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

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

	Joint linkage mapping QTL models
QTL Model	Phenotype	No. markers in linkage map	No. NAM RILs
1^a	original^b	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
A^a	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

^aQTL model 1 and GWAS model A results were previously published [8].
^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.

ISSN: 1471-2164