Table 2.

Summary of the stable QTL detected in 2, 3 and 4 environments (highlighted in bold, italics and bolditalics, respectively. Env environment (1 = IRRI 2012, 2 = IRRI 2013, 3 = PhilRice2012, 4 = PhilRice2013), Chr chromosome, Start/End physical Mb position of the linkage block, Add Effect: estimated additive effect, PVE phenotypic variation explained by the QTL (%), High all Freq Frequency of the higher value allele.

Trait	QTL	Env	Chr	Start Mb	End Mb	− log10P	PVE%	Add. effect	High all Freq
B	qB7.1	1	7	6.06	6.49	8.8	9.7	2.44	0.12
	qB7.1	2	7	6.06	6.49	8.9	11.5	4.03	0.16
Ca	qCa3.1	1	3	16.66	16.92	6.0	9.5	15.12	0.56
	qCa3.1	4	3	16.80	16.90	5.7	5.1	13.52	0.41
	qCa12.2	3	11	27.83	27.83	5.2	4.7	6.03	0.66
	qCa12.2	4	11	27.83	27.83	5.2	3.6	7.89	0.68
Co	qCo7.1	2	7	29.23	29.37	5.5	4.5	0.02	0.14
	qCo7.1	3	7	29.26	29.35	7.2	6.2	0.03	0.14
	qCo7.1	4	7	29.27	29.34	5.4	5.1	0.02	0.14
	qCo8.1	3	8	3.55	3.56	5.5	12.4	0.00	0.09
	qCo8.1	4	8	3.55	3.57	6.2	15.7	0.00	0.90
Fe	qFe1.2	2	1	2.53	2.64	5.9	6.7	0.41	0.60
	qFe1.2	4	1	2.56	2.66	5.6	7.0	0.44	0.82
K	qK6.1	2	6	1.59	1.83	7.8	6.2	255.44	0.13
	qK6.1	3	6	1.70	1.81	5.5	5.0	261.83	0.13
	qK6.1	4	6	1.70	1.83	6.0	4.5	233.69	0.13
Mo	qMo3.3	1	3	26.70	26.83	6.4	7.2	0.67	0.05
	qMo3.3	3	3	26.76	26.78	6.0	6.3	0.17	0.06
	qMo8.1	3	8	0.00	0.25	9.2	10.1	0.12	0.85
	qMo8.1	4	8	0.00	0.33	8.0	9.9	0.07	0.38
	qMo10.2	2	10	5.17	5.28	5.4	4.4	0.10	0.09
	qMo10.2	3	10	5.17	5.36	7.1	7.5	0.59	0.09
Na	qNa1.2	1	1	11.01	11.54	8.9	9.7	10.28	0.27
	qNa1.2	2	1	11.46	11.52	6.3	5.2	2.75	0.77
	qNa11.5	2	11	27.37	27.48	6.2	5.4	5.54	0.05
	qNa11.5	4	11	27.68	27.82	5.2	4.8	10.73	0.16
Zn	qZn7.2	1	7	29.26	29.43	6.3	5.0	4.88	0.11
	qZn7.2	2	7	29.26	29.33	6.4	5.1	3.87	0.16
	qZn7.2	3	7	29.26	29.42	6.9	8.0	2.94	0.19
	qZn7.2	4	7	29.26	29.41	6.1	5.2	7.34	0.06
	qZn7.3	1	7	29.42	29.67	6.5	5.4	6.38	0.08
	qZn7.3	2	7	29.47	29.67	5.5	4.3	4.04	0.12
	qZn7.3	3	7	29.52	29.67	5.4	5.0	4.00	0.07