QTL Analysis for Grain Weight and Shape and Validation of qTGW1.2/qGL1.2

doi:10.16819/j.1001-7216.2021.201205

Abstract

Abstract:

【Objective】 Grain weight and shape have an important impact on the yield and quality of rice. The purpose is to further reveal the genetic mechanism of grain weight and shape in rice by primary mapping of QTLs for grain weight and shape and validating of the newly identified qTGW1.2/qGL1.2 on the long arm of chromosome 1. 【Method】 An F_2:3 population consisting of 277 individuals and a recombinant inbred line (RIL) population with 211 individuals were derived from the cross between the large-grain male parent FM9, and the small-grain female parent EFT. The 1000-grain weight (TGW), grain length (GL) and grain width (GW) were measured. QTL mapping was performed by the inclusive composite interval mapping. As for the qTGW1.2/qGL1.2 region, two residual heterozygotes were screened and self-fertilized to produce segregated populations for QTL validation. 【Results】 A total of 35 QTLs for TGW, GL and GW were detected by QTL primary mapping. Among them, 11 QTLs were detected in both populations, 18 QTLs were detected only in the F_2:3 population, and six QTLs only in the RIL population. The effects of the newly identified qTGW1.2/qGL1.2 on TGW and GL were validated by using the segregated populations derived from the two residual heterozygotes. Additionally, significant variations in the length of glume cells were observed, and qPCR results demonstrated that the expression levels of genes related to cell cycle, auxin metabolism and grain shape were up- or down-regulated significantly. 【Conclusion】 The primary mapping of 35 QTLs and the validating of qTGW1.2/qGL1.2 will contribute to a deep insight into the genetic basis underlying grain weight and shape of rice, and also lay a foundation for gene cloning and marker assisted selection.

Key words: rice, grain weight, grain shape, QTL, residual heterozygote

摘要：

【目的】粒重粒形对水稻的产量和品质均有重要的影响。本研究通过开展水稻粒重粒形QTL的初步定位,并对新鉴定的第1染色体长臂qTGW1.2/qGL1.2区间进行验证,旨在进一步揭示水稻粒重粒形的遗传调控机制。【方法】以大粒的FM9为父本,小粒的EFT为母本,配组衍生遗传群体,先后获得包含277个株系的F_2:3群体和211个株系的重组自交系群体（Recombinant Inbred Lines, RILs）,测定千粒重、粒长和粒宽,采用完备区间作图法进行QTL初定位;针对新鉴定的qTGW1.2/qGL1.2区间,筛选2个剩余杂合体单株,自交衍生分离群体,开展QTL效应验证。【结果】初定位分析共检测到35个调控千粒重、粒长和粒宽的QTL,其中,11个能同时在两个群体中被检测到,18个仅在F_2:3群体中被检测到,6个仅在RIL群体中被检测到;应用两个剩余杂合体衍生的两套分离群体验证了新鉴定的qTGW1.2/qGL1.2区间对千粒重和粒长的效应,并观察到颖壳细胞长度的显著变化。通过qPCR分析,观察到与细胞周期、生长素代谢和粒形相关基因表达发生了显著变化。【结论】初步定位的35个QTL以及验证的qTGW1.2/qGL1.2有利于进一步揭示水稻粒重粒形的遗传控制基础,也为后续的基因克隆及分子标记辅助选择奠定了基础。

关键词: 水稻, 粒重, 粒形, QTL, 剩余杂合体

Chengxing DU, Huali ZHANG, Dongqing DAI, Mingyue WU, Minmin LIANG, Junyu CHEN, Liangyong MA. QTL Analysis for Grain Weight and Shape and Validation of qTGW1.2/qGL1.2 [J]. Chinese Journal OF Rice Science, 2021, 35(4): 359-372.

杜成兴, 张华丽, 戴冬青, 吴明月, 梁敏敏, 陈俊宇, 马良勇. 水稻粒重粒形QTL的定位及qTGW1.2/qGL1.2的验证[J]. 中国水稻科学, 2021, 35(4): 359-372.

Figures/Tables 10

References 56

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群体 Population	性状Trait	F_2:3-TGW	F_2:3-GL	F_2:3-GW	RIL-TGW	RIL-GL
F_2:3	粒长GL	0.679^**
	粒宽GW	0.725^**	0.279^**
RIL	千粒重TGW	-0.053
	粒长GL		0.020		0.753^**
	粒宽GW			-0.163	0.776^**	0.394^**

群体 Population	性状Trait	F_2:3-TGW	F_2:3-GL	F_2:3-GW	RIL-TGW	RIL-GL
F_2:3	粒长GL	0.679^**
	粒宽GW	0.725^**	0.279^**
RIL	千粒重TGW	-0.053
	粒长GL		0.020		0.753^**
	粒宽GW			-0.163	0.776^**	0.394^**

性状	数量性状基因座	标记区间		F_2:3					已克隆QTL^a Cloned QTL^a
Trait	QTL	Marker interval	LOD	PVE/%	Add	LOD	PVE/%	Add	已克隆QTL^a Cloned QTL^a
千粒重	qTGW1.1	RM246-RM1061				3.97	3.25	-0.92
TGW	qTGW1.2	RM315-RM12138	5.28	3.95	-1.08	4.51	4.15	-0.94
	qTGW2	RM145-RM71	59.83	38.33	-3.70	31.8	34.24	-3.00	GW2^[21]
	qTGW3.1	THI351-THI468				4.25	4.24	-1.07
	qTGW3.2	THI1668-THI1701	16.05	6.74	-1.49	8.68	7.60	-1.41	GS3^[22,23]
	qTGW3.3	RM168-RM3867	11.15	5.89	-1.39	5.82	5.92	-1.24	GSA1^[24]
	qTGW5.1	FIF232-FIF345	8.53	3.67	0.95				GS5^[25,26]
	qTGW5.2	FIF426-FIF738	9.86	4.64	1.11	5.95	4.97	1.14	GSE5/GW5/qSW5^{[27,28,29,30,31]}
	qTGW6.1	RM136-RM3	4.19	2.25	-0.87
	qTGW6.2	RM30-RM340	6.12	2.80	-1.04
	qTGW7	RM420-RM172	4.35	1.76	-0.76
	qTGW9.1	RM296-RM7424	4.97	2.68	-0.96				DEP1/DN1/qNGR9^{[32,33,34,35,36,37,38]}
	qTGW9.2	RM7048-RM328				3.26	3.16	-0.91
	qTGW10.1	RM228-RM590	6.70	2.64	-0.92
	qTGW10.2	RM474-TEN400				4.12	3.43	-0.96
	qTGW12	RM1103-RM3226	6.26	2.62	-0.93
粒长	qGL1.1	RM1061-RM128	8.29	4.05	-0.16
GL	qGL1.2	RM315-RM12138	7.47	3.83	-0.15	9.10	8.25	-0.21
	qGL1.3	RM12283-RM12333				2.99	2.42	-0.12
	qGL2	RM145-RM71	12.09	6.35	-0.21	12.82	18.24	-0.32	GW2^[21]
	qGL3.1	THI156-THI214				4.86	4.01	-0.15
	qGL3.2	THI301-THI351	5.06	2.36	-0.12
	qGL3.3	THI1668-THI1701	45.92	32.65	-0.44	24.88	25.95	-0.38	GS3^[22,23]
	qGL3.4	RM168-RM3867	7.62	5.15	-0.18	2.95	2.78	-0.12	GSA1^[24]
	qGL5	RM538-RM480	5.14	2.45	0.13
	qGL6	RM589-RM587	4.26	2.27	0.12
	qGL7	RM351-RM234	5.78	3.32	-0.14
	qGL9	RM296-RM7424	10.43	7.67	-0.22				DEP1/DN1/qNGR9^{[32,33,34,35,36,37,38]}
	qGL11	RM1355-RM209	7.18	3.70	-0.16
粒宽	qGW2	RM145-RM71	48.09	30.95	-0.20	17.85	24.96	-0.17	GW2^[21]
GW	qGW3	RM3867-RM571	5.30	2.93	-0.05				GSA1^[24]
	qGW5.1	FIF426-FIF738	29.68	19.25	0.15	10.84	15.49	0.13	GSE5/GW5/qSW5^{[27,28,29,30,31]}
	qGW5.2	FIF738-FIF801	9.30	4.42	0.07
	qGW11	RM21-RM254	4.44	3.10	-0.06
	qGW12	RM1103-RM3226	7.88	4.01	-0.07

性状	数量性状基因座	标记区间		F_2:3					已克隆QTL^a Cloned QTL^a
Trait	QTL	Marker interval	LOD	PVE/%	Add	LOD	PVE/%	Add	已克隆QTL^a Cloned QTL^a
千粒重	qTGW1.1	RM246-RM1061				3.97	3.25	-0.92
TGW	qTGW1.2	RM315-RM12138	5.28	3.95	-1.08	4.51	4.15	-0.94
	qTGW2	RM145-RM71	59.83	38.33	-3.70	31.8	34.24	-3.00	GW2^[21]
	qTGW3.1	THI351-THI468				4.25	4.24	-1.07
	qTGW3.2	THI1668-THI1701	16.05	6.74	-1.49	8.68	7.60	-1.41	GS3^[22,23]
	qTGW3.3	RM168-RM3867	11.15	5.89	-1.39	5.82	5.92	-1.24	GSA1^[24]
	qTGW5.1	FIF232-FIF345	8.53	3.67	0.95				GS5^[25,26]
	qTGW5.2	FIF426-FIF738	9.86	4.64	1.11	5.95	4.97	1.14	GSE5/GW5/qSW5^{[27,28,29,30,31]}
	qTGW6.1	RM136-RM3	4.19	2.25	-0.87
	qTGW6.2	RM30-RM340	6.12	2.80	-1.04
	qTGW7	RM420-RM172	4.35	1.76	-0.76
	qTGW9.1	RM296-RM7424	4.97	2.68	-0.96				DEP1/DN1/qNGR9^{[32,33,34,35,36,37,38]}
	qTGW9.2	RM7048-RM328				3.26	3.16	-0.91
	qTGW10.1	RM228-RM590	6.70	2.64	-0.92
	qTGW10.2	RM474-TEN400				4.12	3.43	-0.96
	qTGW12	RM1103-RM3226	6.26	2.62	-0.93
粒长	qGL1.1	RM1061-RM128	8.29	4.05	-0.16
GL	qGL1.2	RM315-RM12138	7.47	3.83	-0.15	9.10	8.25	-0.21
	qGL1.3	RM12283-RM12333				2.99	2.42	-0.12
	qGL2	RM145-RM71	12.09	6.35	-0.21	12.82	18.24	-0.32	GW2^[21]
	qGL3.1	THI156-THI214				4.86	4.01	-0.15
	qGL3.2	THI301-THI351	5.06	2.36	-0.12
	qGL3.3	THI1668-THI1701	45.92	32.65	-0.44	24.88	25.95	-0.38	GS3^[22,23]
	qGL3.4	RM168-RM3867	7.62	5.15	-0.18	2.95	2.78	-0.12	GSA1^[24]
	qGL5	RM538-RM480	5.14	2.45	0.13
	qGL6	RM589-RM587	4.26	2.27	0.12
	qGL7	RM351-RM234	5.78	3.32	-0.14
	qGL9	RM296-RM7424	10.43	7.67	-0.22				DEP1/DN1/qNGR9^{[32,33,34,35,36,37,38]}
	qGL11	RM1355-RM209	7.18	3.70	-0.16
粒宽	qGW2	RM145-RM71	48.09	30.95	-0.20	17.85	24.96	-0.17	GW2^[21]
GW	qGW3	RM3867-RM571	5.30	2.93	-0.05				GSA1^[24]
	qGW5.1	FIF426-FIF738	29.68	19.25	0.15	10.84	15.49	0.13	GSE5/GW5/qSW5^{[27,28,29,30,31]}
	qGW5.2	FIF738-FIF801	9.30	4.42	0.07
	qGW11	RM21-RM254	4.44	3.10	-0.06
	qGW12	RM1103-RM3226	7.88	4.01	-0.07

群体 Population	分离区别 Segregated region	性状 Trait	qTGW1.2/qGL1.2^EFT	qTGW1.2/qGL1.2^FM9	P值 P value	加性效应 Additive effect
E1	FIR3596-FIR3892	千粒重TGW/g	33.00±1.09	34.77±1.03	0.0014	-0.89
		粒长GL/mm	9.42±0.17	9.85±0.13	<0.0001	-0.21
		粒宽GW/mm	3.09±0.02	3.08±0.02	0.1703
E2	FIR3596-FIR3892	千粒重TGW/g	33.63±0.87	35.99±0.88	<0.0001	-1.19
		粒长GL/mm	9.67±0.17	10.11±0.11	<0.0001	-0.22
		粒宽GW/mm	3.10±0.03	3.09±0.04	0.7305