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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (5): 1141-1151.doi: 10.3724/SP.J.1006.2022.12024


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

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*()   

  1. Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education / College of Agronomy, Jiangxi Agricultural University / Research Center of Super Rice, Engineering and Technology, Nanchang 330045, Jiangxi, China
  • Received:2021-04-07 Accepted:2021-09-09 Online:2022-05-12 Published:2021-10-15
  • Contact: SUN Xiao-Tang,ZHU Chang-Lan E-mail:wxl0vip@163.com;45101034@qq.com;zhuchanglan@163.com
  • Supported by:
    National Natural Science Foundation of China(31860373);“5511” Superior Science and Technology Innovation Team Project of Jiangxi Province, China(20165BCB19005)


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

Table 1

Planting environments of Changhui 121, Koshihikari, and 208 CSSLs"

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)
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)
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)
May to October in 2016

Table 2

Methods of measuring plant architecture traits"

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

Fig. 1

Plant architecture traits of Changhui 121 and Koshihikari"

Table 3

Plant architecture traits of Changhui 121, Koshihikari, and 208 CSSLs"

亲本Parents 208个染色体片段置换系 208 CSSLs
Changhui 121
(mean ± SD)
(mean ± SD)
Mean ± SD 范围
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
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
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
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
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

Fig. 2

Plant architecture distribution of 208 CSSLs 2015 JXNC: middle-season rice in 2015 in Nanchang, Jiangxi; 2016 HNSY: in 2016 in Sanya, Hainan; 2016 JXNC: middle-season rice in 2016 in Nanchang, Jiangxi."

Table 4

Correlation coefficient of plant architecture traits"

Plant height
Flag leaf length
Flag leaf width
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

Table 5

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

QTL 染色体Chr. 标记区间
Marker interval
LOD score
Phenotypic variation
explained (%)
Additive effects (Add)
E1 E2 E3 E1 E2 E3 E1 E2 E3
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
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
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
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
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

Fig. 3

Chromosomal distribution of the QTL for plant architecture traits detected in 208 CSSLs of Changhui 121/Koshihikari PH: plant height; FLL: flag leaf length; FLW: flag leaf width; FLA: flag leaf angle; TN: tiller numbers. 2015 JXNC: middle-season rice in 2015 in Nanchang, Jiangxi; 2016 SYHN: in 2016 in Sanya, Hainan; 2016 JXNC: middle-season rice in 2016 in Nanchang, Jiangxi."

Table 6

Plant architecture traits of Changhui 121, Koshihikari, and target CSSLs in three environments"

QTL locus
标记Marker 剑叶角表型值 FLA of phenotypic value (o)
RM3646 RM3513 RM2334 RM5891 2015江西南昌中稻季
2015 JXNC
2016 JXNC
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 locus
标记Marker 株高表型值 PH of phenotypic value (cm)
RM3148 RM5423 RM5302 RM3530 2015江西南昌中稻季
2015 JXNC
2016 JXNC
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

Table 7

Regional analysis of the pleiotropic QTL"

Marker interval
Pleiotropic QTLs
Cloning gene
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]
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