Table 2.

Markers associated with different agronomic traits in the mega-environment (composed of three sites evaluated over 2 years) according the GLM corrected for population structure according to principal component covariates, PCA, and Mixed Linear Model, (MLM), corrected with kinship and structure matrices and that in addition fulfill the criteria of a genetic inflation factor lower than 1.25. Marker-trait association was considered significant when the corresponding markers’ q value was lower than the q value cut-off that retrieve less than one false positive estimated for each model tested by false discovery rate test.

Marker	marker_p	markerR2	Map location	ref
Yield
oPt-10734	0.00020351	0.06405	Mrg05	Hizbai et al. (2012)
oPt-12924	0.000035844	0.07632	Mrg12	He et al. (2013)
oPt-5217	0.00025632	0.06187	Mrg03	Tinker et al. (2009)
oPt-8261	0.00042453	0.05877	Mrg23	He et al. (2013)
oPt-9844	0.00033705	0.05992	NA
Biomass
Merge98	0.00049472	0.04305	NA
oPt-15938	0.00077951	0.05059	Mrg15	Tinker et al. (2009)
Harvest Index
Barb2-40	0.00055462	0.08744	NA
MAMA07	0.00040226	0.07294	Mrg13	Wight et al. (2010)
oPt-793146	0.00046858	0.08982	NA
oPt-8261	0.0005373	0.08783	Mrg23	He et al. (2013)
Heading date
MAMA07	0.00034825	0.07102	Mrg13	Wight et al. (2010)
Merge82	0.00017619	0.09703	NA
oPt-10359	0.000015774	0.12598	Mrg12	Tinker et al. (2009)
oPt-10891	0.000027511	0.11923	Mrg08	He et al. (2013)
oPt-1340	0.00055509	0.08356	Mrg08	He et al. (2013)
Crown rust severity
Merge136	0.00031113	0.02328	Mrg18	Howarth (pers com)
oPt-10121	0.00097244	0.02484	Mrg21	Hizbai et al. (2012)
oPt-11494	0.0006268	0.02634	Mrg01	Hizbai et al. (2012)
oPt-12898	0.00057288	0.09602	NA
oPt-388855	0.00034875	0.10272	NA
oPt-794313	0.00015813	0.03099	NA
oPt-9546	0.00113	0.02434	Mrg18	Howarth (pers com)