Table 6.

Summary of QTL observed for mapping population G33 × G43

Trait	Observations (n)	Linkage group	Position (cM)	LODa	PVE	Bayes 95 % CI (cM)	Beneficial allele	Effectb	QTL plot Additional file 8:	Effect plot Additional file 9:
Total seeds Year 2 (NPc)	254	5	22.9 (G104)	3.05*	4.6	0.0–37.0	G33	Dom	Fig. S5a	Fig. S6a
Total seeds Year 3	251	7	30.3 (1398222|12344025)	3.52**	5.9	12.0–38.0	G33	Dom	Fig. S5b	Fig. S6b
		4	8.0	3.19*	5.4	0.0–34.5	G33	Dom		Fig. S6c
100-seed weight Year 1	243	4	40.0	6.12***	9.5	28.0–55.0	G33	Rec	Fig. S5c	Fig. S6d
		2	28.0	5.66***	8.7	24.3–35.0	G33	Dom		Fig. S6e
		11	20.5 (G28)	4.16***	6.3	4.0–37.0	G33	Add		Fig. S6f
100-seed weight Year 2	250	4	35.9 (AG806)	15.09***	18.5	30.0–42.0	G33	Add	Fig. S5d	Fig. S6g
		11	26.0	11.39***	13.5	21.2–27.0	G33	Add		Fig. S6h
		2	23.0	5.35***	6.0	18.0–26.0	G33	Dom		Fig. S6i
		10	3.0	4.39***	4.9	0.0–11.0	G43	Dom		Fig. S6j
100-seed weight Year 3	253	4	41.0	6.82***	8.9	35.9–58.9	G33	Add	Fig. S5e	Fig. S6k
		9	50.8 (1408478|12317739)	4.41***	5.6	42.0–51.5	G33	Dom		Fig. S6l
		11	1.0	3.53***	4.5	0.0–10.0	G33	Rec		Fig. S6m
		2	37.0	3.15**	4.0	15.0–40.0	G33	Dom/OD		Fig. S6n
		11	26.8 (1398998|12324489)	2.96**	3.7	7.0–32.0	G33	Add		Fig. S6o
		10	4.0	2.64**	3.2	0.0–15.0	G43	Dom		Fig. S6p
Oil content Year 2	249	6	24.0	5.62***	7.6	1.0–34.0	G43	Rec	Fig. S5f	Fig. S6q
		10	0.0 (Jcuint152)	4.89***	6.5	0.0–5.0	G43	Add		Fig. S6r
		4	2.5 (1416680|12276533)	4.51***	6.0	0.0–10.0	G33	Dom		Fig. S6s
		5	43.8 (AG517)	4.13***	5.5	27.7–49.0	G33	Dom		Fig. S6t
Oil content Year 3	253	5	48.0 (1407850|12321642)	7.07***	11.5	40.0–51.0	G33	Dom	Fig. S5g	Fig. S6u
		6	45.5 (1406827|12348279)	3.13***	4.9	1.0–51.0	G43	Rec		Fig. S6v

^aThe LOD significance thresholds are *** p = 0.01, ** p = 0.05 or * p = 0.10

^bEffects are overdominant (OD), additive (Add) or dominant (Dom)

^cQTL for total seed yield in year 2 were obtained by performing non-parametric analysis