Table 5.

Summary of the main QTLs (−log₁₀(Pval) ≥ 8) identified for the three traits

Trait	QTL	Chr	Pos	Lower Limit	Upper Limit	R2	Effect	Log	Minor All	Major All	MAF	EnvMax	Nb DiffEnv
DTA	95	3	158,974,594	158,943,646	159,005,990	0.15	1.27	10.03	G	C	0.41	Ner13R	19
plantHT	21	2	130,441,738	129,971,437	130,912,039	0.15	−6.74	9.21	A	G	0.14	Cam12W	3
	71	6	6,614,012	6,593,785	6,636,807	0.13	−4.76	8.39	G	A	0.18	Cam12R	2
	72	6	6,807,230	6,793,841	6,837,747	0.14	−4.87	8.77	T	G	0.18	Cam12R	2
	78	6	20,330,595	12,258,527	20,758,095	0.27	−8.99	17.31	C	T	0.26	Cam12W	4
	79	6	22,905,376	21,037,721	23,951,687	0.19	−5.45	11.42	T	G	0.31	Cam12R	3
	80	6	25,3178,25	24,184,017	26,606,537	0.13	−4.41	8.17	T	C	0.2	Cam12R	2
	81	6	28,130,108	26,695,327	28,659,766	0.16	−5.14	9.84	C	G	0.44	Cam12R	2
	94	6	101,482,646	101,463,249	101,501,936	0.14	−5.98	8.22	T	A	0.17	Cam12W	2
	110	8	12,782,777	12,767,198	12,798,330	0.19	−7.67	12.44	C	T	0.22	Cam12W	3
GY	65	3	141,621,777	140,505,559	144,210,207	0.12	0.42	8.13	A	C	0.27	Gai12W	5
	85	3	187,028,970	186,994,852	187057,772	0.12	−0.48	8.49	A	C	0.28	Kar12W	1
	120	6	5,155,708	5,131,927	5,177,694	0.12	−0.58	8.24	C	T	0.42	Cam12W	2
	122	6	5,638,516	5,623,945	5,659,803	0.12	−0.57	8.11	T	G	0.23	Cam12W	2
	124	6	5,871,000	5,855,407	5,887,383	0.12	−0.56	8.4	T	G	0.42	Cam12W	2
	127	6	6,612,654	6,593,785	6,636,807	0.16	−0.65	10.44	C	A	0.32	Cam12W	2
	128	6	6,807,462	6,793,841	6,837,747	0.12	−0.54	8.41	A	C	0.26	Cam12W	2
	129	6	6,890,199	6,878,877	6,930,838	0.12	0.63	8.06	T	A	0.48	Cam12W	3
	130	6	7,046,773	7,027,497	7,088,575	0.13	0.62	8.71	A	G	0.4	Cam12W	3
	131	6	7,159,714	7,113,662	7,200,479	0.12	0.59	8.24	T	C	0.39	Cam12W	3
	135	6	18,528,943	12,258,527	29,438,316	0.28	−0.78	18.7	G	C	0.31	Cam12W	6
	147	6	101,482,646	101,463,249	101,501,936	0.22	−0.65	15.04	T	A	0.17	Cam12W	5
	173	8	12,782,777	12,767,198	12,798,330	0.17	−0.61	11.8	C	T	0.22	Cam12W	4

“Pos” indicates the physical position in base pair of the SNP with the strongest association on the V2 of reference genome. LowerLimit and UpperLimit indicate the lower and upper physical limits estimated by LD windows (LD_win) for each QTL. The proportion of the variance explained (R²), the effect of the major allele (Effect) as outputted by FastLMM, −log₁₀(Pval) (Log), the minor and major alleles (Minor All and Major All) and the minor allele frequency (MAF) of the most significant SNP within the QTL are shown. The following columns represent environment for which the most associated QTL was observed (EnvMax) and the number of different environments in which QTL are detected (NbDiffEnv) are shown. Note that QTLs 71–72 for the plant height and QTLs 129–130 for the grain yield are genetically close (< 1 cM) and display high mean LD (r²K > 0.5). Hence, QTLs 71–72 and 129–130 can potentially be merged