experiment»: experiments ID with location («Site») and year («year»). In «Experiment», experiments are 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. «plotID»: plot identifier (when available) «treatment»: targeted water regime. «Replicate», «block»: experimental design factors. «Row,» «Column»: 2D coordinates of each plot. «Code_ID», «Variety_ID», «Accession_ID»: three genotype ID where «Code_ID» is a project code of each genotype, «Variety_ID» is the name of the parental accession and «Accession_ID» is the project name of the hybrid. It also contains 9 columns with the phenotypic information at the plot level: «grain.yield»: yiel adjusted at 15% grain moisture, in ton per hectare (t ha-1). «grain.number»: number of grain per square meter. «grain.weight»: individual grain weight (mg). «anthesis»: male flowering (pollen shed), in thermal time cumulated since emergence (d20°C). «silking»: female flowering (silking emergence), in thermal time cumulated since emergence (d20°C). «plant.height»: plant height, from ground level to the base of the flag leaf (highest) leaf (cm). «tassel.height»: plant height including tassel, from ground level to the highest point of the tassel (cm). «ear.height»: ear insertion height, from ground level to ligule of the highest ear leaf (cm).
1-Env_variables_daily-1.tab
Tabular Data - 687.6 KB - Nov 5, 2019 - 87 Downloads
30 Variables, 2633 Observations - UNF:6:ubHZzvd3YZcP64UGsyUaww==
This file contains the environmental characterization of each Location × year combination. Based on the recorded weather, daily environmental variables were calculated. This file contains 30 columns: «year», «Site», «Env»: experiments ID with year of experiment («year»), location («Site»). In «Env», experiments are described by the three first letters of the city’s name followed by the year of experiment. «Date»: Calendar date in the crop cycle. «D20.air», «D20cum.air»: thermal time calculated using the air temperature cumulated per day (D20.air) and cumulated since emergence (D20cum.air) in days equivalent at 20°C (d20°C). «D20.apex», «D20cum.apex»: thermal time calculated using the meristem temperature cumulated per day (D20.apex) and cumulated since emergence (D20cum.apex) in days equivalent at 20°C (d20°C). «Tmin.air», «Tmax.air», «Tmean.air»: minimum, maximum and average air temperature (°C). «Rhmin.air», «Rhmax.air», «Rhmean.air»: minimum, maximum and average air humidity (%). «Raincum»: cumulated rainfall (mm). «Windspeedmax»: maximun wind speed (m.s-1). «ET0.air»: reference Evapo-Transpiration (ET0, in mm) calculated using air temperature with the FAO estimation of the penman-Monteith equation. «Light»: cumulated global light (MJ m -2 d -1). «Inter.Light»: cumulated intercepted light (MJ m -2 d -1), simulated for the reference hybrid using the crop model APSIM. «VPD.air»: mean leaf to air Vapour Pressure Difference (VPD, in kPa) for the three hours in the afternoon during which VPD was maximum (most often 12:00 to 15:00 solar time). «VPD.apex»: mean leaf to leaf Vapour Pressure Difference (VPD, in kPa) for the three hours in the afternoon during which VPD was maximum (most often 12:00 to 15:00 solar time). «Tmaxperiod.apex»: mean meristem temperature (°C) for the two hours in the afternoon during which temperature was maximum (most often 13:00 to 15:00 solar time). «nbHourSupTmax.apex»: number of hours above 30°C, cumulated per day (h). «TmoyNuit»: mean temperature (°C) during night (by considering time course of temperature against the light). «WW.median3060»: median soil water potential between 30 and 60cm depth (cbar) in the watered scenario, averaged per day. «WD.median3060»: median soil water potential between 30 and 60cm depth (cbar) in the rainfed scenario, averaged per day. «WW.30»: soil water potential at 30cm depth (cbar) in the watered scenario, averaged per day. «WW.60»: soil water potential at 60cm depth (cbar) in the watered scenario, averaged per day. «WD.30»: soil water potential at 30cm depth (cbar) in the rainfed scenario, averaged per day. «WD.60»: soil water potential at 60cm depth (cbar) in the rainfed scenario, averaged per day.
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