水稻粒重粒形QTL的定位及qTGW1.2/qGL1.2的验证

doi:10.16819/j.1001-7216.2021.201205

中国水稻科学 ›› 2021, Vol. 35 ›› Issue (4): 359-372.DOI: 10.16819/j.1001-7216.2021.201205

水稻粒重粒形QTL的定位及qTGW1.2/qGL1.2的验证

杜成兴^#, 张华丽^#, 戴冬青, 吴明月, 梁敏敏, 陈俊宇^*(), 马良勇^*()

中国水稻研究所水稻生物学国家重点实验室/国家水稻改良中心,杭州 310006

收稿日期:2020-12-08 修回日期:2021-01-26 出版日期:2021-07-10 发布日期:2021-07-10
通讯作者: 陈俊宇,马良勇
作者简介:
^#共同第一作者
基金资助:
国家自然科学基金青年科学基金资助项目（31701398）;国家863计划资助项目（2014AA10A604-15）;浙江省农业（粮食）新品种选育重大科技专项（2016C02050-4）;国家重点研发计划资助项目（2016YFD0101104）

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

Chengxing DU^#, Huali ZHANG^#, Dongqing DAI, Mingyue WU, Minmin LIANG, Junyu CHEN^*(), Liangyong MA^*()

State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China

Received:2020-12-08 Revised:2021-01-26 Online:2021-07-10 Published:2021-07-10
Contact: Junyu CHEN, Liangyong MA
About author:
^#These authors contributed equally to this work

摘要/Abstract

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

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

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.

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.

图/表 10

图1 群体构建过程

Fig. 1. Development of the rice materials used in the study.

图2 两个剩余杂合体单株RHL17和RHL124与目标qTGW1.2/qGL1.2区间的基因型组成

Fig. 2. Schematic genotypes of two residual heterozygotes RHL17 and RHL124 and the targeted region of qTGW1.2/qGL1.2.

图3 两个亲本材料EFT和FM9的千粒重、粒长和粒宽的比较**表示在 0.01水平上显著。

Fig. 3. Comparison of 1000-grain weight, grain length and grain width of the parents EFT and FM9.** Significant at 0.01 level.

图4 EFT/FM9衍生的F2:3和RIL群体的粒重粒形性状的频率分布

Fig. 4. Frequency distribution of grain weight and shape of EFT/FM9 derived F2:3 and RIL populations.

表1 EFT/FM9 F2:3和RIL群体粒型性状相关性分析

Table 1 Correlationship analysis on grain shape traits in EFT/FM9 F2:3 and RIL population.

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^**

表2 F2:3和RIL群体中检测到的粒重粒形QTL

Table 2 QTLs for grain weight and shape detected in the F2:3 and RIL populations.

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

表2 F2:3和RIL群体中检测到的粒重粒形QTL

Table 2 QTLs for grain weight and shape detected in the F2:3 and RIL populations.

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

图5 在F2:3和RIL群体中检测到的粒重和粒形QTL

Fig. 5. QTLs for grain weight and shape detected in F2:3 and RIL populations.

图6 高世代分离群体D1（A-C）和D2群体（D-F）中qTGW1.2/qGL1.2不同基因型间的株型、粒形和粒重的比较**表示在0.01水平上差异显著。

Fig. 6. Comparison of plant architecture, grain shape and grain weight among different genotypes of qTGW1.2/qGL1.2 in the D1 population (A-C) and the D2 population (D-F) of advanced generations. **Significant at 0.01 level.

表3 高世代分离群体E1和E2中qTGW1.2/qGL1.2的效应分析

Table 3 Effect of qTGW1.2/qGL1.2 estimated in E1 and E2 populations of advanced generations.

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

图7 携带qTGW1.2/qGL1.2的FM9纯合型（qTGW1.2/qGL1.2FM9）和EFT纯合型（qTGW1.2/qGL1.2EFT）材料的颖壳表皮细胞扫描电镜观察和相关基因的表达分析A- qTGW1.2/qGL1.2FM9和qTGW1.2/qGL1.2EFT的颖壳细胞（标尺：200 μm）;B-外颖细胞长度和宽度的比较（*, **分别表示在 0.05 和 0.01 水平上显著相关,n=30）;C- qTGW1.2/qGL1.2FM9和qTGW1.2/qGL1.2EFT幼穗中细胞周期与粒形相关基因的表达水平比较。CDKA1-A型细胞周期蛋白依赖性激酶1;CDKB2;1-B型周期蛋白依赖性激酶2;CYCA1;1- A型周期蛋白依赖性激酶1-1;CYCA2; 2-A型周期蛋白依赖性激酶2-1;CYCB1;1-B型周期蛋白依赖性激酶1-1;CYCB2; 2-B型周期蛋白依赖性激酶2-2;CYCD4;1-D型周期蛋白依赖性激酶4-1;CYCD4; 2-D型周期蛋白依赖性激酶4-2;KN-突触融合蛋白相关蛋白KNOLLE;CYCT1- T型细胞周期蛋白依赖性激酶1;CYCU4; 3-U型细胞周期蛋白依赖性激酶4-3;CDT2-U型细胞周期蛋白依赖性激酶4-1;MAD2-细胞扩增相关基因MAD2;E2F2- E2F转录因子2;MAPK-丝裂原活化蛋白激酶;MCM2-微型染色体维持蛋白2;MCM3-微型染色体维持蛋白3;MCM4-微型染色体维持蛋白4;GW2-粒宽基因;GS3-粒长基因;GW5 -粒宽基因;OsPIN1a-PIN蛋白1a;OsPIN1- PIN蛋白1;BG1-大粒基因;OsIAA11-Aux/IAA蛋白11;OsARF19-生长素应答因子19;TSG1-色氨酸转氨酶。

Fig. 7. Scanning electron observation and quantitative expression analysis of related genes in qTGW1.2/qGL1.2FM9 and qTGW1.2/qGL1.2EFT. A, Local outer surfaces of qTGW1.2/qGL1.2FM9 and qTGW1.2/qGL1.2EFT spikelet hulls. (Bars = 200 µm); B, Comparison of the cell length and width of outer glume cells (*, **Significant at 0.05 and 0.01 levels, respectively, n=30); C, Two parental homozygous genotypes qTGW1.2/qGL1.2FM9 and qTGW1.2/qGL1.2EFT are involved in the expression levels of cell cycle- and grain shape-related genes in young panicles. CDKA1, Cyclin-dependent kinase A-1; CDKB2;1, B-type cyclin-dependent kinase 2;1; CYCA1;1, A-type cyclin 1;1; CYCA2; 2, A-type cyclin 3;1; CYCB1;1, B-type cyclin 1; CYCB2; 2, B-type cyclin 2;2; CYCD4;1, D-type cyclin 4;1; CYCD4; 2, D-type cyclin 4;2; KN, Syntaxin-related protein KNOLLE; CYCT1, T-type cyclin 1; CYCU4; 3, U-type cyclin 4;3; CDT2, Cadmium tolerant 2; MAD2, Cell expansion-related gene MAD2; E2F2, E2F transcription factor 2; MAPK, Mitogen-activated protein kinase; MCM2, Mini-chromosome maintenance protein 2; MCM3, Mini-chromosome maintenance protein 3; MCM4, Mini-chromosome maintenance protein 4; GW2, Grain weight 2; GS3, Grain size 3; GW5, Grain width 5; OsPIN1a, Pin protein 1a; OsPIN1, Pin-formed 1b; BG1, Big grain 1; OsIAA11, Aux/IAA protein 11; OsARF19, Auxin response factor 19; TSG1, Tillering and small grain 1.

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水稻粒重粒形QTL的定位及qTGW1.2/qGL1.2的验证

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

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