Identification of QTL for Panicle Traits under Multiple Environments in Rice(Oryza sativa L.)

doi:10.16819/j.1001-7216.2019.8100

Abstract

Abstract:

【Objective】It is important to explore new panicle and grain traits QTL related to yield for further cloning and utilization of high yield genes. 【Method】A recombinant inbred line (RIL) population derived from the cross between Longdao 5 (super high-yielding japonica) and Zhongyouzao 8 (typical indica) was used to identify QTL for panicle traits in multiple environments.【Result】Sixty-three QTLs were detected on chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 10 and 12. Among them, 27, 27, 18 and 35 QTLs were detected in four ecological environments, respectively. Among these QTLs, 16 QTLs were detected in two environments, 12 QTLs were detected in more than three environments, namely 25.40% and 19.05% were stably and reliably detected across multi-environments. The QTLs with pleiotropic genetic overlap effect clustered on chromosomes 1, 3, 4 and 5 were detected in multi-environments, indicating they have significant effects on panicle traits. 【Conclusion】 qSNP3 (STS3.3-STS3.6) on chromosome 3 and qSNP4.1 (RM5688-RM1359) on chromosome 4 may be two novel pleiotropic QTL clusters controlling panicle traits. In addition, epistatic effect plays an important role in the regulation of panicle traits.

Key words: rice(Oryza sativa L.), environment, panicle traits, epistasis interaction

摘要：

【目的】发掘与产量相关的穗粒性状QTL对进一步克隆和利用高产基因具有重要意义。【方法】以超级粳稻龙稻5号和典型高产籼稻中优早8号杂交衍生的重组自交系群体为试材,在4种环境下对穗部性状进行比较和QTL分析。【结果】共检测到63个穗部性状QTL,分布于除第9染色体外的11条染色体上。在4个环境下分别检测到27、27、18和35个QTL。其中,16个QTL能在2个环境下被检测到,12个在3个以上环境下稳定表达,分别占QTL总数的25.40%和19.05%;第1、3、4和5染色体的多效QTL簇能在不同环境下稳定表达,对穗部性状具有明显的调控作用。【结论】第3染色体STS3.3-STS3.6区间的qSNP3、第4染色体RM5688-RM1359区间的qSNP4.1是2个新的稳定表达的多效性QTL簇。此外,上位性效应是调控穗部性状的重要组分。

关键词: 水稻, 生态环境, 穗部性状, 上位性效应

CLC Number:

Jin LIU, Xiaoyun YAO, Dan LIU, Liqin YU, Hui LI, Qi WANG, Jiayu WANG, Maomao LI. Identification of QTL for Panicle Traits under Multiple Environments in Rice(Oryza sativa L.)[J]. Chinese Journal OF Rice Science, 2019, 33(2): 124-134.

刘进, 姚晓云, 刘丹, 余丽琴, 李慧, 王棋, 王嘉宇, 黎毛毛. 不同生态环境下水稻穗部性状QTL鉴定[J]. 中国水稻科学, 2019, 33(2): 124-134.

Figures/Tables 7

References 35

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性状 Trait	环境 Environment	亲本 Parent		重组自交系群体 RIL population
性状 Trait	环境 Environment	龙稻5号 Longdao 5	中优早8号 Zhongyouzao 8	平均值±标准差 βMean±SD	变幅 Range	峰度 Skewness	偏度 Kurtosis
穗长PL / cm	E₁	20.1±1.0	23.5±1.5^**	21.4±2.9	15.5~29.0	0.08	-0.63
	E₂	21.5±1.5	24.5±2.1^**	21.9±2.5	9.0~27.6	-0.75	2.99
	E₃	21.6±0.3	22.2±2.3^*	22.8±2.4	9.0~28.5	-0.98	4.91
	E₄	19.7±1.2	24.4±1.7^**	22.6±2.9	12.0~28.4	-0.61	0.55
一次枝梗数PRBN	E₁	9.0±0.6	10.2±0.4	9.8±2.5	5.6~16.8	0.28	-0.79
	E₂	13.0±0.5	13.0±0.2	11.6±2.0	5.6~17.0	-0.03	0.27
	E₃	9.8±0.5	9.2±0.2	9.6±1.8	5.4~15.0	0.45	0.33
	E₄	12.0±1.0	11.8±0.5	12.3±3.3	5.4~35.2	2.42	14.72
二次枝梗数SRBN	E₁	17.2±1.5	41.6±4.5^**	25.8±9.8	3.0~66.0	1.07	1.81
	E₂	31.0±4.0	42.0±5.0^**	29.7±10.3	7.2~57.6	0.29	-0.43
	E₃	9.2±2.0	20.4±4.5^**	13.0±7.1	1.2~51.0	1.37	4.16
	E₄	17.6±3.5	28.8±3.5^**	20.0±10.0	2.6~51.0	0.54	-0.10
每穗颖花数GN	E₁	112.0±11.2	267.8±16.3^**	145.3±48.6	46.6~308.0	0.57	0.41
	E₂	163.0±12.2	211.0±20.2^**	160.7±45.2	82.2~284.2	0.45	-0.18
	E₃	112.4±10.1	139.2±15.3^**	122.9±36.0	33.5~231.0	0.46	0.09
	E₄	119.8±10.5	158.8±15.8^**	132.7±43.2	44.2~276.2	0.40	0.06
每穗实粒数FGN	E₁	95.6±8.5	183.6±16.4^**	94.8±43.1	9.2~211.8	0.35	-0.04
	E₂	160.0±10.6	175.0±15.1^**	111.8±34.8	28.6~218.0	0.42	0.03
	E₃	88.8±9.2	71.2±12.1^*	75.5±23.1	33.5~156.4	0.46	0.82
	E₄	109.4±9.7	93.5±25.1^*	90.7±28.0	25.0~163.4	0.25	-0.17
结实率SSR / %	E₁	85.4±7.4	68.6±8.5^**	64.7±19.0	6.8~95.8	-0.96	0.54
	E₂	98.2±1.5	82.9±8.2^**	70.6±14.9	27.7~96.3	-0.52	-0.37
	E₃	79.0±7.2	51.1±12.3^**	62.4±13.0	10.5~95.2	-0.38	0.80
	E₄	91.3±5.6	58.9±6.6^**	69.8±12.4	27.7~95.5	-0.36	0.02
着粒密度	E₁	5.8±0.3	11.4±0.9^*	6.8±2.1	2.7~13.1	0.49	0.05
SD / (grain∙cm^-1)	E₂	7.6±0.5	8.6±0.7^*	7.4±2.2	3.5~13.5	0.43	-0.34
	E₃	5.2±0.2	6.3±0.4^*	5.4±1.6	1.6~10.9	0.68	0.68
	E₄	6.1±0.2	6.5±0.6^*	5.9±1.8	2.6~11.0	0.52	-0.15
千粒重TGW / g	E₁	19.62±1.52	24.85±1.23^**	23.85±4.52	12.50~35.28	0.17	-0.12
	E₂	23.62±0.92	26.82±2.01^**	24.54±3.12	16.50~28.28	0.14	-0.15
	E₃	19.42±1.32	23.87±1.25^**	22.54±2.42	16.50~26.40	0.19	-0.27
	E₄	22.62±0.63	25.83±1.51^**	24.53±4.02	15.50~30.28	0.16	-0.14

性状 Trait	环境 Environment	亲本 Parent		重组自交系群体 RIL population
性状 Trait	环境 Environment	龙稻5号 Longdao 5	中优早8号 Zhongyouzao 8	平均值±标准差 βMean±SD	变幅 Range	峰度 Skewness	偏度 Kurtosis
穗长PL / cm	E₁	20.1±1.0	23.5±1.5^**	21.4±2.9	15.5~29.0	0.08	-0.63
	E₂	21.5±1.5	24.5±2.1^**	21.9±2.5	9.0~27.6	-0.75	2.99
	E₃	21.6±0.3	22.2±2.3^*	22.8±2.4	9.0~28.5	-0.98	4.91
	E₄	19.7±1.2	24.4±1.7^**	22.6±2.9	12.0~28.4	-0.61	0.55
一次枝梗数PRBN	E₁	9.0±0.6	10.2±0.4	9.8±2.5	5.6~16.8	0.28	-0.79
	E₂	13.0±0.5	13.0±0.2	11.6±2.0	5.6~17.0	-0.03	0.27
	E₃	9.8±0.5	9.2±0.2	9.6±1.8	5.4~15.0	0.45	0.33
	E₄	12.0±1.0	11.8±0.5	12.3±3.3	5.4~35.2	2.42	14.72
二次枝梗数SRBN	E₁	17.2±1.5	41.6±4.5^**	25.8±9.8	3.0~66.0	1.07	1.81
	E₂	31.0±4.0	42.0±5.0^**	29.7±10.3	7.2~57.6	0.29	-0.43
	E₃	9.2±2.0	20.4±4.5^**	13.0±7.1	1.2~51.0	1.37	4.16
	E₄	17.6±3.5	28.8±3.5^**	20.0±10.0	2.6~51.0	0.54	-0.10
每穗颖花数GN	E₁	112.0±11.2	267.8±16.3^**	145.3±48.6	46.6~308.0	0.57	0.41
	E₂	163.0±12.2	211.0±20.2^**	160.7±45.2	82.2~284.2	0.45	-0.18
	E₃	112.4±10.1	139.2±15.3^**	122.9±36.0	33.5~231.0	0.46	0.09
	E₄	119.8±10.5	158.8±15.8^**	132.7±43.2	44.2~276.2	0.40	0.06
每穗实粒数FGN	E₁	95.6±8.5	183.6±16.4^**	94.8±43.1	9.2~211.8	0.35	-0.04
	E₂	160.0±10.6	175.0±15.1^**	111.8±34.8	28.6~218.0	0.42	0.03
	E₃	88.8±9.2	71.2±12.1^*	75.5±23.1	33.5~156.4	0.46	0.82
	E₄	109.4±9.7	93.5±25.1^*	90.7±28.0	25.0~163.4	0.25	-0.17
结实率SSR / %	E₁	85.4±7.4	68.6±8.5^**	64.7±19.0	6.8~95.8	-0.96	0.54
	E₂	98.2±1.5	82.9±8.2^**	70.6±14.9	27.7~96.3	-0.52	-0.37
	E₃	79.0±7.2	51.1±12.3^**	62.4±13.0	10.5~95.2	-0.38	0.80
	E₄	91.3±5.6	58.9±6.6^**	69.8±12.4	27.7~95.5	-0.36	0.02
着粒密度	E₁	5.8±0.3	11.4±0.9^*	6.8±2.1	2.7~13.1	0.49	0.05
SD / (grain∙cm^-1)	E₂	7.6±0.5	8.6±0.7^*	7.4±2.2	3.5~13.5	0.43	-0.34
	E₃	5.2±0.2	6.3±0.4^*	5.4±1.6	1.6~10.9	0.68	0.68
	E₄	6.1±0.2	6.5±0.6^*	5.9±1.8	2.6~11.0	0.52	-0.15
千粒重TGW / g	E₁	19.62±1.52	24.85±1.23^**	23.85±4.52	12.50~35.28	0.17	-0.12
	E₂	23.62±0.92	26.82±2.01^**	24.54±3.12	16.50~28.28	0.14	-0.15
	E₃	19.42±1.32	23.87±1.25^**	22.54±2.42	16.50~26.40	0.19	-0.27
	E₄	22.62±0.63	25.83±1.51^**	24.53±4.02	15.50~30.28	0.16	-0.14

性状 Trait	环境Environment	PL	PRBN	SRBN	GN	FGN	SSR	SD
一次枝梗数PRBN	E₁	0.556^**
	E₂	0.161
	E₃	0.274^*
	E₄	0.345^**
二次枝梗数SRBN	E₁	0.370^**	0.662^**
	E₂	0.123	0.512^**
	E₃	0.167	0.349^**
	E₄	0.312^**	0.342^**
每穗颖花数GN	E₁	0.366^**	0.653^**	0.799^**
	E₂	0.086	0.573^**	0.927^**
	E₃	0.196^*	0.576^**	0.763^**
	E₄	0.408^**	0.472^**	0.960^**
每穗实粒数FGN	E₁	0.190^*	0.505^**	0.525^**	0.763^**
	E₂	0.048^**	0.379^**	0.654^**	0.715^**
	E₃	0.095	0.525^**	0.465^**	0.755^**
	E₄	0.272^*	0.375^**	0.694^**	0.813^**
结实率SSR	E₁	-0.098	0.657^**	-0.058	0.685^**	0.672^**
	E₂	0.046	-0.176	-0.236^*	-0.244^*	0.475^**
	E₃	-0.018	-0.022	-0.341^*	-0.249^*	0.406^**
	E₄	-0.236^*	-0.232^*	-0.398^*	-0.369^**	0.270^*
着粒密度SD	E₁	-0.045	0.462^**	0.670^**	0.904^**	0.731^**	-0.136
	E₂	-0.334^**	0.473^**	0.818^**	0.902^**	0.642^**	-0.227^*
	E₃	-0.212^*	0.480^**	0.673^**	0.903^**	0.703^**	-0.197^*
	E₄	0.029	0.384^**	0.851^**	0.915^**	0.795^**	-0.275^*
千粒重TGW	E₁	0.168	-0.088	-0.095	-0.223^*	0.098	0.126	-0.198^*
	E₂	0.230^*	-0.101	-0.161	-0.154	0.110	0.067	-0.234^*
	E₃	0.045	-0.147	-0.138	-0.216^*	-0.208^*	0.012	-0.229^*
	E₄	-0.092	-0.092	-0.176	-0.173	-0.185	0.110	0.248^*

性状 Trait	环境Environment	PL	PRBN	SRBN	GN	FGN	SSR	SD
一次枝梗数PRBN	E₁	0.556^**
	E₂	0.161
	E₃	0.274^*
	E₄	0.345^**
二次枝梗数SRBN	E₁	0.370^**	0.662^**
	E₂	0.123	0.512^**
	E₃	0.167	0.349^**
	E₄	0.312^**	0.342^**
每穗颖花数GN	E₁	0.366^**	0.653^**	0.799^**
	E₂	0.086	0.573^**	0.927^**
	E₃	0.196^*	0.576^**	0.763^**
	E₄	0.408^**	0.472^**	0.960^**
每穗实粒数FGN	E₁	0.190^*	0.505^**	0.525^**	0.763^**
	E₂	0.048^**	0.379^**	0.654^**	0.715^**
	E₃	0.095	0.525^**	0.465^**	0.755^**
	E₄	0.272^*	0.375^**	0.694^**	0.813^**
结实率SSR	E₁	-0.098	0.657^**	-0.058	0.685^**	0.672^**
	E₂	0.046	-0.176	-0.236^*	-0.244^*	0.475^**
	E₃	-0.018	-0.022	-0.341^*	-0.249^*	0.406^**
	E₄	-0.236^*	-0.232^*	-0.398^*	-0.369^**	0.270^*
着粒密度SD	E₁	-0.045	0.462^**	0.670^**	0.904^**	0.731^**	-0.136
	E₂	-0.334^**	0.473^**	0.818^**	0.902^**	0.642^**	-0.227^*
	E₃	-0.212^*	0.480^**	0.673^**	0.903^**	0.703^**	-0.197^*
	E₄	0.029	0.384^**	0.851^**	0.915^**	0.795^**	-0.275^*
千粒重TGW	E₁	0.168	-0.088	-0.095	-0.223^*	0.098	0.126	-0.198^*
	E₂	0.230^*	-0.101	-0.161	-0.154	0.110	0.067	-0.234^*
	E₃	0.045	-0.147	-0.138	-0.216^*	-0.208^*	0.012	-0.229^*
	E₄	-0.092	-0.092	-0.176	-0.173	-0.185	0.110	0.248^*

性状Trait	位点 Locus	位置 Position	标记 Marker	LOD值 LOD value				贡献率PEV/%				加性效应Additive effect
性状Trait	位点 Locus	位置 Position	标记 Marker	E₁	E₂	E₃	E₄	E₁	E₂	E₃	E₄	E₁	E₂	E₃	E₄
穗长	qPL2	26.5	RM3732-RM1361	3.96				7.98				-1.11
PL	qPL3.1	29.5	RM5480-R3M10	10.82	2.53	2.54	6.06	28.06	8.41	9.90	25.68	1.31	0.83	0.86	1.33
	qPL3.2	62.5	STS3.3-RM6676	10.01			6.39	23.13			13.99	1.78			1.13
	qPL6.1	21.4	RM217-RM111	2.98				5.58				-0.75
	qPL6.2	47.4	R6M14-RM3827	3.16			3.38	8.77			7.64	-0.87			-0.80
	qPL8	111.5	RM3571-RM3754		3.97				9.77				-0.79
	qPL12	24.0	RM247-RM7003				4.16				9.85				-0.91
一次枝梗数	qPRBN1	18.5	RM6902-RM428		5.49	2.90			10.82	7.12			0.67	0.48
PRBN	qPRBN3.1	7.5	RM523-STS3.1		10.57	2.81	2.92		25.25	7.13	5.87		1.04	0.48	0.82
	qPRBN3.2	62.5	STS3.3-RM6676	4.89				9.88				0.85
	qPRBN3.3	101.5	RM3513-RM1350	3.43				7.30				-0.67
	qPRBN4	88.1	RM2441-R4M50		4.21	3.25	3.25		8.48	8.73	10.08		-0.60	-0.53	-1.06
	qPRBN6	50.4	R6M14-RM3827	13.04				40.10				-1.58
	qPRBN7	116.2	RM1306-RM248		5.34				10.94				0.67
	qPRBN8	36.5	RM5556-RM6208		2.79				5.22				-0.54
	qPRBN10	54.6	RM5620-R10M40				5.77				17.34				1.38
	qPRBN11.1	19.0	STS11.1-RM1124	4.77				8.37				0.73
	qPRBN11.2	93.0	R11M23-RM206		2.98				8.60				-0.59
二次枝梗数	qSRBN1.1	18.5	RM6902-RM428	5.54	7.69	2.92	6.53	12.64	17.12	9.05	13.65	3.51	4.29	2.17	3.74
SRBN	qSRBN1.2	81.5	STS1.1-RM306				3.30				9.81				3.42
	qSRBN2	123.5	ID4-RM6933			2.55	3.07			7.93	5.33			2.00	2.31
	qSRBN3.1	48.5	STS3.3-STS3.5	2.85		3.98		6.19		27.54		3.07		4.70
	qSRBN4.1	57.1	RM1359-R4M43	4.32	4.59		6.91	11.52	12.56		22.36	-3.44	-4.08		-4.84
	qSRBN4.2	93.1	RM2441-R4M50				3.46				5.87				-2.46
	qSRBN5	38.0	RM17954-STS5.2				3.81				9.14				3.02
	qSRBN6	57.4	R6M14-RM3827	2.71	3.62			12.16	8.58			-3.41	3.30
	qSRBN7	42.2	RM5711-STS7.1		3.53				14.40				-3.90
	qSRBN8	27.5	RM1376-RM4085				4.10				8.49				-3.29
	qSRBN10	52.6	RM467-RM6737	3.15			3.29	8.80			8.87	2.94			2.99
每穗颖花数	qGN1.1	20.5	RM428-RM323	3.84	6.67	3.74	7.29	10.43	14.86	9.24	14.17	15.93	17.58	11.04	16.41
GN	qGN1.2	83.5	STS1.1-RM306				4.91				16.09				18.85
	qGN2	122.5	ID4-RM6933			2.69				8.53				10.51
	qGN4.1	56.1	RM1359-R4M43	3.64	5.86		5.53	9.75	14.99		14.87	-15.74	-19.47		-17.00
	qGN4.2	88.1	RM2441-RM348		2.48	3.42	6.40		4.59	9.37	12.64		-9.80	-11.08	-15.42
	qGN6	31.4	RM111-STS6.2		4.68				10.73				16.29
	qGN10	54.6	RM5620-R10M40				9.27				22.91				20.70