Table 2. Common quantitative trait loci (QTL) detected between the joint inclusive composite interval mapping (JICIM) in nested association mapping of 10 RIL populations, and inclusive composite interval mapping (ICIM) methods in individual populations for stem rust adult plant resistance in four environments.

Chra	Pos (cM)b	Populationc	Env	Left Marker	Right Marker	LODd	R2 (%)e	Addf
1A	33	Joint	SA12	1A_53256976	1A_214244842	10.26	3.05
	35	Kulungu	Ken13	1A_64961094	1A_101708352	4.12	1.84	-0.15
	36	Fahari	SA12	1A_184159449	1A_50973716	15.36	38.71	0.22
	36	Joint	StP12	1A_168260073	1A_50914673	5.86	4.22
	37	Romany	SA12	1A_39856840	1A_235277072	3.22	2.20	0.09
1D	20	Gem	StP12	1D_96967944	1D_11687876	4.01	1.26	0.15
	23	Joint	Ken13	1D_95968008	1D_62309262	5.01	8.16
2A	16	Joint	StP12	2A_13651965	2A_195408664	4.49	8.78
	17	Romany	SA12	2A_11044893	2A_152187592	3.06	1.31	-0.04
	17	Joint	Ken13	2A_118236938	2A_152187592	6.68	10.63
	20	Romany	SA12	2A_85264302	2A_96999682	13.96	6.54	-0.16
	144	Joint	StP12	2A_254280385	2A_226128547	5.31	2.40
	145	Ada	StP12	2A_254280385	2A_226128547	3.52	7.86	0.05
2B	53	Joint	SA12	2B_295548243	2B_4526688	18.27	1.52
	55	Romany	SA12	2B_14347146	2B_326925659	3.57	2.21	0.07
	60	Ada	StP13	2B_328392028	2B_344339504	3.00	3.15	-0.14
	60	Joint	StP13	2B_309579404	2B_313124463	6.62	6.73
	60	Joint	StP12	2B_309579404	2B_313124463	4.68	6.91
3B	108	Pasa	StP13	3B_647995685	3B_584832142	9.82	10.93	-0.05
	108	Joint	StP12	3B_673326253	3B_82601403	4.90	3.16
	108	Joint	StP13	3B_673326253	3B_82601403	6.89	5.00
	109	Pasa	StP12	3B_647995685	3B_584832142	7.12	9.91	-0.05
	121	Gem	StP13	3B_496875398	3B_554937272	5.70	19.89	-0.07
	121	Joint	SA12	3B_538190692	3B_554937272	13.40	4.43
	121	Joint	StP12	3B_538190692	3B_554937272	5.75	6.24
	124	Kudu	StP12	3B_591992271	3B_909961	3.65	17.15	-0.12
	124	Kudu	StP13	3B_591992271	3B_909961	4.21	29.22	-0.09
	124	Kudu	Ken13	3B_591992271	3B_909961	3.10	10.93	-0.12
4B	51	Romany	StP13	4B_299160842	4B_210047150	3.57	1.06	0.14
	51	Joint	StP13	4B_282191767	4B_203809435	5.89	8.27
4D	21	Kulungu	Ken13	4D_50470445	4D_59436083	3.51	1.93	-0.16
	21	Joint	StP12	4D_61244682	4D_58434790	4.62	7.73
5B	51	Joint	StP13	5B_258358007	5B_233185212	7.69	8.42
	53	Gem	StP12	5B_257695597	5B_155513783	4.94	1.28	-0.14
5D	47	Joint	Ken13	5D_145713577	5D_101495576	6.28	13.20
	48	Kulungu	Ken13	5D_27462012	5D_91682679	3.33	1.88	-0.16
6A	21	Pasa	SA12	6A_41412787	6A_49007339	11.68	6.71	-0.02
	21	Joint	StP13	6A_12874936	6A_16883183	4.87	4.33
7A	3	Gem	StP12	7A_92272971	7A_134846357	3.94	1.05	-0.15
	3	Joint	StP13	7A_5990339	7A_2150377	5.96	3.15

^a Chromosome location of the QTL.

^b Position (centiMorgan) of the detected QTL peak in Chromosome ‘Chr’. Positions are sorted in ascending order.

^c Result of JICIM is shown in bold; result of ICIM is shown in italics.

^d Logarithm of odds scores for the QTL detected at position ‘Pos’, based on joint mapping.

^e Percentage of phenotypic variation explained by the observed QTL, based on joint mapping.

^f Additive effect for JICIM is not shown as JICIM reports additive effect for each parent individually; see S1 File for more information.