越冬栽培稻产量性状相关QTL定位

doi:10.3724/SP.J.1006.2019.82045

Abstract

Abstract:

Overwintering cultivated rice is a type of special rice that can survive through cold-winter season, germinate in spring of the coming year, seed and be harvested. In this study, four genetic linkage maps contained 108, 116, 111, and 184 SSR markers were constructed using three half-sib F₂ populations from overwintering cultivated rice for the identification of QTLs affecting yield traits, respectively. Phenotypic values for yield traits were investigated for QTL mapping and other statistical analysis using Microsoft Excel 2003, GraphPadPrism 5.0, and QTL IciMapping 4.10. The phenotypic values for yield traits exhibited a continuously normal distribution and might be controlled by quantitative trait locus (QTL). A total of 37 QTLs affecting 15 yield traits and 26 epistatic QTL pairs with one or more interactions were detected in the three populations, explaining the wide phenotypic variance ranging from 2.32% to 36.31% and from 1.04% to 2.05% respectively. Among these QTLs, nine QTLs affecting two or more traits were detected on chromosomes 1, 3, 6, 8, 11, and 12 respectively. Thirteen QTLs affecting yield-related traits were detected by nested association mapping (NAM) mapping; four out of thirteen were overlapped with QTLs detected in single mapping population. The additive-dominance QTL affecting yield traits played an important role than that of epistatic QTL. Overall, this research lays a good foundation for the mining of yield-related genes from overwintering cultivated rice and their breeding innovation and utilization.

Key words: QTL mapping, yield traits, overwintering cultivated rice

YAN Chao,ZHENG Jian,DUAN Wen-Jing,NAN Wen-Bin,QIN Xiao-Jian,ZHANG Han-Ma,LIANG Yong-Shu. Locating QTL controlling yield traits in overwintering cultivated rice[J].Acta Agronomica Sinica, 2019, 45(4): 522-537.

Figures/Tables 9

Fig. 1

Table 1

Field performance of yield traits in the biparents, hybrid F1, and F2 populations"

性状 Trait	亲本 Parent				T测验值 T-test value			杂种F₁Hybrid F₁			平均值±标准差 Means±SD			变幅 Range
性状 Trait	绵恢725 Mianhui 725	W1	W2	W3	W1	W2	W3	OW1	OW2	OW3	OW1	OW2	OW3	OW1	OW2	OW3
株高PH (cm)	122.67	139.13	99.79	115.70	2.26	3.27^*	3.01^*	155.58	143.75	142.80	133.51±19.58	112.97±15.50	128.22±18.88	89.80-174.80	84.20-151.3	88.50-176.50
有效穗数PN	12	17	21	23	2.38	4.92^**	3.31^*	18	16	115	15.63±5.92	13.26±5.08	13.10±6.54	5-29	5-29	4-43
穗长PL (cm)	29.27	27.43	19.67	19.23	3.76^*	18.02^**	29.96^**	32.50	24.50	26.50	27.75±2.84	22.70±2.79	25.41±3.43	20.86-30.57	18.23-29.87	18.75-33.21
穗实粒数 NFG	334	188	192	142	6.41^**	6.27^**	25.56^**	105	95	87	144.06±80.47	133.47±75.20	142.14±78.10	2-379	6-308	2-327
穗空粒数NEG	16.33	47.38	39.00	40.80	3.19^*	1.07	3.90^*	282	226	215	118.15±73.44	135.90±67.83	140.75±91.52	24-387	26-310	6-423
穗总粒数SPP	350	235	231	183	5.76^**	5.63^**	14.07^**	387	321	302	262.22±77.31	269.37±70.59	280.20±86.51	76-442	108-441	133-603
结实率 SSR (%)	95.33	79.86	83.10	77.68	3.42^*	1.33	7.12^**	27.13	29.60	28.81	51.80±12.90	46.44±9.67	50.64±4.82	7.69-60.98	14.29-52.53	25.00-55.88
穗粒密度GSD	11.96	8.57	11.70	7.90	5.13^**	0.31	4.23^**	11.90	13.10	11.35	9.47±2.94	11.96±3.25	11.02±3.06	2.84-15.13	5.80-20.31	4.71-19.82
粒长GL (mm)	9.74	7.11	7.13	6.84	15.65^**	10.58^**	16.16^**	8.11	8.25	8.30	8.27±0.57	7.83±0.83	7.94±0.43	7.16-9.66	2.80-9.41	7.11-9.20
粒宽GW (mm)	2.34	3.43	3.42	3.26	11.61^**	8.14^**	13.29^**	3.25	3.18	3.20	2.84±0.26	2.88±0.61	2.89±0.28	2.27-3.65	2.15-7.67	2.38-3.60
粒厚GT (mm)	1.92	2.44	2.41	2.20	2.25	5.77^**	6.60^**	2.55	2.45	2.35	2.01±0.09	2.05±0.13	2.06±0.16	1.82-2.21	1.70-2.34	1.60-2.59
粒长宽比LWR	4.18	2.08	2.09	2.09	17.65^**	14.25^**	13.90^**	2.20	2.60	2.60	2.93±0.33	2.78±0.44	2.78±0.31	2.32-3.69	0.98-3.95	2.14-3.46
千粒重TGW (g)	21.06	22.49	23.33	24.78	2.38	1.49	7.95^**	24.70	25.50	24.80	21.76±1.85	20.94±1.57	23.34±1.84	15.0-31.90	15.10-49.50	16.20-40.00
主穗重MPW (g)	7.26	4.15	3.43	3.36	8.52^**	10.10^**	25.81^**	2.45	2.04	1.85	3.83±1.84	3.47±1.56	3.94±1.83	0.45-8.77	0.90-7.10	1.06-9.87
单株产量GYP (g)	69.02	59.43	55.85	50.47	0.93	0.26	1.50	47.85	37.56	33.56	32.71±24.28	24.79±20.13	30.60±31.11	0.39-126.30	0.46-76.96	0.78-188.85

Table 1

Fig. 2

Table 2

Correlation (r) coefficients among yield traits in three populations"

性状 Trait	群体 Population	穗数 NP	穗长 PL	穗实粒数 NFG	穗空粒数 NEG	穗总粒数 SPP	结实率 SSR	穗粒密度 GSD	粒长 GL	粒宽 GW	粒厚 GT	长宽比 LWR	单穗重 MPW	千粒重 TGW	单株重 GYP
株高 PH	OW1	0.17^*	0.45^**	0.36^**	0.01	0.38^**	0.23^**	0.25^**	0.17^*	0.02	-0.18^*	0.10	0.48^**	0.12	0.31^**
	OW2	0.12	0.55^**	0.22^**	0.06	0.29^**	0.12	0.04	0.18^*	-0.15^*	-0.14	0.25^**	0.27^**	-0.05	0.25^**
	OW3	0.34^**	0.63^**	0.16^*	0.18^*	0.32^**	-0.04	0.10	0.06	0.06	-0.10	-0.04	0.03	0.21^**	0.26^**
穗数 NP	OW1		-0.01	0.16^*	-0.09	0.08	0.18^*	0.10	-0.02	-0.02	-0.05	0.00	0.18^*	-0.03	0.55^**
	OW2		0.02	0.29^**	-0.12	0.19^*	0.18^*	0.18^*	0.08	-0.12	-0.01	0.15^*	0.23^**	0.01	0.63^**
	OW3		0.38^**	0.31^**	-0.04	0.23^**	0.17^*	0.08	-0.06	0.10	-0.02	-0.07	0.17^*	0.04	0.73^**
穗长PL	OW1			0.18^*	0.04	0.23^**	0.10	-0.09	0.21^**	0.04	0.09	0.09	0.21^**	-0.09	0.11
	OW2			0.06	0.12	0.18^*	0.03	-0.25^**	0.16^*	-0.22^**	-0.16^*	0.27^**	0.18^*	0.01	0.11
	OW3			0.29^**	0.17^*	0.43^**	0.04	0.02	0.24^**	0.08	-0.21^**	0.13	0.07	0.17^*	0.38^**
穗实粒数 NFG	OW1				-0.50^**	0.57^**	0.84^**	0.51^**	0.02	-0.15^*	0.00	0.09	0.94^**	0.02	0.69^**
	OW2				-0.52^**	0.57^**	0.88^**	0.54^**	0.16^*	-0.08	-0.11	0.23^**	0.88^**	-0.19^*	0.78^**
	OW3				-0.45^**	0.41^**	0.81^**	0.32^**	0.01	0.05	0.15^*	0.03	0.21^**	0.08	0.67^**
穗空粒数 NEG	OW1					0.43^**	-0.81^**	0.43^**	-0.07	0.11	-0.17^*	-0.12	-0.36^**	-0.02	-0.37^**
	OW2					0.41^**	-0.81^**	0.34^**	-0.12	0.07	-0.07	-0.22^**	-0.43^**	0.07	-0.45^**
	OW3					0.63^**	-0.83^**	0.62^**	-0.01	-0.11	-0.27^**	0.20^**	-0.13	-0.20^**	-0.35^**
穗总粒数 SPP	OW1						0.11	0.95^**	-0.05	-0.05	-0.16^*	-0.01	0.64^**	0.00	0.36^**
	OW2						0.16^*	0.90^**	0.05	-0.02	-0.18^*	0.03	0.53^**	-0.13	0.40^**
	OW3						-0.14	0.90^**	0.00	-0.08	-0.14	0.22^**	0.05	-0.13	0.22^**
结实率 SSR	OW1							0.07	0.05	-0.13	0.17^*	0.11	0.74^**	0.03	0.60^**
	OW2							0.16^*	0.13	-0.09	-0.03	0.24^**	0.76^**	-0.19^*	0.68^**
	OW3							-0.17^*	0.01	0.11	0.28^**	-0.10	0.21^**	0.22^**	0.57^**
穗粒密度 GSD	OW1								-0.13	-0.06	-0.20^**	-0.05	0.58^**	0.02	0.34^**
	OW2								-0.01	0.09	-0.10	-0.09	0.44^**	-0.14	0.35^**
	OW3								-0.12	-0.11	-0.06	0.18^*	0.03	-0.21^**	0.07
粒长 GL	OW1									0.04	-0.02	0.59^**	0.10	0.24^**	0.07
	OW2									0.06	-0.12	0.62^**	0.23^**	0.05	0.19^*
	OW3										-0.05	-0.24^**	0.42^**	-0.14	0.03
粒宽GW	OW1										0.36^**	-0.78^**	-0.04	0.23^**	-0.06
	OW2										0.14	-0.66^**	-0.04	0.16^*	-0.12
	OW3										-0.02	-0.71^**	0.06	0.01	0.21^**
粒厚 GT	OW1											-0.30^**	0.03	0.09	0.07
	OW2											-0.32^**	0.00	0.38^**	-0.11
	OW3											-0.20^**	0.05	0.39^**	0.08
长宽比 LWR	OW1												0.06	-0.04	0.06
	OW2												0.18^*	-0.23^**	0.25^**
	OW3												-0.24^**	-0.25^**	-0.16^*
单穗重 MPW	OW1													0.10	0.68^**
	OW2													0.09	0.78^**
	OW3													0.16^*	0.16^*
千粒重TGW	OW1														0.20^**
	OW2														-0.02
	OW3														0.15^*

Table 2

Table 3

Locating QTLs for yield traits in three populations"

性状 Trait	群体 Population	QTL	染色体 Chr.	标记区间 Marker interval	LOD值 LOD value	加性效应 Additive	显性效应 Dominant	贡献率 R²(%)	作图群体或参考文献Mapping populations
株高 PH	OW1	qPH1	1	RM3362-RM3738	7.18	18.19	15.29	36.31	[30]
穗数 PN	OW2	qPN10	10	RM1146-RM25664	3.10	2.43	-3.09	5.42
穗数 PN	OW2	qPN12	12	RM7018-RM1227	3.17	4.53	-4.84	15.70	W2
穗数 PN	OW3	qPN11	11	RM5599-RM7240	3.35	-6.39	-8.75	5.11
穗空粒数NEG	OW1	qNEG1	1	RM7405-RM8084	5.48	71.96	-85.60	8.67
穗空粒数NEG	OW1	qNEG5	5	RM6517-RM3170	7.25	69.77	-112.64	9.22
穗空粒数NEG	OW1	qNEG6a	6	RM276-RM1369	3.44	89.52	-71.69	8.43
穗空粒数NEG	OW2	qNEG11	11	RM4746-RM254	3.83	-12.01	113.53	2.93
穗空粒数NEG	OW3	qNEG6b	6	RM8242-RM3138	3.71	-30.06	81.06	20.68	Mianhui 725
穗总粒数SPP	OW1	qSPP1	1	RM3604-RM5359	3.19	-61.55	-16.63	20.99	[31]
结实率SSR	OW1	qSSR3a	3	RM5686-RM6291	3.58	1.57	-23.13	14.23	W1
结实率SSR	OW1	qSSR5	5	RM3170-RM3348	3.44	8.62	11.50	9.33	W1
结实率SSR	OW1	qSSR8	8	RM22418-RM6838	3.94	0.44	-21.23	12.41
结实率SSR	OW2	qSSR3b	3	RM1350-RM487	3.54	-11.85	-6.74	9.91
性状 Trait	群体 Population	QTL	染色体 Chr.	标记区间 Marker interval	LOD值 LOD value	加性效应 Additive	显性效应 Dominant	贡献率 R²(%)	作图群体或参考文献Mapping populations
结实率SSR	OW3	qSSR6	6	RM8242-RM3138	3.22	8.82	-29.68	16.24	[35]
穗粒密度 GSD	OW1	qGSD1	1	RM3604-RM5359	4.49	-2.39	-0.49	26.30
粒长 GL	OW1	qGL3	3	RM6291-RM6038	4.87	-0.47	-0.09	25.30	[32]
粒长 GL	OW2	qGL7	7	RM3859-RM1306	3.23	2.52	2.64	2.32
粒宽 GW	OW1	qGW3a	3	RM15281-RM6959	3.70	0.16	0.02	16.06	[33-34]
粒宽 GW	OW1	qGW5	5	RM1024-RM6517	4.99	0.19	-0.01	25.56	[39]
粒宽GW	OW2	qGW3b	3	RM5639-RM1284	3.25	-1.22	1.30	6.69
粒宽 GW	OW2	qGW11	11	RM26652-RM4746	21.43	-0.05	4.82	25.02
粒长宽比LWR	OW1	qLWR3	3	RM15281-RM6959	7.69	-0.26	-0.12	23.81	[36-37]
粒长宽比 LWR	OW1	qLWR4	4	RM6540-RM5979	3.06	-0.07	0.24	10.18	[38]
粒长宽比LWR	OW1	qLWR6	6	RM276-RM1369	3.51	-0.20	0.12	12.92	Mianhui 725
粒长宽比LWR	OW3	qLWR8	8	RM5637-RM6948	4.84	-1.21	1.35	5.10
千粒重TGW	OW1	qTGW1a	1	RM3362-RM3738	6.04	10.26	10.00	5.17
千粒重TGW	OW1	qTGW1b	1	RM3738-RM6887	6.56	10.39	9.74	5.19
千粒重TGW	OW1	qTGW3a	3	RM6509-RM85	9.72	-10.66	8.70	5.40
千粒重TGW	OW1	qTGW3b	3	RM85-RM186	9.80	-11.60	7.26	6.20
千粒重TGW	OW1	qTGW6	6	RM1370-RM6395	3.43	-9.84	10.39	3.81	[40]
单株产量 GYP	OW2	qGYP3a	3	RM1350-RM487	3.24	-19.29	-18.18	6.19
单株产量 GYP	OW2	qGYP3b	3	RM487-RM6484	4.52	-19.23	-22.11	6.28
单株产量 GYP	OW2	qGYP11	11	RM4746-RM254	4.24	1.33	39.74	7.01
单株产量 GYP	OW2	qGYP12	12	RM7018-RM1227	6.23	22.07	-20.40	6.50	[41]
单株产量 GYP	OW3	qGYP5	5	RM5994-RM1237	3.77	-59.59	-57.78	7.06
单株产量 GYP	OW3	qGYP8	8	RM5637-RM6948	5.31	49.58	-57.95	8.04

Table 3

Fig. 3

Table 4

Table 5

Epistasis QTL underlying yield traits in te three populations"

名称 ID	群体 Population	性状 Trait	染色体 Chr.	区间1 Interval 1	染色体 Chr.	区间2 Interval 2	LOD值 LOD value	贡献率 R²(%)	加性1 Add 1	加性2 Add 2	显性1 Dom 1	显性2 Dom 2	加性-加性 Add by Add	加性-显性 Add by Dom	显性-加性 Dom by Add	显性-显性 Dom by Dom
IA-1	OW1	TGW	3	RM85-RM186	1	RM7405-RM8084	15.43	1.32	3.65	2.92	11.06	8.17	-6.49	-2.29	-5.61	-14.63
IA-2	OW1	TGW	3	RM85-RM186	8	RM6976-RM7631	14.55	1.22	-0.20	-0.15	-1.15	-7.33	1.01	-12.62	-1.49	7.11
IA-3	OW1	NEG	5	RM6517-RM3170	11	RM5599-RM202	7.90	1.23	54.35	52.43	29.34	-17.72	66.90	-96.47	-111.77	-52.55
IA-4	OW1	NEG	6	RM276-RM1369	1	RM7405-RM8084	8.73	1.34	66.13	64.19	-156.91	-93.93	-17.74	-39.60	-63.95	96.94
IA-5	OW2	NEG	5	RM6229-RM289	7	RM3859-RM1306	5.28	1.92	16.05	4.43	78.99	17.93	13.54	-59.95	77.93	10.25
IA-6	OW2	NEG	11	RM4746-RM254	3	RM1350-RM487	5.49	2.05	20.12	1.88	39.89	130.61	-12.33	33.49	-75.32	-146.32
IA-7	OW2	NEG	11	RM4746-RM254	10	RM1146-RM25664	5.01	1.67	18.62	-30.10	-34.46	43.81	10.42	-97.83	36.29	71.52
IA-8	OW2	SSR	3	RM1350-RM487	1	RM572-RM129	5.43	2.04	0.47	5.70	17.32	22.18	-21.60	3.53	-14.12	-54.89
IA-9	OW2	SSR	3	RM1350-RM487	6	RM6395-RM1340	5.71	2.45	-9.59	-15.15	-0.19	-7.41	-7.56	-22.14	34.33	6.11
IA-10	OW2	SSR	5	RM1024-RM163	7	RM3859-RM1306	5.44	2.35	2.47	-6.13	-13.23	13.23	12.19	5.73	5.066	-41.14
IA-11	OW2	SSR	5	RM1024-RM163	9	RM6497-RM24085	5.67	2.23	1.21	-0.00	42.36	10.05	11.01	-24.85	-4.23	-37.28
IA-12	OW2	SSR	5	RM1024-RM163	10	RM590-RM1146	5.49	2.29	11.22	-9.96	-9.73	-14.86	-2.95	-36.15	37.65	11.41
IA-13	OW2	GL	7	RM3859-RM1306	11	RM4746-RM254	10.63	1.43	1.05	1.51	1.46	0.77	-1.19	-0.44	-1.49	-0.03
IA-14	OW2	GW	3	RM5639-RM1284	5	RM6229-RM289	17.48	1.18	0.46	0.75	-0.63	-1.88	0.68	-1.61	-0.85	2.20
IA-15	OW2	GW	3	RM5639-RM1284	12	RM7018-RM1227	17.57	1.18	-0.11	-1.15	0.08	-0.37	-1.31	-0.02	1.30	0.12
IA-16	OW2	GW	11	RM26652-RM4746	5	RM6229-RM289	25.85	1.91	-0.04	-0.06	-0.07	2.45	0.10	2.42	0.10	-2.32
IA-17	OW2	GW	11	RM26652-RM4746	8	RM6838-RM22418	28.02	2.03	0.17	-0.06	-0.08	2.12	-0.05	-2.86	0.07	-1.84
IA-18	OW2	TGW	8	RM6838-RM22418	7	RM3859-RM1306	13.57	1.39	-7.92	6.58	-19.26	-8.18	-5.14	7.88	2.00	19.47
IA-19	OW2	TGW	8	RM6838-RM22418	11	RM4746-RM254	13.12	1.56	4.33	9.93	-7.15	-16.13	5.78	6.95	-10.99	13.79
IA-20	OW2	GYP	3	RM1350-RM487	7	RM3859-RM1306	10.88	1.33	-7.87	1.96	-37.45	-37.77	15.86	1.93	-3.76	52.98
IA-21	OW2	GYP	3	RM1350-RM487	11	RM4746-RM254	8.69	1.30	-24.38	5.65	-12.24	6.35	-8.16	45.26	4.54	-8.83
IA-22	OW3	PN	11	RM5599-RM7240	1	RM3604-RM1287	6.27	1.82	-6.87	-8.03	-0.70	2.06	5.14	0.02	7.39	-10.36
IA-23	OW3	LWR	8	RM5637-RM6948	9	RM1328-RM1189	9.37	1.04	-0.02	0.07	-0.14	-1.38	-0.06	-1.17	-0.35	1.50
IA-24	OW3	GYP	5	RM5994-RM1237	1	RM3738-RM6470	7.80	1.22	-2.53	7.25	39.42	-13.38	-10.94	0.65	-74.54	-35.93
IA-25	OW3	GYP	5	RM5994-RM1237	6	RM8242-RM3138	9.46	1.45	7.72	15.93	-30.03	27.63	0.44	-75.59	-11.40	-11.70
IA-26	OW3	GYP	11	RM5599-RM7240	5	RM5994-RM1237	8.26	1.41	4.01	-19.14	-29.06	29.10	-1.18	-73.32	14.84	-9.05

Table 5

Table 6

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Locating QTL controlling yield traits in overwintering cultivated rice

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性状 Trait	Chr.	标记区间 Marker intervals	LOD值 LOD value	贡献率 R²(%)	LOD_OW1	LOD_OW2	LOD_OW3	Add_OW1	Add_OW2	Add_OW3
株高 PH	7	RM3859-RM20882	3.17	4.71	0.05	2.53	0.59	-1.48	8.27	4.56
穗长PL	1	RM493-RM7075	3.10	4.30	0.20	2.39	0.51	-0.28	-0.95	0.52
穗长PL	2	RM6611-RM6509	3.14	5.95	3.03	0.10	0.00	-1.40	-0.30	0.05
穗长PL	6	RM3827-RM3138	3.79	6.83	1.86	0.05	1.88	-0.99	0.17	-1.24
穗空粒数NEG	11	RM1341-RM206	3.40	7.73	0.12	1.26	2.03	5.48	-16.72	-29.72
结实率SSR	5	RM1366-RM289	3.42	5.97	3.27	0.15	0.00	21.44	-3.52	-0.33
结实率SSR	5	RM6229-RM18452	3.19	1.04	2.94	0.08	0.17	9.02	-1.54	2.36
穗粒密度GSD	8	RM7356-RM7631	4.02	5.84	1.91	0.80	1.30	-1.00	-0.94	-0.96
粒长GL	3	RM3545-RM6038	3.44	8.48	2.79	0.51	0.14	-0.20	-0.13	-0.04
粒长GL	3	RM6929-RM15281	3.35	8.53	2.78	0.36	0.20	-0.18	-0.10	0.04
粒宽GW	6	RM6818-RM20092	3.19	0.87	3.06	0.01	0.13	0.10	0.01	-0.22
粒厚GT	7	RM6776-RM418	3.33	5.31	2.12	0.75	0.47	0.03	-0.02	0.02
长宽比LWR	3	RM15281-RM1350	6.33	7.34	4.78	0.99	0.56	-0.19	-0.11	-0.08

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