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Table 1 Inputs for joint linkage mapping QTL analysis and GWAS models

From: Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population

  Joint linkage mapping QTL models   
QTL Model Phenotype No. markers in linkage map No. NAM RILs
1a originalb 1106 4694
2 original 1106 4354
3 updated 1106 4694
4 updated 1106 4354
5 original 7386 4354
6 updated 7386 4354
7 updated 7386 4413
GWAS models
GWAS Model QTL model used to adjust phenotypes Variants tested for association p value threshold
Aa 1 1.6 M HM1 SNPs 1E-4
B 1 1.6 M HM1 SNPs 1E-7
C 1 28.2 M HM1/2 SNPs + 0.2 M RDVs 1E-7
D 7 1.6 M HM1 SNPs 1E-7
E 7 28.2 M HM1/2 SNPs + 0.2 M RDVs 1E-7
  1. aQTL model 1 and GWAS model A results were previously published [8].
  2. bOriginal phenotype inputs were RIL BLUPs across 3 environments, based on a model with a common flowering time covariate; updated phenotype inputs were RIL BLUPs across 3 environments based on a model with environment-specific flowering time covariates.