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

摘要/Abstract

摘要：

【目的】通过对水稻籽粒大小相关性状进行QTL定位及候选基因的筛选,为水稻籽粒大小相关基因的精细定位、克隆及基因功能等研究奠定基础。【方法】以籼稻品种特华占搭载高空气球空间诱变后产生的特异矮秆突变体CHA-1为母本,以籼稻品种航恢7号搭载“神州八号”飞船经空间诱变后筛选出的突变体H335为父本杂交衍生出的275个RIL群体作为供试材料,利用GBS测序技术构建高密度遗传图谱,RIL群体及亲本分别于2017年早季和2017年晚季在华南农业大学实验教学基地种植。成熟收获后通过扫描仪获取水稻籽粒图像,利用SmartGrain软件获取籽粒大小相关性状表型数据。采用QTL IciMapping v 4.0软件基于完备复合区间作图法,对水稻籽粒大小相关性状进行QTL定位。【结果】构建的高密度遗传图谱包含2 498个Bin标记,总图距2 371.84 cM,标记间平均遗传图距为0.95 cM。两季共检测到26个籽粒大小相关QTL,分布于第1、2、3、4、7和9染色体上,单一QTL贡献率为0.16%—14.41%。在第1、2、3、7染色体上检测到5个QTL簇（qGS1、qGS2、qGS3-1、qGS3-2和qGS7）。其中qGS1、qGS3-2和qGS7与前人报道相似,qGS2和qGS3-1是新发现的籽粒大小相关QTL,qGS2在2个季别的不同性状中被检测在同一标记区间附近,LOD值介于4.00—8.08,贡献率为6.67%—11.38%。qGS3-1在2个季别下均检测到与籽粒厚度相关,LOD值介于2.94—8.59,贡献率为4.69%—14.41%。使用的高密度遗传图谱定位区间较小,结合功能注释和CREP数据库表达谱,在qGS2位点筛选到4个潜在的与籽粒大小相关的注释基因LOC_Os02g42310、LOC_Os02g42314、LOC_Os02g42370和LOC_Os02g42380。其中LOC_Os02g42310编码一个丝氨酸羧肽酶;LOC_Os02g42314编码一个泛素E2结合酶;LOC_Os02g42370编码一个类受体蛋白激酶;LOC_Os02g42380编码一个TCP转录因子。在qGS3-1位点筛选到3个潜在的与籽粒大小相关的注释基因LOC_Os03g39020、LOC_Os03g39150和LOC_Os03g39230。其中LOC_Os03g39020编码一个驱动蛋白结构域;LOC_Os03g39150编码一个蛋白激酶结构域;LOC_Os03g39230编码一个具有去蛋白质泛素化功能的OTU-like半胱氨酸肽酶。其中编码泛素E2结合酶的LOC_Os02g42314和编码驱动蛋白结构域的LOC_Os03g39020在幼穗和授粉后的胚乳中表达量较高,推测其为最可能的调控籽粒大小的候选基因。【结论】共检测到26个水稻籽粒大小相关QTL。在第1、2、3和7染色体上检测到5个QTL簇（qGS1、qGS2、qGS3-1、qGS3-2和qGS7）,其中qGS2和qGS3-1为新发现的控制籽粒大小QTL,并在该位点筛选到2个可能调控水稻籽粒大小相关的候选基因。

关键词: 水稻, RIL群体, 高密度遗传图谱, 籽粒大小, QTL定位, 候选基因

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

张健,杨靖,王豪,李冬秀,杨瑰丽,黄翠红,周丹华,郭涛,陈志强,王慧. 基于高密度遗传图谱定位水稻籽粒大小相关性状QTL[J]. 中国农业科学, 2020, 53(2): 225-238.

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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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]