基于染色体片段置换系群体检测水稻株型性状QTL

doi:10.3724/SP.J.1006.2022.12024

Abstract

Abstract:

Plant architecture is a compound trait integrated with multiple morphological and physiological traits, and it is closely related to rice yield. Deciphering excellent plant architecture alleles or QTLs is of great significance for high-yield rice breeding. In this study, we constructed a set of Changhui 121/Koshihikari chromosome segment substitution lines (CSSLs) with the size of 208 in our laboratory. QTLs controlling plant height, flag leaf morphology, and tiller numbers were detected under three environments. A total of 35 QTLs for rice architecture were identified on 11 chromosomes except chromosome 9, and the range of the phenotypic variation explaining was 2.00%-22.86%. It was worth noting that qPH-1-1, qFLW-6, and qFLA-3 could be detected in three environments, among which qFLW-6 was a newly identified QTL of the flag leaf width. Phenotypic identification verified that the additive effects and environmental stability of the two locus alleles by the replacement lines carrying qPH-1-1 and sites. The results of this study laid the foundation for further fine mapping and cloning of QTLs for rice plant architecture and the molecular marker-assisted selection (MAS) in rice breeding.

Key words: rice, chromosome segment substitution lines, plant architecture, quantitative trait locus

WANG Xiao-Lei, LI Wei-Xing, OU-YANG Lin-Juan, XU Jie, CHEN Xiao-Rong, BIAN Jian-Min, HU Li-Fang, PENG Xiao-Song, HE Xiao-Peng, FU Jun-Ru, ZHOU Da-Hu, HE Hao-Hua, SUN Xiao-Tang, ZHU Chang-Lan. QTL mapping for plant architecture in rice based on chromosome segment substitution lines[J].Acta Agronomica Sinica, 2022, 48(5): 1141-1151.

Figures/Tables 10

Table 1

Table 2

Fig. 1

Table 3

Fig. 2

Table 4

Table 5

QTLs controlling plant architecture traits detected in Changhui 121/Koshihikari 208 CSSLs"

性状 Trait	QTL	染色体Chr.	标记区间 Marker interval	LOD值 LOD score			表型贡献率 Phenotypic variation explained (%)			加性效应 Additive effects (Add)
性状 Trait	QTL	染色体Chr.	标记区间 Marker interval	E1	E2	E3	E1	E2	E3	E1	E2	E3
株高 Plant height	qPH-1-1	1	RM5423-RM5302	6.60	6.04	4.10	9.27	7.17	3.44	18.58	11.92	15.42
	qPH-1-2	1	RM5389-RM6696	9.59	11.51	—	13.93	14.53	—	13.97	10.42	—
	qPH-2-1	2	RM5812-RM1211	—	3.69	—	—	4.27	—	—	5.04	—
	qPH-2-2	2	RM7451-RM154	—	—	4.14	—	—	3.48	—	—	15.52
	qPH-3	3	RM5891-RM5475	3.62	—	5.30	4.92	—	4.51	6.61	—	14.50
	qPH-4	4	RM5503-RM5879	3.54	—	—	4.80	—	—	7.88	—	—
	qPH-5	5	RM3345-RM7444	—	8.39	—	—	10.22	—	—	8.74	—
	qPH-7	7	RM8262-RM7273	—	3.07	—	—	3.53	—	—	5.97	—
	qPH-12	12	RM6288-RM19	—	4.25	—	—	4.94	—	—	4.42	—
剑叶长 Flag leaf length	qFLL-5-1	5	RM3476-RM178	—	10.00	—	—	7.41	—	—	9.42	—
	qFLL-5-2	5	RM3790-RM7423	—	19.15	—	—	15.80	—	—	9.74	—
	qFLL-6	6	RM7641-RM3138	—	—	2.59	—	—	4.79	—	—	-2.49
	qFLL-7	7	RM5711-RM8263	—	2.96	—	—	2.03	—	—	1.59	—
	qFLL-12	12	RM6869-RM3331	6.86	—	—	13.97	—	—	6.97	—	—
剑叶宽 Flag leaf width	qFLW-1	1	RM3530-RM8111	—	5.50	4.39	—	4.97	7.48	—	0.12	0.10
	qFLW-3	3	RM1164-RM3646	—	4.03	—	—	3.59	—	—	0.09	—
	qFLW-4	4	RM6089-RM5503	—	2.64	6.32	—	2.31	11.01	—	0.05	0.11
	qFLW-5	5	RM3345-RM7444	—	21.11	6.13	—	22.86	10.64	—	0.16	0.09
	qFLW-6	6	RM3628-RM5371	15.83	3.31	9.88	16.17	2.94	9.38	6.91	1.95	0.32
	qFLW-7	7	RM3394-RM5752	—	3.58	—	—	3.16	—	—	0.06	—
	qFLW-10	10	RM484-RM591	3.97	—	—	3.55	—	—	1.49	—	—
剑叶夹角 Flag leaf angle	qFLA-1-1	1	RM6387-RM5389	5.67	—	—	5.16	—	—	2.78	—	—
	qFLA-1-2	1	RM6296-RM5362	—	13.59	—	—	21.11	—	—	11.02	—
	qFLA-2	2	RM1358-RM5812	9.74	—	9.76	7.03	—	8.42	5.09	—	7.78
	qFLA-3	3	RM3513-RM2334	10.07	9.98	12.87	9.63	14.87	11.51	3.31	6.61	3.86
	qFLA-4	4	RM5412-RM3471	—	—	6.97	—	—	5.82	—	—	2.68
	qFLA-5	5	RM3328-RM2998	—	—	9.76	—	—	8.42	—	—	4.34
	qFLA-6	6	RM3628-RM5371	15.83	—	—	16.17	—	—	6.91	—	—
	qFLA-10	10	RM484-RM591	3.97	—	—	3.55	—	—	1.49	—	—
分蘖数 Tiller numbers	qTN-1	1	RM259-RM5496	—	3.35	—	—	7.02	—	—	1.22	—
	qTN-5-1	5	RM1237-RM305	—	5.11	—	—	10.93	—	—	1.69	—
	qTN-5-2	5	RM3328-RM2998	—	—	7.42	—	—	2.89	—	—	1.38
	qTN-6	6	RM6275-RM3628	2.70	4.02	—	5.06	7.64	—	0.97	2.89	—
	qTN-8	8	RM4085-RM6838	—	2.80	7.90	—	5.83	2.00	—	0.73	1.58
	qTN-11	11	RM3717-RM1812	2.60	—	—	4.87	—	—	0.95	—	—

Table 5

Fig. 3

Table 6

Table 7

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环境Environment	重复数Replication	种植地点Crop location	种植季节Crop season
E1	3	江西南昌(北纬28.45°, 东经115.50°) Nanchang, Jiangxi (28.45°N, 115.50°E)	2015年5月-10月 May to October in 2015
E2	3	三亚海南(北纬18.14°, 东经109.31°) Sanya, Hainan (18.14°N, 109.31°E)	2015年12月-2016年5月 December 2015 to May 2016
E3	3	江西南昌(北纬28.45°, 东经115.50° ) Nanchang, Jiangxi (28.45°N, 115.50°E)	2016年5月-10月 May to October in 2016

性状Trait	考察记录方法 Investigation method
株高Plant height (cm)	穗颖尖到地面的高度 Height of spike tip to ground
剑叶长Flag leaf length (cm)	剑叶基部到顶端的长度 The length of the flag leaf from base to tip
剑叶宽Flag leaf width (cm)	剑叶最宽处的长度 The length of the widest point of the flag leaf
剑叶夹角Flag leaf angel (^o)	剑叶与叶枕的连线与主茎延长线所成角度 The angle between the flag leaf and the main stem
分蘖数Tiller numbers (tillers per plant)	成熟期能抽穗且能结实10粒以上的分蘖数 Tillers that can produce more than 10 grains at maturity are called effective tillers

性状 Trait	环境 Environment	亲本Parents		208个染色体片段置换系 208 CSSLs
性状 Trait	环境 Environment	昌恢121 Changhui 121 (mean ± SD)	Koshihikari (mean ± SD)	Mean ± SD	范围 Range	峰度 Kurtosis	偏度 Skewness	遗传率 h_B²
株高 Plant height (cm)	E1	128.20 ± 2.12^**	107.20 ± 2.30	128.40 ± 0.42	76.00-174.30	1.40	0.89	0.98
	E2	97.20 ± 0.41^**	86.00 ± 0.76	92.70 ± 0.28	72.30-128.00	0.25	0.77	0.99
	E3	124.00 ± 2.28^**	97.70 ± 5.17	121.00 ± 11.80	91.00-155.00	0.14	0.77	0.75
剑叶长 Flag leaf length (cm)	E1	29.90 ± 2.15	31.70 ±1.86	31.60 ± 0.29	18.30-43.10	1.53	0.71	0.89
	E2	25.40 ± 1.63	24.72 ± 1.22	22.93 ± 0.12	16.60-51.30	1.90	0.69	0.97
	E3	37.00 ± 0.14^*	30.70 ± 0.17	33.80 ± 3.72	25.20-51.80	2.02	0.46	0.83
剑叶宽 Flag leaf width (cm)	E1	1.80 ± 0.58^**	1.30 ± 0.58	1.80 ± 0.58	1.00-2.20	0.80	0.69	0.97
	E2	1.80 ± 0.08^**	1.24 ± 0.06	1.41 ± 0.00	1.00-2.00	1.89	0.41	0.99
	E3	2.00 ± 0.01^**	1.20 ± 1.00	1.60 ± 0.14	1.00-2.20	1.21	0.12	0.78
剑叶夹角 Flag leaf angle (^o)	E1	13.00 ± 1.53	40.00 ± 14.71^**	11.00 ± 0.00	4.00-51.00	0.88	1.49	0.52
	E2	13.78 ± 1.40	35.22 ± 1.64^**	15.14 ± 0.20	4.00-51.30	1.79	0.97	0.89
	E3	9.00 ± 1.00	30.30 ± 1.33^**	15.00 ± 5.52	4.00-38.00	1.42	0.85	0.92
分蘖数 Tiller numbers	E1	9.00 ± 2.08	11.00 ± 2.00	8.00 ± 0.00	5.00-14.00	0.15	0.96	0.97
	E2	10.00 ± 0.47	14.00 ± 0.63^*	8.00 ± 0.23	4.00-15.00	1.17	0.45	0.99
	E3	10.00 ± 1.13	12.00 ± 1.34	8.00 ± 1.61	5.00-13.00	1.66	1.14	0.97

QTL位点 QTL locus	株系 Line	标记Marker				剑叶角表型值 FLA of phenotypic value (^o)
QTL位点 QTL locus	株系 Line	RM3646	RM3513	RM2334	RM5891	2015江西南昌中稻季 2015 JXNC	2016海南三亚 2016 JXNC	2016江西南昌中稻季 2016 JXNC
qFLA-3	CH121	A	A	A	A	13.0	13.8	9.0
	CSSL8	B	B	B	B	51.2^**	36.0^**	17.7^**
	CSSL90	B	B	B	A	19.3^**	26.0^**	13.8^*
	CSSL115	A	B	B	B	21.6^**	35.3^**	25.9^**
	Koshihikari	B	B	B	B	40.0	35.2	30.3
QTL位点 QTL locus	株系 Line	标记Marker				株高表型值 PH of phenotypic value (cm)
QTL位点 QTL locus	株系 Line	RM3148	RM5423	RM5302	RM3530	2015江西南昌中稻季 2015 JXNC	2016海南三亚 2016 JXNC	2016江西南昌中稻季 2016 JXNC
PH-1-1	CH121	A	A	A	A	128.2	97.2	124.0
	CSSL21	A	B	B	B	105.4^**	78.7^**	103.1^**
	CSSL49	B	B	B	B	93.2^**	74.3^**	91.1^**
	CSSL161	B	B	B	A	112.4^**	77.0^**	103.2^**
	Koshihikari	B	B	B	B	107.2	86.0	92.7

染色体 Chr.	标记区间 Marker interval	性状 Trait	多效性QTL Pleiotropic QTLs	已克隆的基因 Cloning gene	参考文献 Reference
5	RM3345-RM7444	PH, FLW	qPH-5, qFLW-5	EUI1^[31]	—
5	RM3328-RM2998	FLA, TN	qFLA-5, qTN-5-2	—	Yang and Xing^[32]
6	RM3628-RM5371	FLW, FLA	qFLW-6, qFLA-6	OsSPX1^[33], LC3^[34]	Hong et al.^[35], Mei and Luo^[36]
10	RM484-RM591	FLW, FLA	qFLW-10, qFLA-10	—	Mei and Li^[37]

QTL mapping for plant architecture in rice based on chromosome segment substitution lines

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性状 Trait	环境 Environment	株高 Plant height	剑叶长 Flag leaf length	剑叶宽 Flag leaf width	剑叶夹角 Flag leaf angle
剑叶长 Flag leaf length	E1	0.305^**	—	—	—
	E2	0.177^*	—	—	—
	E3	0.207^**	—	—	—
剑叶宽 Flag leaf width	E1	0.115	0.308^**	—	—
	E2	0.135	0.401^**	—	—
	E3	0.156	0.243^**	—	—
剑叶夹角 Flag leaf angle	E1	0.238^**	0.124	0.146	—
	E2	0.209^**	0.087	0.038	—
	E3	0.315^**	0.172	0.153	—
分蘖数 Tiller numbers	E1	0.098	0.097	0.194	0.106
	E2	0.009	0.117	0.078	0.056
	E3	0.106	0.108	0.112	0.083

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