Table 2. Rootstock QTLs identified from the ‘M9’ × ‘R5’ population that influence the growth and flowering of the grafted scion. QTLs are derived from three replicates (Rep1–3) of the first population and a subset of the second population. For each QTL detected with the MQM the LOD score is given by the number before ‘/’. For QTLs detected with the Kruskal–Wallis test, the significance level (indicated by asterisks: *P<0.01; ***P<0.005, ****P<0.0001) is given. The percentage of variance explained by each QTL is indicated by the number after ‘/’.

		Trait	Map	LG3	LG5	LG6	LG8	LG9	LG10	LG11	LG12	LG14	LG15	LG16
Population 1	Rep1	DW%	‘M9’		****/50.2					****/11.4
			‘R5’						***/7.6		*/5.4
		Flowering	‘M9’		****/21.1			*/6.8		****/16.5
			‘R5’			***/9.0
		TCA year 2	‘M9’		3.1/7.1					2.4/5.4
			‘R5’			1.8/5.3						2.0/7.4
		TCA increase years 2–3	‘M9’		11.3/36.3
			‘R5’
		TCA increase years 3–4	‘M9’		11.5/34.4					2.7/6.6
			‘R5’
		TCA increase years 4–5	‘M9’		13.3/39.9					2.5/5.7
			‘R5’
		TCA increase years 5–6	‘M9’		12.8/38.9					1.6/4.2
			‘R5’
		TCA increase years 6–7	‘M9’		8.2/23.9			2.4/6.2		2.0/5.2
			‘R5’
		TCA increase years 2–7	‘M9’		14.2/40.7					2.9/6.3
			‘R5’						1.9/8.0
	Rep2	TCA increase years 4–5	‘M9’		21.6/57.2
			‘R5’						1.8/7.1
		TCA increase years 5–6	‘M9’		12.4/39.8					2.2/11.7
			‘R5’						2.2/8.7
	Rep3	TCA increase years 4–5	‘M9’		9.8/56.5					1.6/10.1
			‘R5’						1.7/14.9
		TCA increase years 5–6	‘M9’		9.8/57.1
			‘R5’
Population 2		Height year 1	‘M9’							3.8/17.8			3.1/17.3
			‘R5’			1.6/8.8
		Node number year 1	‘M9’				2.2/15.8			2.4/11.3				2.6/12.5
			‘R5’			2.6/13.7
		Average internode length	‘M9’	3.3/14	3.1/13					1.8/7.5			2.0/8.3
			‘R5’								1.6/11.4

Abbreviation: MQM, multiple QTL model.