基于高密度遗传图谱对水稻粒形QTL定位及分析

doi:10.3724/SP.J.1006.2022.12069

Abstract

Abstract:

In this study, QTL mapping of grain size related traits and pyramided effect analysis of different sites were carried out to lay a foundation for marker-assisted breeding and fine mapping of grain size related genes. A total of 192 recombinant inbred lines derived from indica rice cultivars Modasui and Hanghui 315 were planted in three different seasons. A high-density genetic map was constructed based on whole-genome resequencing technology, and the QTLs for grain shape traits were mapped by complete interval mapping (ICIM) and verified by composite interval mapping (CIM). QTL mapping was carried out for grain length, grain width, length-width ratio, 1000-grain weight, cross-sectional area, and grain circumference. 50 and 81 QTLs were detected by ICIM and CIM, respectively, and 43 QTLs could be detected simultaneously. They were clustered on chromosome 2, 3, 5, 7, 8, and 9. Their highest phenotypic contribution rates were 15.74%, 54.07%, and 15.89%, respectively. These loci could be the candidate loci for subsequent gene function studies. According to the genotyping of bin markers, different progenies were divided into Hanghui 315 type and Modasui type in each QTL interval. Further data processing and analysis were performed to analyze the pyramided effect of QTLs. It was found that individuals with more pyramided synergistic alleles showed higher phenotypic values in different environments. The identified lines with multiple synergistic alleles can be used as donor parents in breeding practices.

Key words: rice, recombinant inbred lines, high density genetic map, grain size, QTL mapping

SONG Bo-Wen, WANG Chao-Huan, ZHAO Zhe, CHEN Chun, HUANG Ming, CHEN Wei-Xiong, LIANG Ke-Qin, XIAO Wu-Ming. Mapping and analysis of QTLs for grain size in rice based on high density genetic map[J].Acta Agronomica Sinica, 2022, 48(11): 2813-2825.

Figures/Tables 8

Table 1

Fig. 1

Table 2

Table 3

Information of grain size-related QTLs in RILs under three environments"

性状 Trait	QTL	染色体 Chr.	位置 Position	LOD值 LOD score	加性效应 Additive	贡献率 PVE (%)	环境 Environment	置信区间 Confidence interval (cM)	标记区间 Marker interval
粒长 GL	qGL2-1	2	56.2	7.36	-0.13	3.12	2020L	55.75-56.95	bin550-bin551
	qGL2-2	2	70.9	8.03	-0.15	4.23	2019L	70.65-71.25	bin579-bin580
	qGL2-3	2	95.1	3.83	-0.10	2.29	2020E	94.75-97.05	bin622-bin623
	qGL3	3	8.9	5.96	0.13	3.06	2019L	7.75-9.45	bin700-bin701
	qGL5-1	5	94.1	11.33	-0.18	6.22	2019L	93.85-94.35	bin1179-bin1180
	qGL5-1	5	94.1	4.27	-0.10	2.57	2020E	93.85-94.35	bin1179-bin1180
	qGL5-2	5	95.6	6.69	-0.12	2.81	2020L	95.15-95.95	bin1182-bin1183
	qGL7	7	93.6	54.3	-0.54	53.42	2019L	93.45-93.95	bin1444-bin1445
			93.6	52.13	-0.49	59.48	2020E
			93.6	66.74	-0.59	64.97	2020L
	qGL8-1	8	38.2	4.91	-0.10	2.02	2020L	37.75-38.25	bin1520-bin1521
粒长 GL	qGL8-2	8	39.9	7.05	-0.14	3.67	2019L	39.05-41.85	bin1524-bin1525
	qGL8-2	8	40.8	8.70	-0.15	5.62	2020E	39.05-41.85	bin1524-bin1525
	qGL9-1	9	82.0	5.17	-0.11	3.17	2020E	80.85-86.85	bin1743-bin1744
	qGL9-1	9	82.6	6.37	-0.14	3.39	2019L	80.85-86.85	bin1743-bin1744
	qGL9-2	9	91.3	12.4	-0.19	6.35	2020L	88.45-93.85	bin1744-bin1745
	qGL12-1	12	14.1	5.15	-0.11	2.13	2020L	13.65-14.55	bin396-bin397
	qGL12-2	12	36.9	5.03	-0.12	2.56	2019L	36.85-37.25	bin424-bin426
粒宽 GW	qGW2	2	30.8	3.60	-0.02	2.09	2019L	30.15-31.75	bin523-bin524
	qGW3-1	3	137.8	42.68	-0.10	20.62	2020L	137.75-138.15	bin847-bin848
	qGW3-2	3	138.8	34.26	0.08	14.40	2020L	138.45-139.35	bin850-bin851
	qGW4-1	4	58.1	9.56	-0.04	2.90	2020L	57.95-58.55	bin1028-bin1029
	qGW4-2	4	62.9	5.35	-0.04	4.44	2020E	62.65-63.35	bin1013-bin1033
	qGW4-3	4	65.2	9.36	-0.04	5.84	2019L	65.05-65.35	bin1011-bin1010
	qGW5-1	5	96.5	4.25	-0.03	2.49	2019L	95.95-97.05	bin1185-bin1186
	qGW5-2	5	109.1	4.17	-0.03	1.61	2020L	99.75-114.55	bin1191-bin1192
	qGW7	7	93.3	45.47	0.13	61.86	2020E	93.05-93.65	bin1443-bin1445
			93.5	61.42	0.14	38.26	2020L
			93.6	55.35	0.13	63.57	2019L
长宽比 LWR	qLWR1-1	1	137.0	4.07	-0.07	1.07	2020L	135.85-138.95	bin170-bin171
	qLWR1-2	1	166.1	3.30	-0.08	1.50	2020E	165.85-166.75	bin185-bin186
	qLWR4-1	4	68.9	7.93	0.10	2.18	2020L	68.35-68.95	bin1004-bin1002
	qLWR4-2	4	73.2	10.32	0.12	3.62	2019L	72.75-73.45	bin991-bin992
	qLWR4-2	4	73.2	5.41	0.11	2.53	2020E	72.75-73.45	bin991-bin992
	qLWR7	7	93.6	82.93	-0.53	81.10	2019L	93.45-93.95	bin1444-bin1445
			93.6	66.96	-0.55	72.45	2020E
			93.6	91.42	-0.58	84.89	2020L
	qLWR11	11	52.8	3.55	0.08	1.62	2020E	52.15-52.95	bin356-bin357
千粒重 TGW	qTGW2-1	2	30.5	4.22	-0.38	4.47	2019L	29.45-33.25	bin523-bin526
	qTGW2-1	2	32.6	5.26	-0.54	6.76	2020L	29.45-33.25	bin523-bin526
	qTGW2-2	2	77.9	3.27	-0.36	3.45	2020E	77.35-77.95	bin594-bin596
	qTGW3	3	137.2	4.10	-0.40	4.38	2020E	136.85-137.65	bin846-bin847
	qTGW4-1	4	58.0	5.59	-0.58	7.08	2020L	57.95-58.65	bin1027-bin1028
	qTGW4-2	4	64.8	5.36	-0.48	6.23	2019L	64.15-65.15	bin1033-bin1012
	qTGW5	5	96.5	4.19	-0.40	4.46	2020E	95.95-98.65	bin1185-bin1186
			97.0	6.91	-0.49	7.37	2019L
			97.0	5.28	-0.54	6.67	2020L
	qTGW7-1	7	67.6	3.78	0.36	3.99	2019L	67.45-67.75	bin1400-bin1399
	qTGW7-2	7	93.5	16.32	0.80	19.64	2019L	93.05-93.65	bin1444-bin1445
			93.5	18.70	0.93	23.88	2020E
			93.5	12.35	0.86	17.12	2020L
	qTGW8-1	8	40.3	3.99	-0.37	4.24	2019L	39.35-41.55	bin1524-bin1525
	qTGW8-2	8	65.4	5.34	-0.46	5.75	2020E	65.35-66.15	bin1576-bin1577
千粒重 TGW	qTGW8-3	8	75.2	4.74	-0.51	5.96	2020L	74.65-75.65	bin1589-bin1590
	qTGW9-1	9	9.9	3.26	0.42	4.02	2020L	9.35-10.65	bin1651-bin1652
	qTGW9-2	9	89.9	8.71	-0.64	11.14	2020E	86.85-94.4	bin1744-bin1745
			91.4	11.59	-0.70	14.64	2019L
			93.2	6.08	-0.61	8.45	2020L
谷粒截面积 GAS	qGAS2-1	2	31.5	4.02	-0.25	5.90	2020E	30.85-33.25	bin524-bin525
	qGAS2-1	2	31.5	5.32	-0.29	6.38	2020L	30.85-33.25	bin524-bin525
	qGAS2-2	2	74.8	6.96	-0.43	10.61	2019L	74.45-75.15	bin588-bin589
	qGAS4-1	4	63.1	3.30	-0.27	5.74	2020E	62.65-63.55	bin1013-bin1033
	qGAS4-2	4	65.3	4.58	-0.28	5.32	2020L	65.15-65.55	bin1011-bin1010
	qGAS5	5	95.7	5.54	-0.29	7.98	2020E	95.15-96.45	bin1183-bin1184
			95.7	7.95	-0.35	9.59	2020L
			95.9	9.97	-0.51	15.78	2019L
	qGAS7	7	16.3	4.69	-0.26	5.44	2020L	15.65-16.35	bin1344-bin1345
	qGAS8-1	8	43.7	4.88	-0.27	5.71	2020L	42.65-43.95	bin1530-bin1531
	qGAS8-2	8	53.8	3.62	-0.30	5.30	2019L	53.35-54.15	bin1551-bin1552
	qGAS8-2	8	53.8	8.70	-0.38	13.07	2020E	53.35-54.15	bin1551-bin1552
	qGAS9-1	9	6.7	3.95	0.24	5.61	2020E	6.05-7.25	bin1644-bin1645
	qGAS9-2	9	23.2	3.85	0.24	4.53	2020L	21.35-23.65	bin1666-bin1667
	qGAS9-3	9	92.1	3.53	-0.25	5.81	2020E	86.85-94.4	bin1744-bin1745
	qGAS9-3	9	92.1	10.78	-0.45	15.43	2020L	86.85-94.4	bin1744-bin1745
谷粒周长 GPL	qGPL2-1	2	30.9	4.09	-0.22	2.89	2020E	30.15-31.75	bin524-bin525
	qGPL2-2	2	70.9	8.18	-0.31	4.36	2020L	70.65-71.25	bin579-bin580
	qGPL2-3	2	74.8	7.54	-0.34	5.50	2019L	74.45-75.15	bin588-bin589
	qGPL2-4	2	95.2	3.99	-0.22	2.85	2020E	94.75-96.95	bin623-bin624
	qGPL3	3	9.4	3.44	0.22	2.38	2019L	7.75-9.45	bin700-bin701
	qGPL5-1	5	94.1	10.64	-0.41	8.04	2019L	93.85-94.35	bin1179-bin1180
	qGPL5-1	5	94.1	3.95	-0.21	2.76	2020E	93.85-94.35	bin1179-bin1180
	qGPL5-2	5	95.6	8.07	-0.30	4.29	2020L	95.15-95.95	bin1182-bin1183
	qGPL7-1	7	93.2	41.92	-1.00	47.97	2019L	92.75-93.75	bin1443-bin1445
	qGPL7-1	7	93.5	57.95	-1.14	60.17	2020L	92.75-93.75	bin1443-bin1445
	qGPL7-2	7	94.1	44.88	-0.95	54.04	2020E	93.95-94.75	bin1447-bin1448
	qGPL8	8	39.9	5.90	-0.30	4.18	2019L	39.85-41.85	bin1524-bin1526
			41.2	7.14	-0.29	5.28	2020E
			41.8	4.5	-0.22	2.29	2020L
	qGPL9-1	9	81.9	5.84	-0.26	4.19	2020E	80.85-86.85	bin1743-bin1744
	qGPL9-1	9	85.1	3.55	-0.23	2.57	2019L	80.85-86.85	bin1743-bin1744
	qGPL9-2	9	91.1	9.64	-0.36	5.98	2020L	87.95-93.95	bin1744-bin1745
	qGPL12	12	34.4	4.20	-0.21	2.13	2020L	33.55-35.75	bin420-bin421

Table 3

Table 4

Fig. 2

Fig. 3

Table 5

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性状 Trait	季节 Season	亲本Parents		重组自交系RILs						广义遗传力 h²(%)
性状 Trait	季节 Season	R315	MDS	均值±标准差 Mean ± SD	变异系数 CV (%)	最大值 Maximum	最小值 Minimum	偏度 Skewness	峰度 Kurtosis	广义遗传力 h²(%)
粒长 GL (mm)	2019L	10.93^**	8.62	9.59±0.72	7.54	11.37	7.97	0.09	-0.56	96.68
	2020E	10.70^**	8.57	9.69±0.65	6.65	11.21	8.24	-0.05	-0.68
	2020L	11.06^**	8.57	9.66±0.72	7.49	11.22	8.10	-0.06	-0.78
粒宽 GW (mm)	2019L	2.11	2.27^**	2.14±0.16	7.64	2.52	1.81	0.22	-0.76	94.14
	2020E	1.99	2.17^**	2.11±0.17	7.94	2.52	1.73	0.06	-1.02
	2020L	2.06	2.22^**	2.09±0.16	7.83	2.61	1.78	0.28	-0.74
长宽比 GLWR	2019L	5.20^**	3.82	4.55±0.58	12.81	6.03	3.43	0.01	-1.34	97.28
	2020E	5.42^**	3.96	4.66±0.62	13.21	5.86	3.60	0.08	-1.41
	2020L	5.40^**	3.89	4.70±0.64	13.56	5.81	3.64	-0.03	-1.54
千粒重 TGW (g)	2019L	18.86^**	18.47	17.85±1.91	10.69	23.20	13.10	0.22	-0.32	92.69
	2020E	20.49^**	19.09	19.48±1.89	9.68	24.04	14.43	-0.08	-0.23
	2020L	21.60^**	20.01	19.37±2.14	11.03	26.67	12.00	0.05	0.77
谷粒截面积 GAS (mm²)	2019L	17.89^**	15.53	16.07±1.28	7.98	19.25	12.70	0.20	-0.26	88.80
	2020E	16.66^*	14.79	16.00±1.03	6.43	18.87	13.30	0.19	-0.11
	2020L	17.73^**	14.85	15.77±1.11	7.05	18.22	13.10	0.13	-0.44
谷粒周长 GPL (mm)	2019L	24.67^**	19.92	21.78±1.48	6.79	25.54	18.39	0.10	-0.35	96.30
	2020E	24.08^**	19.75	21.99±1.30	5.91	25.39	18.82	-0.04	-0.48
	2020L	24.94^**	19.76	21.97±1.48	6.75	25.16	18.57	-0.07	-0.62

性状 Trait	粒长 GL	粒宽 GW	长宽比 GLWR	千粒重 TGW	谷粒截面积 GAS	谷粒周长 GPL
粒长GL	1	-0.592^**	0.887^**	-0.049	0.454^**	0.997^**
粒宽GW	-0.592^**	1	-0.895^**	0.731^**	0.443^**	-0.535^**
长宽比GLWR	0.887^**	-0.895^**	1	-0.446^**	-0.005	0.853^**
千粒重TGW	-0.049	0.731^**	-0.446^**	1	0.755^**	0.01
谷粒截面积GAS	0.454^**	0.443^**	-0.005	0.755^**	1	0.514^**
谷粒周长GPL	0.997^**	-0.535^**	0.853^**	0.010	0.514^**	1

QTL簇 QTL cluster	染色体 Chr.	表型贡献率 PVE (%)	标记区间 Marker range	遗传区间 Genetic interval	相关性状 Related traits	已报道基因 Reported genes
Loci2	2	2.09-6.76	bin523-bin526	29.45-33.25	GW, TGW, GAS, GPL
Loci3	3	2.38-3.06	Bin700-bin701	8.90-9.40	GL, GPL
Loci5	5	2.49-15.78	bin1179-bin1186	93.85-98.65	GL, GPL, GW, TGW, GAS	OsPUP7^[13]
Loci7	7	17.12-84.89	bin1443-bin1448	92.75-94.75	GL, GW, LWR, TGW, GPL	GL7/GW7^[11-12]
Loci8	8	2.29-5.62	bin1524-bin1525	39.05-41.85	GL, TGW, GPL
Loci9	9	2.57-15.43	bin1743-bin1745	80.85-94.40	GL, TGW, GAS, GPL	APX9^[14]

株系类型 Type of lines	QTL			株系数 No. of line	粒长 GL (mm)	粒宽 GW (mm)	长宽比 LWR	谷粒截面积 GAS (mm²)	谷粒周长 GPL (mm)	千粒重 TGW (g)
株系类型 Type of lines	Loci5	Loci7	Loci9	株系数 No. of line	粒长 GL (mm)	粒宽 GW (mm)	长宽比 LWR	谷粒截面积 GAS (mm²)	谷粒周长 GPL (mm)	千粒重 TGW (g)
MDS	MDS	MDS	MDS	1	8.62±0.04	2.24±0.02	3.86±0.03	15.26±0.30	19.89±0.10	19.19±0.63
Line.1	MDS	MDS	MDS	14	8.73±0.33	2.18±0.07	4.03±0.21	14.86±0.72	20.01±0.70	18.19±1.34
Line.2	MDS	MDS	R315	20	9.01±0.30	2.24±0.07	4.06±0.18	15.76±0.77	20.63±0.64	19.40±1.37
Line.3	MDS	R315	MDS	14	9.80±0.24	1.96±0.08	5.04±0.24	15.10±0.64	22.12±0.51	16.74±1.42
Line.4	MDS	R315	R315	25	10.23±0.33	1.97±0.09	5.24±0.31	15.87±0.78	23.03±0.68	18.33±1.38
Line.5	R315	MDS	MDS	13	8.92±0.33	2.27±0.09	3.96±0.19	15.76±0.94	20.50±0.78	19.67±1.60
Line.6	R315	MDS	R315	15	9.50±0.19	2.29±0.08	4.17±0.16	17.09±0.71	21.75±0.42	21.22±1.19
Line.7	R315	R315	MDS	17	10.17±0.28	2.00±0.05	5.12±0.14	16.04±0.75	22.93±0.62	17.57±1.37
Line.8	R315	R315	R315	22	10.42±0.43	2.01±0.08	5.23±0.17	16.47±1.16	23.46±1.00	19.17±1.30
R315	R315	R315	R315	1	10.97±0.07	2.07±0.03	5.33±0.09	17.67±0.21	24.70±0.19	20.32±1.13
增效位点来源^aSource of favorable alleles ^a					R315	R315	—	R315	R315	R315
					R315	MDS	R315	—	R315	MDS
					R315	—	—	R315	R315	R315

Mapping and analysis of QTLs for grain size in rice based on high density genetic map

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