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Supplemental Material for Ta et al., 2020
dataset
posted on 2020-09-28, 14:57 authored by James Ta, Christine Palmer, Marcus Brock, Matthew J. Rubin, Cynthia Weinig, Julin MaloofJulin Maloof, Daniel RuncieDaniel RuncieFile 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.