cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/iasstn/cqdq8b
title: 4-Genotypic_variables.tab

description: 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).
DOI: 10.15454/iasstn/nbw8k5
title: 0_Data_outline.pdf

description: This file contains the outline of the files organization and content. It describes the different measurement scales available: Weather and soil water data at daily time step (1). Phenotypic data at the plot level in each experiment (2a) and at the genotypic level in each experiments (2b and 3). Variable calculated at the genotype level (4). Phenotypic data at the plant level in each experiment for the reference genotype (5 and 6). Genotyping data available for each genotype (7a and 7b). Description of the genotypic material used (8). The map of the experimental sites has been drawn with the R package ggmap (Kahle and Wickham, 2013, doi:10.32614/RJ-2013-014). The maize 3D canopy is adapted from Pradal et al., 2008 (https://doi.org/10.1071/FP08084). The maize 3D plant is adapted from Fournier and Andrieu, 1999 (http://dx.doi.org/10.1051/agro:19990311).
DOI: 10.15454/iasstn/4q5k3m
title: 1-Env_variables_daily-1.tab

description: 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.
DOI: 10.15454/iasstn/vqcl95
title: 2a-GrainYield_components_Plot_level-1.tab

description: 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).
DOI: 10.15454/iasstn/totpky
title: 6-Plant_Ref_Geno_level-1.tab

description: 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.
DOI: 10.57745/o4ojvp
title: 2a-GrainYield_components_Plot_level.tab

description: 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 13 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»: three genotype ID where «Code_ID» is a project code of each genotype, «Variety_ID» is the name of the parental accession and «Accession» is the project name of the hybrid. «type»: the type of set in the genomic prediction study (Millet et al. 2019). It can be part of the cross validation set (CrossValidation), or the external test set (GnE_ext). NOTE: there is no plot data for the external test set “nGnE_ext”.
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).
DOI: 10.57745/rretio
title: 2b-GrainYield_components_BLUEs_level-1.tab

description: This file contains the genotypic means (Best Linear Unbiased Estimation, BLUEs), with one value per experiment (Location × year × water regime) per genotype. It contains 7 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. «type»: the type of set in the genomic prediction study (Millet et al. 2019). It can be part of the cross validation set (CrossValidation), or the external test set (GnE_ext or nGnE_ext). 
It also contains 8 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).
DOI: 10.57745/1riega
title: 3-Indices_GenoEnv_level-1.tab

description: 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 6 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.
DOI: 10.57745/xpijk2
title: 3b-Indices_Env_level.tab

description: This file contains the mean environmental indices (Supplementary Table S1 in Millet et al. 2016). An environmental index is calculated as the average or the sum of one environmental variable in a period over 20 days at 20°C encompassing flowering time of the reference hybrid. The environmental variables used to calculate these indices can be found in the file «1-Env_variables_daily». 
It contains 5 columns of experiment metadata: «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. «Lat», «Long» latitude and longitude of the experimental site. «EC_water» and «EC_temp» are the environmental classification using soil water potential and temperature respectively (see Millet et al. 2016 for details). 
It also contains 6 columns with the indices (see file «1-Env_variables_daily» for environmental variables descirption). Column «type» indicates the type of dataset for the genomic prediction study (Millet et al. 2019): cross-validation (CrossValidation) or external test set (nE_ext).
DOI: 10.57745/kfzccx
title: 8-Info_Maize_variety-1.tab

description: 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 14 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”). «type»: the type of set in the genomic prediction study. It can be part of the cross validation set (CrossValidation), or the external test set (nG_ext). «holding», «Holding name»: Identifiers of the holing institutions.
DOI: 10.57745/httdob
title: 7c-Genotyping_50K_41722_nG.tab

description: This file contains the genotyping of 41,722 loci on the 56 parental lines of the external test set (nG_ext). Format is the same as file «7a-Genotyping_50K_41722.csv» and description of loci can be found in «7b-InfoSNP_50K_41722.csv».
DOI: 10.57745/984p0i
title: 9a-CrossValidation_Sets_Geno.tab

description: This file contains the 10 sampling sets of genotypes for the cross-validation in the genomic prediction study (Millet et al.2019). A random stratified sampling was repeated ten times by selecting 80% and discarding 20% of the 246 hybrids in each genetic group. The file contains 5 columns of genotype identification described in file «8-Info_Maize_variety.csv». It also 10 columns, one per sampling, with “yes” when the genotype was selected in the training set and “no” when the genotype was kept in the validation set.
DOI: 10.57745/l7f21w
title: 9b-CrossValidation_Sets_Exp.tab

description: This file contains the 10 sampling sets of experiments for the cross-validation in the genomic prediction study (Millet et al.2019). A random stratified sampling was repeated ten times by selecting selecting 80% and discarding 20% of the 25 experiments in each environmental scenario defined in Millet et al. 2016. The file contains 2 columns of experiment identification: «Experiment» described in previous files and «EC» the environmental classification. It also contains 10 columns, one per sampling, with “yes” when the experiment was selected in the training set and “no” when the experiment was left in the validation set.
DOI: 10.57745/begjhm
title: 1-Env_variables_daily.tab

description: This file contains the environmental characterization of each Location × year combination. Based on the recorded weather, daily environmental variables were calculated. This file contains 31 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. «Rad»: cumulated global radiation (MJ m -2 d -1). «Ri»: cumulated intercepted radiation (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). «Tmax.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). «Tnight»: 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. «type»: the type of set in the genomic prediction study (Millet et al. 2019). It can be part of the cross validation set (CrossValidation), or the external test set (nE_ext).
DOI: 10.57745/y1tn0o
title: 8-Info-BiologicalMaterial.tab

description: 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 14 columns: «Variety_ID», «AccessionID, «AccessionHolding»: 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”). «type»: the type of set in the genomic prediction study. It can be part of the cross validation set (CrossValidation), or the external test set (nG_ext). «holding», «Holding name»: Identifiers of the holing institutions. The Following columns have been added to comply to MIAPPE: MaterialSourceDOI: DOI of the Accession identifying this variety, MaterialSourceID: ID of the Accession identifying this variety, BiologicalMaterialID: ID used in the data files, Organism:NCBI Taxonomy identifier, Genus, Species, InfraspecificName: variety name
DOI: 10.57745/ywn6g7
title: 10-Info-ObservedVariable.tab

description: List of phenotypic and environmental variables used in the dataset, following the MIAPPE data standard (https://www.miappe.org/)
DOI: 10.57745/d8n1ra
title: 12a-Info-EIPO-Environmental_Traits.csv

description: Ontology referenced in the Observed Variable file. This Ontology is here for traceability and to ensure an unambiguous versioning. The 10-Info-ObservedVariable.tab should be sufficient in most cases.
DOI: 10.57745/0kiqdq
title: 12b-Info-MIPO-Maize_traits.csv

description: Ontology referenced in the Observed Variable file. This Ontology is here for traceability and to ensure an unambiguous versioning. The 10-Info-ObservedVariable.tab should be sufficient in most cases.
DOI: 10.57745/gvfa3d
title: 11-Info-Study.tab

description: List of studies, including locations, used in the dataset, following the MIAPPE data standard (https://www.miappe.org/)
DOI: 10.57745/e7sqdi
title: 12a-Info-EIPO-Environmental_Traits.csv

description: Ontology referenced in the Observed Variable file. This Ontology is here for traceability and to ensure an unambiguous versioning. The 10-Info-ObservedVariable.tab should be sufficient in most cases.
DOI: 10.57745/ditiav
title: 0b-MIAPPE-metadata-description.xlsx

description: :unav