Multi-environment QTL studies suggest a role for cysteine-rich protein kinase genes in quantitative resistance to blackleg disease in Brassica napus

Larkan, Nicholas J.; Raman, Harsh; Lydiate, Derek J.; Robinson, Stephen J.; Yu, Fengqun; Barbulescu, Denise M.; Raman, Rosy; Luckett, David J.; Burton, Wayne; Wratten, Neil; Salisbury, Philip A.; Rimmer, S. Roger; Borhan, M. Hossein

doi:10.1186/s12870-016-0877-2

Table 2 Clustered single and multi-environment QTL detected in TC and TS populations

From: Multi-environment QTL studies suggest a role for cysteine-rich protein kinase genes in quantitative resistance to blackleg disease in Brassica napus

Trait^a	Chrom.	QTL Int. (cM)	Support interval	Peak (cM)	Peak interval	LOD	σ² (%)	Add	σ² _A	σ² _E	h ²
A) Topas/AG-Castle
W09 S	A01	54–67.5	sR9564 - sN12790	59	sN11665 - sN12790	5.20	8.32	4.61
H09 S	A01	68–69	sN12790 - sN4638	69	sR8420 - sN4638	17.20	15.84	7.80
W10 S	A01	68–69	sN12790 - sN4638	69	sR8420 - sN4638	24.25	29.90	9.31
W10 II	A01	68–69	sN12790 - sN4638	69	sR8420 - sN4638	9.08	11.52	4.90
MET II	A01	69	sR8420 - sN4638	69	sR8420 - sN4638	34.85	20.55	6.53	12.06	8.49	0.59
MET S	A01	68.5–69	sN12790 - sN4638	69	sR8420-sN4638	41.47	15.84	5.79	10.80	5.04	0.68
H09 II	A01	69–69.5	sR8420 - sN12176	69.5	sN4638 - sN12176	25.71	31.77	14.01
CotQTL	A07	73.5–74	sNRA59 - sR12387b	73.5	Rlm3 - sR12829	72.37	72.18	23.29
H09 S	A08	34.5–42.5	sN4513Fa - sNRB88	39	sN4513Fa - sNRG04	8.96	7.63	5.49
W09 S	A08	34.5–42.5	sN4513Fa - sNRB88	39	sN4513Fa - sNRG04	4.45	7.05	4.32
MET S	A08	37.5–42	sN4513Fa - sNRB88	39	sN4513Fa - sNRG04	13.59	5.13	3.51	3.85	1.28	0.75
H09 II	A08	39.5–47.5	sNRG04 - sN12352a	41	sNRG04 - sNRB88	7.42	7.85	7.08
MET II	A08	39.5–46.5	sNRG04 - sN12352a	41.5	sNRG04 - sNRB88	10.29	5.26	3.39	3.16	2.10	0.60
W10 S	A08	43–50.5	sNRB88 - sR9433	46	sNRB88 - sN12352a	8.34	9.08	5.19
W09 II	C06b	21–22	brPb - 841625 - brPb - 841355	21.5	brPb - 841625 - brPb - 841355	3.04	5.17	3.50
H09 S	C06b	23.5–45	brPb - 841355 - sN12461Ix	40	brPb - 841355 - sN12461Ix	14.59	14.08	7.42
CotQTL	C06b	23.5–45	brPb - 841355 - sN12461Ix	40	brPb - 841355 - sN12461Ix	4.71	9.26	7.25
MET S	C06b	36.5–45	brPb - 841355 - sN12461Ix	42.5	brPb - 841355 - sN12461Ix	25.99	9.22	5.06	8.12	1.10	0.88
W10 II	C06b	23.5–45	brPb - 841355 - sN12461Ix	44.5	brPb - 841355 - sN12461Ix	5.88	7.35	3.94
H09 II	C06b	23.5–45	brPb - 841355 - sN12461Ix	45	brPb - 841355 - sN12461Ix	10.44	11.07	8.34
W10 S	C06b	23.5–45	brPb - 841355 - sN12461Ix	45	brPb - 841355 - sN12461Ix	10.00	10.83	5.65
MET II	C06b	38–45	brPb - 841355 - sN12461Ix	45	brPb - 841355 - sN12461Ix	16.44	7.83	4.30	5.14	2.70	0.66
B) Topas/AV-Sapphire
H12 S	A01	30.5–39	sR9228a - sR9555x	36.5	sR6202b - sR9555x	4.3901	10.10	5.33
MET S	A01	33.5–39	sR9228a - sR9555x	36.5	sR6202b - sR9555x	13.1741	10.07	5.04	8.71	1.36	0.86
W11 II	A01	30.5–39	sR9228a - sR9555x	37.5	sR6202b - sR9555x	3.4382	11.07	4.39
W11 S	A01	30.5–39	sR9228a - sR9555x	39	sR6202b - sR9555x	6.352	18.47	8.21
H12 II	A01	36.5–40	sR6202b - sN12176	39.5	sR9555x - sN12176	3.3711	9.00	4.08
MET II	A01	36.5–40	sR6202b - sN12176	40	sR9555x - sN12176	7.8313	5.02	4.20	4.74	0.28	0.94
CotQTL	A07	48–56.5	sN2555Ra - Rlm4	56	sN2555Ra - Rlm4	30.80	48.92	19.16
W11 II	A09	5–19.5	sS2212 - sR9373	8	sR6410 - sR9373	5.35	16.38	5.41
H12 II	A09	6.5–14.5	sS2212 - sR9373	8	sR6410 - sR9373	3.05	8.12	3.92
W11 S	A09	5–19.5	sS2212 - sR9373	8	sR6410 - sR9373	5.34	15.00	7.48
MET S	A09	6.5–12.5	sS2212 - sR9373	8	sR6410 - sR9373	10.41	9.18	4.67	7.33	1.86	0.80
W09 II	A09	8–11.5	sR6410 - sR9373	8.5	sR6410 - sR9373	2.89	11.83	6.68
MET II	A09	8–14	sR6410 - sR9373	9.5	sR6410 - sR9373	13.97	9.66	5.88	9.10	0.56	0.94
H08 II	A09	21–29	sR9373 - sR6966	25	sR9373 - sR6966	3.43	12.31	9.82
H12 S	A09	21.5–33.5	sR9373 - sR12078a	27.5	sR9373 - sR6966	3.41	9.47	5.19
H08 II	C06	38–60	sS2486a - sN5088F	52.5	sS2486a - sR12387a	4.79	19.31	12.24
H12 S	C06	35.5–60	sS2486a - sN5088F	54.5	sS2486a - sR12387a	6.91	22.18	7.88
H12 II	C06	40.5–60	sS2486a - sN5088F	56.5	sS2486a - sR12387a	4.55	13.63	5.00
MET II	C06	50.5–58.5	sS2486a - sN5088F	57	sS2486a - sR12387a	10.84	9.67	4.97	6.69	2.98	0.69
H08 S	C06	43–60	sS2486a - sN5088F	58	sS2486a - sR12387a	4.58	15.26	4.73
MET S	C06	53.5–58.5	sS2486a - sN5088F	58	sS2486a - sR12387a	14.65	9.34	5.04	8.76	0.58	0.94

Significant QTL shown only (Single environment QTL > 5 σ²(%), MET QTL > 5 σ²(%) and h ² > 0.5)
^aSingle environment (plain) and multi-environment (bold) QTL, single-environment trait names given as location (H = Horsham, W = Wagga Wagga), year (08–12 = 2008–2012) and metric (S = survival, II = internal infection), MET = Multi-environment traits (all environments) for S (survival) and MET II (internal infection) metrics, CotQTL = single-isolate cotyledon tests. Chrom. = B. napus chromosome; QTL Int. (cM) = QTL interval (in centiMorgans); Support Interval = map interval, defined by flanking markers, which contains QTL (LOD > significance threshold); Peak (cM) = Position of Peak LOD value (in centiMorgans); Peak Interval = map interval containing QTL peak LOD; LOD = peak logarithm of odds; σ²(%) = variance (total percentage); Add = additive effect (positive score indicates net genetic contribution from AG-Castle or AV-Sapphire parent); σ² _A variance (additive) portion (%), σ² _E variance (environmental) portion (%), h ² heritability (σ² _A/σ² (%))

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ISSN: 1471-2229

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