DOI: 10.6084/m9.figshare.23789685
title: In Silico Sorghum GxExM Dataset For Prediction Algorithm Comparisons

description: <br># In Silico Sorghum GxExM Dataset For Prediction Algorithm Comparisons<br>## BackgroundA simulated Multi-Environment Trial (MET) dataset to stimulate the development and comparisons of predictive algorithms to deconvolute genotype-by-environment-by-management interactions in plant breeding. Contains Genomic (SNP & QTL) & Phenotypic Data for Multiple Traits.<br>### Data##### Map<i>map.csv</i>Positional Information on the Causal (Quantitative Trait Loci - QTL) and Non-Causal (Single Nucleotide Polymorphisms - SNP) Genomic Sites within and across chromosomesColumn 1: Chromosome NumberColumn 2: Marker IDColumn 3: Position (Morgans)##### Genotype<i>qtl_effects.csv</i>Information on Causal Genomic Sites (Quantitative Trait Loci - QTL) & their Effect Sizes on Component Traits;- Column 1: QTL Effect Sizes For Propensity To Tiller (ptt)- Column 2: QTL Effect Sizes For Canopy (ams)- Column 3: QTL Effect Sizes For Maturity (mtu)<br>*QtlIndex.csv*Information on QTL position for each Component Trait. Position Number connects to Column order in qtl.csv- Column 1: Per Component Trait QTL Index- Column 2: QTL Positions For Propensity To Tiller (ptt)- Column 3: QTL Positions For Canopy (ams)- Column 4: QTL Positions For Maturity (mtu)<br>*qtl.csv*Information on Number of Gene Copies (Alleles) at each QTL for each individual- 1st Column: Individual ID- 2nd Column Onnwards: QTL Allele Counts<br>*markers.csv*Information on the number of Gene Copies (Alleles) at each SNP (Non-Causal Genomic Sites) for each individual- 1st Column: Individual ID- 2nd Column Onwards: SNP Allele Counts<br>##### Trait Records<br>*trait_data.csv*Trait Records for each individual- Column 1: Genotype ID- Column 2: Phenotype (without error) for Propensity of Tiller (ptt)- Column 3: Phenotype (without error) for Canopy (ams)- Column 4: Phenotype (without error) for Maturity (mtu)- Column 5: Plant Population/Plot Density- Column 6: Environment/Site where Crop was grown- Column 7: Phenotype (without error) for Biomass- Column 8: Phenotype (without error) for Grain Yield<br>*trait_data_H2_0.3.csv*Trait Records for each individual- Columns 1- 8: same as trait_data.csv- Column 9: Replicate ID- Column 10: Simulated Error for Grain Yield Observations in Column 11- Column 11: Phenotype (with error) for Grain Yield (Broad Sense Heritability=0.3)<br>*trait_data_H2_0.5.csv*Trait Records for each individual- Columns 1- 8: same as trait_data.csv- Column 9: Replicate ID- Column 10: Simulated Error for Grain Yield Observations in Column 11- Column 11: Phenotype (with error) for Grain Yield (Broad Sense Heritability=0.5)<br>*trait_data_H2_0.8.csv*Trait Records for each individual- Columns 1- 8: same as trait_data.csv- Column 9: Replicate ID- Column 10: Simulated Error for Grain Yield Observations in Column 11- Column 11: Phenotype (with error) for Grain Yield (Broad Sense Heritability=0.8)<br>*trait_data_H2_0.99.csv*Trait Records for each individual- Columns 1- 8: same as trait_data.csv- Column 9: Replicate ID- Column 10: Simulated Error for Grain Yield Observations in Column 11- Column 11: Phenotype (with error) for Grain Yield (Broad Sense Heritability=0.99)##### Longitudinal Trait Records*StageReports.csv*Trait Records for each individual by Developmental Stage- Column 1: Genotype ID- Column 2: Plant Population/Plot Density- Column 3: Days after sowing- Column 4: Developmental Stage- Column 5: Average maximum temperature per developmental stage- Column 6: Average minimum temperature per developmental stage- Column 7: Average radiation per developmental stage- Column 8: Total rainfall per developmental stage- Column 9: Total potential evapotranspiration per developmental stage<br>*WeeklyReports.csv*Trait Records for each individual by Developmental Stage- Column 1: Genotype ID- Column 2: Plant Population/Plot Density- Column 3: Days after sowing- Column 4: Developmental Stage- Column 5: Developmental Stage Continuous Format- Column 6: biomass (g/m2)- Column 7: grain yield (g/m2)- Column 8: Leaf Area Index- Column 9: Leaf Cover - Column 10: Fertile Tiller Number- Column 11: Number of Leaves- Column 12: Extractable Soil Water- Column 13: Plant Available Water (mm/mm)- Column 14: Mean maximum temperature per week- Column 15: Mean minimum temperature per week- Column 16: Mean radiation per week- Column 17: Total rainfall per week- Column 18: Total potential evapotranspiration per week<br>