Phenotypic Data and GWA Results for ALL, INDICA and JAPONICA

SMA = Single Marker Analysis
Yellow rectangle on Manhattan Plot (MP) = IR64 x Azucena QTL
Pink rectangle on MP = legacy QTL
Red bar between MP and chromosome = GWA peak detected in ALL and/or clades
Blue bar between MP and chromosome = GWA peak detected uniquely in subpopulation(s)
Green triangle = POCRE SNP

Element	Tissue	ALL _____________________	INDICA _____________________	JAPONICA _____________________
As (Arsenic)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
B (Boron)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Ca (Calcium)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Cd (Cadmium)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Co (Cobalt)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Cr (Chromium)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Cu (Copper)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Fe (Iron)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
K (Potassium)	root shoot	p-values NA	plot NA	p-values NA	plot NA	p-values NA	plot NA
Mg (Magnesium)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Mn (Manganese)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Mo (Molybdenum)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Na (Sodium)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
P (Phosphorus)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Pb (Lead)	root shoot	p-values NA	plot NA	p-values NA	plot NA	p-values NA	plot NA
S (Sulfur)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Se (Selenium)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Si (Silicon)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Sr (Strontium)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot
Zn (Zinc)	root shoot	p-values p-values	plot plot	p-values p-values	plot plot	p-values p-values	plot plot

Element

Tissue

ALL _____________________

INDICA _____________________

JAPONICA _____________________

SMA

p-values

Manhattan/

Q-Q Plots

SMA

p-values

Manhattan/