MagicBeans

The files in these directories respresent the analyses and data used in the manuscript "The effect of genetic distance and genetic diversity on genomic prediction accuracy for soybean quantitative disease resistance to Phytophthora sojae"

Rolling, W. R., Lake, R., Dorrance, A. E., & McHale, L. K. (2024). The Effects of Genetic Distance and Genetic Diversity on Genomic Prediction Accuracy for Soybean Quantitative Disease Resistance to Phytophthora sojae. PhytoFrontiers™, PHYTOFR-07. https://doi.org/10.1094/PHYTOFR-07-23-0093-SC

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The data includes:

1. C2.2018.hmp.csv = Hapmap formatted genotypic data for germplasm panels C2.SK, C2.US, and C2.GRIN.
2. OH.2018.hmp.csv = Hapmap formatted genotypic data for germplasm panels OH.SK, OH.US, and OH.GRIN.
3. SK.2016.hmp.csv = Hapmap formatted genotypic data for the 2016.SK germplasm panel.
4. C2.2018.pheno.csv = Inoculated shoot weight BLUE value for germplasm panels C2.SK, C2.US, and C2.GRIN.
5. OH.2018.pheno.csv = Inoculated shoot weight BLUE value for ermplasm panels OH.SK, OH.US, and OH.GRIN.
6. SK.2016.pheno.csv = Inoculated shoot weight BLUE value for the 2016.SK germplasm panel.
7. Experiment_Panel.IDs.csv = Identification of which panels each plant introduction belongs to.
8. Correlation.Fst.Accuracy.csv = Data used to measure the correlation between genetic distance and genomic prediction accuracy.
9. Mod.dat.csv = Data used in regression analyses to identify which aspects of the training and validation panel have a significant effect on genomic prediction.

The R scripts include:

1. GeneticDiversityCombinedPanels.R - Analyses used to create Supplemental Figure 1, calculate Fst, and He
2. MakePhenotypeViolinPlots.R - Analyses used to create Supplemental Figure 1
3. SKtrainingpop.R - Analyses used to create Supplemental Table 1
4. UStrainingpop.R - Analyses used to create Supplemental Table 1
5. GRINtrainingpop.R - Analyses used to create Supplemental Table 1
6. CombineTwopanelstoTrain.R - Analyses used to create Supplemental Table 1
7. USGRIN.Train2016SK.R - Analyses used to create Supplemental Table 1
8. 2016SKvalidate.R - Analyses used to create Supplemental Table 1
9. Correlation_Fst_Accuracy.R - Used to calculate correlation between Fst and genomic prediction accuracy.
10. Regression.R - Used to complete regression analyses to identify which aspects of the training and validation panel have a significant effect on genomic prediction and create Figure 1, and provide data for supplemental table 2.
11. AddRelated.OHSK2OHUS.R - Analyses used to create Table 2
12. AddRelated.OHUS2OHSk.R - Analyses used to create Table 2
13. AddRelated.US2GRIN.R - Analyses used to create Table 2
14. GeneticDiversityCombinedPanels.R - Analyses used to calculate He and Fst when two panels were combined to create training panel. Results in Supplemental Table 2.