TABLE 1.

Quantitative trait loci (QTL) identified by multiple QTL mapping for flowering time, growth habit and branching index in four populations grown in different environments.

Population	Place	Year	Traita	Condb	QTL	LODc	PVEd	Markere	LGf	Earlyg	Lateg	Thrh
CRIL2	Hobart	2016	DTF	LD, P	DTF3C	2.9	9.6	S1202p50545	3	29	30.3	2.8
				SD, P	DTF3A	50.2	85.2	FTa1	3	66.2	128.6	2.6
		2016	GH	SD, P	GH3	34	66.6	FTa1	3	3.4	1.6	2.6
					GH4	5.5	5.9	S360p1277380	4	2.8	2.2	3.1
		2016	BI	SD, P	BI3	10.6	33.1	FTa1	3	0.4	0.9	2.6
				LD, P	BI3	5.4	18.4	FTa1	3	0.2	0.5	2.5
RIP12	Cordoba	2001	DTF	GLH	DTF3A	10.8	46.9	FTa1	3	14.1	39.6	3.1
				Field	DTF3A	4.5	22	FTa1	3	60.4	68.6	2.9
		2004	DTF	Field	DTF3A	14.8	51.1	FTa1	3	8.9i	21.7i	2.9
					DTF4B	3.6	9.2	STMS11	4	17.9i	12.6i	3.3
		2008	DTF	Field	DTF3B	6.3	29.6	COLh	3	70.3	76.8	2.9
		2014	DTF	Field	DTF3A	8.4	29.8	FTa1	3	58.3	64.2	3
					DTF4A	5.3	17.3	GAA47	4	63.5	59	2.8
RIP5	Cordoba	2003	DTF	Field	DTF3D	9.6	38.7	WRKY	3	60.4	64.8	2.7
	Cordoba				DTF3A	3	8.7	FTa1/2	3	61.3	63.9	2.7
	Mengibar				DTF3A	5.7	26.9	FTa1/2	3	64.2	66.7	2.8
RIP8	Rep1	2003	DTF	Field	DTF3D	7.5	29.2	TA125	3	84.3	87.3	2.6
	Rep2				DTF3D	6.8	29.0	TA125	3	84.6	87.3	2.7

^aTrait analyzed: DTF, flowering time; GH, growth habit; BI, branching index. ^bCondition: LD, long days; SD, short days; P, phytotron; GLH, glasshouse. ^cThe LOD scores for each QTL. ^dPVE, Phenotypic variation explained. ^eMarker nearest to the peak LOD score. ^fLG, linkage group harboring the QTL. ^gMarker genotype class means for early (C. arietinum accessions ICC4958, ICCL81001 and WR315 for CRIL2, RIP12, and RIP5/8, respectively) and late (C. reticulatum accessions PI489777 and Cr5-9 in CRIL2 and RIP12 and C. arietinum ILC3279 in the case of RIP5/8) parents, calculated for the marker with higher LOD. ^hThreshold LOD for a 0.995 confidence value, calculated through permutation test for each trait and linkage group. ⁱFlowering time in 2004 is a relative value, as specified in Supplementary Figure 2.