In Silico Sorghum GxExM Dataset For Prediction Algorithm Comparisons

# In Silico Sorghum GxExM Dataset For Prediction Algorithm Comparisons ## Background A 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. ### Data ##### Genotype *qtl_effects.csv* 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 1: QTL Effect Sizes For Canopy (ams) - Column 1: QTL Effect Sizes For Maturity (mtu) - Column 2: QTL Order - Column 3: Effect Size of each QTL - Column 4: Location Information of each QTL (ChromosomeNumber_WithinChromosomeIndex) *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) *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 *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 ##### Trait Records *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: Environment/Site where crop was grown - Column 6: Phenotype (without error) for Biomass - Column 7: Phenotype (without error) for Grain Yield - Column 8: Simulated Error for Grain Yield Observations in Column 9 - Column 9: Phenotype (with error) for Grain Yield (Heritability=0.99)