基于高密度遗传图谱定位水稻籽粒大小相关性状QTL

doi:10.3864/j.issn.0578-1752.2020.02.001

Abstract

Abstract:

【Objective】Combine QTL mapping for grain size and related traits and screening for candidate genes to lay a good foundation for dissecting genes regulating rice grain size and related traits.【Method】A dwarf mutant CHA-1 screened from the progeny of the indica rice variety Tehuazhan carried by high altitude balloon was hybridized with another mutant H335 selected from the progeny of the indica rice variety Hanghui 7 induced by “Shenzhou 8” spaceflight. A population of 275 recombinant inbred lines (RILs) was structured from CHA-1 ×H335. A high-density genetic map was constructed using genotyping by sequencing (GBS) technology. The RIL population and parents were grown in the experimental base of South China Agricultural University consecutively in the early and late season in 2017. After ripening, rice grain images were scanned, and the grain size and related traits was obtained by SmartGrain software. QTL mapping for rice grain size and related traits was done with QTL IciMapping v 4.0 software based on inclusive composite interval mapping (ICIM).【Result】The constructed high-density genetic map contains 2498 Bin markers ,and all the markers covers 2371.84 cM with an average genetic distance of 0.95 cM/marker. A total of 26 grain-size related QTLs were repeatedly detected on Chr.1, Chr.2, Chr.3, Chr.4, Chr.7 and Chr.9 in the two seasons with single QTL contribution rate ranged from 0.16% to 14.41%. Five QTL clusters (qGS1, qGS2, qGS3-1, qGS3-2, qGS7) were detected on Chr.1, Chr.2, Chr.3, and Chr.7. Among them, qGS1, qGS3-2, and qGS7 have been previously reported. qGS2 and qGS3-1 were novel grain-size related QTLs. qGS2 was repeatedly detected in the same marker interval in the two seasons, and its LOD values in the early and late season were 8.08 and 4.00 with the phenotypic contribution rate 11.38% and 6.67%, respectively. qGS3-1 was detected to be correlated with grain thickness in the two seasons, and its LOD values in the early and late season were 2.94 and 8.59 with the phenotypic contribution rates 4.69% and 14.41%, respectively. Combined with functional annotation and CREP database of gene expression profiles, four candidate grain-size related genes including LOC_Os02g42310, LOC_Os02g42314, LOC_Os02g42370 and LOC_Os02g42380 were screened out in the qGS2 locus. LOC_Os02g42310 encodes a serine carboxypeptidase homologue; LOC_Os02g42314 encodes a ubiquitin-conjugating enzyme; LOC_Os02g42370 encodes a protein kinase domain containing protein; LOC_Os02g42380 encodes a TCP domain containing protein. Three candidate grain-size related genes including LOC_Os03g39020, LOC_Os03g39150 and LOC_Os03g39230 were screened out in the qGS3-1 locus. LOC_Os03g39020 encodes a kinesin motor domain containing protein; LOC_Os03g39150 encodes a protein kinase domain containing protein; LOC_Os03g39230 encodes an OTU-like cysteine protease family protein. Among the genes, LOC_Os02g42314 and LOC_Os03g39020 were highly expressed in the young panicle and endosperm after pollination and recognized as the most possible candidate genes for regulating grain size.【Conclusion】 26 rice grain-size related QTLs were detected. Five QTL clusters (qGS1, qGS2, qGS3-1, qGS3-2, qGS7) were detected on Chr1, Chr.2, Chr.3, and Chr.7, and qGS2 and qGS3-1 were novel QTLs for regulating grain size, and two candidate genes were screened out in this locus.

Key words: rice, RIL population, high-density genetic map, grain size, grain shape, QTL mapping, candidate gene

ZHANG Jian,YANG Jing,WANG Hao,LI DongXiu,YANG GuiLi,HUANG CuiHong,ZHOU DanHua,GUO Tao,CHEN ZhiQiang,WANG Hui. QTL Mapping for Grain Size Related Traits Based on a High-Density Map in Rice[J].Scientia Agricultura Sinica, 2020, 53(2): 225-238.

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References 38

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性状 Trait	季节 Season	亲本Parents		重组自交系RIL
性状 Trait	季节 Season	CHA-1	H335	均值+标准差 Mean±SD	变幅 Range	变异系数 CV (%)	峰度 Kurtosis	偏度 Skewness
粒长 GL(mm)	2017E	8.59	9.15*	9.33±0.44	7.41—10.47	4.71	1.13	-0.27
粒长 GL(mm)	2017L	8.83	9.71*	9.89±0.61	7.54—12.08	6.13	3.13	0.33
粒宽 GW(mm)	2017E	1.92	2.27**	2.46±0.12	2.11—3.04	4.88	1.57	0.31
粒宽 GW(mm)	2017L	2.14	2.47**	2.50±0.16	2.12—3.27	6.34	2.55	0.84
粒厚 GT(mm)	2017E	1.74	1.92**	1.88±0.05	1.74—2.02	3.17	0.12	-0.15
粒厚 GT(mm)	2017L	1.68	1.89**	1.89±0.06	1.71—2.07	3.42	-0.05	-0.16
长宽比 GLWR	2017E	4.4	4.03**	3.82±0.25	2.68—4.55	6.54	3.49	-0.82
长宽比 GLWR	2017L	4.13	3.94**	3.99±0.27	2.33—4.85	6.89	6.93	-1.53
籽粒圆度 CS	2017E	0.43	0.46*	0.48±0.03	0.41—0.62	6.25	5.94	1.32
籽粒圆度 CS	2017L	0.44	0.46*	0.46±0.03	0.38—0.65	5.99	12.46	2.42
籽粒周长 PL(mm)	2017E	19.58	20.86**	21.50±0.96	17.72—23.83	4.47	0.52	-0.09
籽粒周长 PL(mm)	2017L	20.35	22.58**	22.84±1.33	18.18—27.83	5.81	2.75	0.53
籽粒截面积 AS(mm²)	2017E	13.59	16.04**	17.79±1.28	14.30—21.09	7.19	-0.01	0.08
籽粒截面积 AS(mm²)	2017L	14.64	18.75**	19.11±1.96	14.70—28.93	10.25	5.17	1.45
千粒重 TGW(g)	2017E	15.29	22.25**	21.87±1.96	15.50—32.00	8.95	2.78	0.41
千粒重 TGW(g)	2017L	16.02	24.13**	23.02±2.24	14.86—28.50	9.73	0.46	-0.12

性状 Traits	粒长 GL	粒宽 GW	粒厚 GT	谷粒截面积 AS	谷粒周长 PL	长宽比 GLWR	谷粒圆度 CS	千粒重 TGW
粒长GL		0.293**	0.291**	0.825* *	0.991**	0.577**	-0.586**	0.448**
粒宽GW	0.062		0.555**	0.724**	0.385**	-0.598**	0.555**	0.488**
粒厚GT	0.256**	0.368**		0.475**	0.339**	-0.237**	0.193**	0.749**
谷粒截面积AS	0.739**	0.686 **	0.428**		0.875**	0.045	-0.043	0.559**
谷粒周长PL	0.987**	0.188**	0.295**	0.819 **		0.490**	-0.510**	0.490**
长宽比GLWR	0.651**	-0.709**	-0.107	-0.01	0.548 **		-0.967**	-0.059
谷粒圆度CS	-0.674**	0.656 **	0.087	-0.02	-0.583**	-0.974**		0.012
千粒重TGW	0.498**	0.377 **	0.666**	0.616 **	0.536 **	0.043	-0.063

连锁群编号 Linkage group ID	总标记数 Total marker	总图距 Total distance (cM)	平均图距 Average distance (cM)	最大Gap Max gap (cM)	Gap ＜5 cM (%)
Chr.1	251	219.89	0.88	2.85	100.00
Chr.2	316	196.26	0.62	6.69	99.37
Chr.3	313	217.40	0.70	5.54	99.68
Chr.4	309	207.84	0.67	11.89	99.68
Chr.5	138	238.62	1.74	6.83	99.27
Chr.6	212	202.72	0.96	10.02	99.05
Chr.7	156	171.16	1.10	5.17	99.35
Chr.8	141	111.26	0.79	5.77	99.29
Chr.9	192	181.65	0.95	4.07	100.00
Chr.10	185	326.27	1.77	25.61	98.37
Chr.11	140	89.95	0.65	1.82	100.00
Chr.12	145	208.82	1.45	3.24	100.00
总计Total	2498	2371.84	0.95	25.61	99.51

性状 Trait	季别 Season	QTL	染色体 Chr.	位置 Position (cM)	标记区间 Marker interval	LOD	贡献率 PVE (%)	加性效应 Add.
粒长 GL	2017E	qGL1	1	81	Block391— Block433	2.70	4.13	0.89
		qGL2-1	2	112	Block3789— Block3802	6.57	10.37	1.38
	2017L	qGL2-2	2	135	Block3934—Block3940	96.99	11.07	10.47
		qGL2-3	2	139	Block3954— Block3957	86.71	8.87	-9.38
		qGL9	9	151	Block15927— Block15938	3.45	0.16	-1.26
粒宽 GW	2017E	qGW3-2	3	204	Block6009—Block6012	3.92	6.50	0.32
	2017L	qGW3-1	3	36	Block5332— Block5419	2.94	5.29	0.35
谷粒截面积 AS	2017E	qAS2-2	2	112	Block3789— Block3802	6.57	11.36	40.48
		qAS3	3	34	Block5273— Block5280	2.86	4.87	26.75
	2017L	qAS2-1	2	111	Block3794— Block3802	4.00	7.08	47.52
谷粒周长 PL	2017E	qPL1	1	81	Block391—Block433	3.33	4.50	2.08
		qPL2-2	2	112	Block3789— Block3802	8.08	11.38	3.27
	2017L	qPL2-1	2	111	Block3794— Block3802	4.07	6.67	3.30
		qPL9	9	137	Block15834— Block15856	3.22	5.25	-2.93
长宽比 GLWR	2017E	qGLWR3	3	203	Block6004— Block6012	2.53	4.22	-0.05
	2017L	qGLWR7	7	164	Block12538— Block12681	2.85	4.81	0.06
谷粒圆度 CS	2017L	qCS7	7	164	Block12538—Block12681	2.69	4.58	-0.01
粒厚 GT	2017E	qGT3-1	3	37	Block5421- Block5424	3.06	4.69	0.01
		qGT3-2	3	216	Block6268— Block6282	4.68	7.27	0.01
		qGT4-2	4	135	Block7726— Block7769	3.16	4.88	0.01
		qGT7	7	166	Block12689— Block12716	4.16	6.42	-0.01
	2017L	qGT3-1	3	37	Block5421— Block5424	8.59	14.41	0.02
		qGT4-1	4	13	Block6302—Block6677	3.23	5.21	0.01
千粒重 TGW	2017E	qTGW2-2	2	133	Block3892— Block3931	4.35	6.75	0.50
	2017L	qTGW2-1	2	128	Block3805— Block3823	5.72	9.92	0.62
		qTGW4	4	33	Block6738— Block6765	2.73	4.62	0.42

QTL簇 QTL cluster	染色体 Chr.	标记区间 Marker interval	物理区间 Physical interval (bp)	相关性状 Involved trait	LOD	贡献率 PVE (%)	报道QTL QTL reported
qGS1	1	Block391—Block433	9107381—10916140	GL、PL	2.70—3.33	4.13—4.50	YGL8^[28]
qGS2	2	Block3789—Block3802	25385152—25530071	GL、AS、PL	4.00—8.08	6.67—11.38
qGS3-1	3	Block5421—Bloc5424	21695710—21786126	GW、GT	2.94—8.59	4.69—14.41
qGS3-2	3	Block6004—Block6012	31084034—31304364	GW、GLWR	2.53—3.92	4.22—6.50	qST3^[29]
qGS7	7	Block12538—Block12716	24107455—28343282	GT、GLWR、CS	2.69—4.16	4.58—6.42	GL7; GW7^[4]

QTL Mapping for Grain Size Related Traits Based on a High-Density Map in Rice

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