Supplemental Material for Ta et al., 2020
datasetposted on 28.09.2020 by James Ta, Christine Palmer, Marcus Brock, Matthew J. Rubin, Cynthia Weinig, Julin Maloof, Daniel Runcie
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
File S1 contains the transformed and standardized phenotype data. File S2 contains the posterior means for the genotype and GxE random effects used for QTL mapping. File S3 contains the markers used for the GridLMM analysis. File S4 contains the genotype file used for the GEMMA analysis. File S5 contains the phenotypes (bolting day shade responses) used for the GEMMA analysis. File S6 contains the family covariate used for the GEMMA analysis. File S7 contains the SNP annotation file used for the GEMMA analysis. File S8 contains the genotype file used for the TASSEL analysis. File S9 contains the phenotypes (bolting day shade responses) and family covariate data used for the TASSEL analysis. File S10 contains the phenotype and genotype information used for the QTL IciMapping analysis. File S11 contains the trait data in sun/shade conditions used for path analysis. File S12 - Contains the equations for the QTL-path scans and the lavaan equations, as well as a brief example of the estimation of direct and indirect QTL effects. Supplementary Material R1 contains Figures S1-S3. Table S1 contains the names of about 100 natural accessions grown in addition to the NAM population. Table S2 contains the 95% credible intervals for the shelf fixed effects, G-PVE, and GxE-PVE. Table S3 contains the significant markers detected for the bolting day shade response BLUPs using TASSEL. Table S4 contains the summary statistics from the fitted Bayesian mixed models. Table S5 contains the trait effects - estimated from the path models - for the different populations in the sun condition. Table S6 contains the trait effects - estimated from the path models - for the different populations in the shade condition. Table S7 contains the QTL found for the genotype random effects using GridLMM.