QTLs underlying natural variation of root growth angle among rice cultivars with the same functional allele of DEEPER ROOTING 1

Rice

Table 1 Putative QTLs for the ratio of deep rooting detected in the MoK-F2, YuK-F2, TaK-F2 populations.

Population	Trait	Chr.	Closest marker	Mb^a	cM^b	LOD	AE(%)^c	DE(%)^d	R ^{2 e}
MoK-F2	RDR50	1	ad01004243	10.06	0.0	3.98	4.5	−0.6	6.3
		2	P0269	34.00	1.1	4.73	4.7	−1.4	6.4
		4	AE04005953	29.07	0.0	10.41*	9.0	3.3	20.3
		7	ah07001638	28.25	2.6	5.64	7.4	1.3	13.6
									51.8^f
	RDR70	2	P0269	34.00	1.1	3.48	3.7	−0.8	8.3
		4	AE04005953	29.07	0.8	4.40	4.2	0.1	9.4
		7	RM1357	28.85	1.9	4.61	4.6	1.0	12.4
		10	RM6745-1	19.42	0.0	3.17	−2.0	5.2	10.6
									37.7^f
YuK-F2	RDR50	2	RM6424	29.63	1.7	7.46*	6.2	0.4	13.0
		3	AE03005102	22.31	0.0	5.34	8.7	−1.6	15.5
		4	RM3276	30.68	0.2	7.48*	5.6	2.3	13.0
		8	P0400_1	4.50	4.7	3.77	−4.8	−0.9	8.5
									52.2^f
	RDR70	1	ad01009345	20.42	2.7	3.67	−2.6	−1.3	6.4
		2	ad02013805	28.91	1.5	9.20*	5.4	−1.7	19.9
		6	AE06006239	30.14	0.0	9.32*	−5.6	−2.6	23.5
		8	RM6215	19.07	1.3	4.17	−3.8	−0.9	11.1
		11	AE11001189	14.86	0.0	3.00	2.5	−0.8	4.4
									51.3^f
TaK-F2	RDR50	2	RM3421	29.92	0.0	3.81	4.5	−0.4	9.3
		10	AE10002762	12.08	0.0	4.35	−5.0	−2.1	10.3
		11	ah11000388	10.22	0.0	3.08	1.7	−5.4	6.4
									25.4^f
	RDR70	2	RM3421	29.92	0.0	9.43*	7.3	−4.3	24.8
		3	RM5477	6.55	0.2	3.15	3.1	−3.7	7.5
		3	ah03002113	28.32	4.1	4.02	4.0	0.7	7.8
		4	RM3337	21.90	4.9	3.57	−3.5	0.4	5.7
		10	P0468	17.49	0.0	3.12	−3.5	−3.0	6.2
									48.2^f

^aPhysical map position of each marker based on the latest version of the RAP-DB (IRGSP-1.0; http://rapdb.dna.affrc.go.jp).
^bGenetic distance from the QTL LOD peak to the closest marker.
^cAdditive effect of the allele from Kinandang Patong in comparison with that from the paternal line.
^dDominance effect of the allele from Kinandang Patong in comparison with that from the paternal line.
^ePercentage of the phenotypic variance explained by each QTL.
^fPercentage of the phenotypic variance explained by multiple QTLs.
*Putative QTL with a significant LOD score based on 1000 permutation tests at the 5% level.