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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (3): 451-461.doi: 10.3724/SP.J.1006.2021.92002


Identification of an excellent rice chromosome segment substitution line Z746 and QTL mapping and verification of important agronomic traits

SHEN Wen-Qiang(), ZHAO Bing-Bing(), YU Guo-Ling, LI Feng-Fei, ZHU Xiao-Yan, MA Fu-Ying, LI Yun-Feng, HE Guang-Hua, ZHAO Fang-Ming*()   

  1. Rice Research Institute, Southwest University / Academy of Agricultural Sciences, Southwest University / Transgenic Plants and Safety Control, Chongqing Key Laboratory, Chongqing 400715, China
  • Received:2019-01-09 Accepted:2020-10-14 Online:2021-03-12 Published:2020-11-02
  • Contact: ZHAO Fang-Ming E-mail:412588538@qq.com;977276044@qq.com;zhaofangming2004@163.com
  • Supported by:
    National Key Research and Development Program of China(2017YFD0100202);Project of Chongqing Science & Technology Commission Grants(cstc2016shms-ztzx0017);Project of Chongqing Science & Technology Commission Grants(CSTCCXLJRC201713);Southwest University Innovation Team Project(XDJK2017A004)


The important agronomic traits, such as grain type, plant height, and panicle composition, are closely related to rice yield, and their gene inheritance is complex. Chromosome segment substitution lines (CSSLs) are useful materials for studying these complex traits. An excellent CSSL, Z746, containing seven substitution segments and with an average substitution length of 3.99 Mb, was identified from Nipponbare as a recipient and ‘Xihui 18’ as a donor parent. There were significant differences in plant height, panicle composition and grain size between Z746 and Nipponbare. Furthermore, a total of 36 quantitative trait loci (QTL) were detected on chromosomes 2, 3, 4, 6, and 11 in the secondary F2 population constructed by hybridization between Nipponbare and Z746. Five of them may be alleles of the cloned genes, such as qPH3-1, and eight can be detected by multiple times, indicating that these were genetically stable major QTLs. The grain length in Z746 was mainly controlled by four QTLs (qGL3, qGL4, qGL2, and qGL6), and the phenotypic variation of qGL3 and qGL4 for grain length was 60.28% and 27.47%, respectively. Plant height was controlled by five QTLs, panicle length by four QTLs, grain number per panicle by two QTLs, and the 1000-grain weight by two QTLs. Eight single segment substitution lines (SSSLs) were developed in F3 population by molecular marker-assisted selection (MAS), and relevant QTLs verification was conducted in F4. Finally, 24 QTLs were detected by 8 SSSLs and the repeat detection rate was 66.7%, indicating that these QTLs were genetically stable. These results provide a good foundation for further research on genetic mechanisms of the target QTLs and molecular design breeding.

Key words: rice (Oryza sativa L.), chromosome segment substitution line, grain length, plant height, spike composition, QTL mapping

Fig. 1

Substitution segments and detected QTL of chromosome segment substition line Z746 Physical distances (Mb) and mapped QTL are marked at the left of each chromosome; markers substitution interval squared by frame, and substitution length (black arrow direction) are displayed at the right of each chromosome."

Fig. 2

Plant type, panicle type, and grain of Nipponbare and Z746 at maturity stage A: plant type of Nipponbare (left) and Z746 (right). Scale bar, 10 cm; B: main panicle of Nipponbare (left) and Z746 (right). Scale bar, 5 cm; C, D: grains of Nipponbare (C) and Z746 (D). Scale bar, 5 mm; E, F: brown grains of Nipponbare (E) and Z746 (F). Scale bar, 5 mm."

Table 1

Statistical parameters of different traits in Nipponbare, Z746, and the F2 population"

Mean±SD (parents)
F2 population
Z746 平均值±标准差
株高Plant height (cm) 87.93±5.32 96.70±2.11** 89.61±8.43 78.00-124.00 2.16 5.33
有效穗数Panicle number per panicle 18.40±5.55 17.70±5.42 14.41±4.56 6.00-28.00 0.67 0.23
穗长Panicle length (cm) 19.68±0.88 20.64±0.62 19.38±1.70 15.86-29.25 1.93 6.44
一次枝梗数Number of primary branch 7.42±0.43 8.05±0.67* 8.36±1.49 6.67-14.47 2.75 7.62
二次枝梗数Number of secondary branch 14.62±1.67 22.99±2.42** 14.59±4.38 7.17-34.73 2.20 6.71
粒长Grain length (mm) 7.40±0.08 8.93±0.19** 7.71±0.57 7.03-9.42 1.16 0.19
粒宽Grain width (mm) 3.44±0.06 2.85±0.11** 3.26±0.56 2.63-3.48 10.85 132.05
长宽比Ratio of length to width 2.15±0.03 3.13±0.15** 2.40±0.34 2.11-3.53 0.56 4.21
结实率Seed-setting rate (%) 91.79±2.02 89.01±2.34* 87.00±11.02 30.00-96.05 -3.25 11.54
每穗总粒数Spikelets per panicle 97.70±23.84 122.66±10.99* 91.75±18.10 62.56-182.67 2.24 7.62
每穗实粒数Grains per panicle 89.68±22.56 109.23±10.58* 78.77±15.17 26.11-166.73 0.90 7.86
千粒重1000-grain weight (g) 25.41±0.91 26.09±0.71 25.34±1.58 18.33-30.10 0.04 2.15
单株产量Yield per plant (g) 38.44±10.23 44.42±15.42 28.87±11.46 9.91-64.25 0.89 0.36

Table 2

QTLs for agronomic important traits in rice"

QTL 染色体
Linked marker
Var. (%)
Plant height (cm)
qPH2-1 2 RM1075 -5.06 15.06 < 0.0001
qPH2-2 2 RM6378 4.11 13.70 0.0037
qPH3-1 3 RM14389 3.17 2.71 0.0108
qPH3-2 3 RM6266 1.92 5.06 0.0258
qPH4 4 RM1155 4.71 16.67 < 0.0001
qPH6-1 6 RM7412 3.01 13.59 0.0009
qPH6-2 6 RM103 -4.13 26.98 0.0075
Panicle length (cm)
qPL2 2 RM1075 -0.99 13.12 < 0.0001
qPL3 3 RM6266 0.39 4.85 0.0346
qPL4 4 RM1155 0.49 4.16 0.0276
qPL6 6 RM7412 0.64 13.81 0.0011
Number of primary branch
qNPB2-1 2 RM1075 -0.49 4.19 0.0198
qNPB2-2 2 RM6378 0.70 11.59 0.0074
qNPB2-3 2 RM13262 -0.47 5.43 0.0449
qNPB3 3 RM14389 0.46 5.92 0.0424
qNPB4 4 RM1155 1.10 27.43 < 0.0001
qNPB6-1 6 RM7412 0.57 14.32 0.0007
qNPB6-2 6 RM103 -0.87 35.15 0.0023
qNPB6-3 6 RM494 0.63 18.95 0.0165
Number of secondary branch
qNSB2-1 2 RM1075 -1.42 3.35 0.0366
qNSB2-2 2 RM6378 1.76 7.10 0.0284
qNSB4 4 RM1155 2.01 8.73 0.0015
qNSB6 6 RM7412 1.80 13.81 0.0011
length (mm)
qGL2 2 RM1075 -0.11 3.63 0.0302
qGL3 3 RM6266 0.34 60.28 < 0.0001
qGL4 4 RM1155 0.26 27.47 < 0.0001
qGL6 6 RM7412 0.08 4.77 0.0467
Ratio of length
to width
qRLW2 2 RM13262 0.16 12.97 0.0017
qRLW3 3 RM6266 0.13 14.23 0.0004
qRLW4 4 RM1155 0.15 10.41 0.0005
qRLW6 6 RM7412 0.08 5.30 0.0414
Seed-setting rate (%)
qSSR4 4 RM1155 -0.07 17.33 < 0.0001
Spikelets per panicle
qSP4 4 RM1155 6.24 4.73 0.0122
qSP6 6 RM7412 4.33 4.51 0.0481
1000-grain weight (g)
qGWT2 2 RM13262 -0.88 14.82 0.0009
qGWT3 3 RM6266 1.13 40.50 < 0.0001

Table 3

Additive effect analysis of QTLs in SSSLs"

SSSL code
代换片段 b
Substitution segment b
Length (Mb)
QTL 均值±标准差
N a 株高
Plant height (cm)
S1 RM2770--RM6378--RM1075 1.04 2 qPH2-1 101.06±1.65 5.23 2.86E-06
S2 RM6378--RM1075--RM5699 2.58 2 qPH2-2 128.12±3.46 18.76 2.58E-13
S3 RM132--RM14389--RM175 7.34 3 qPH3-1 101.15±1.54 5.28 2.31E-06
S4 RM5928--RM6266--RM157 1.43 3 qPH3-2 110.65±3.48 10.02 4.55E-08
S5 RM5688--RM1155--RM17078 2.95 4 qPH4 108.66±3.19 9.03 1.40E-08
S6 RM7412--RM103--RM494 0.90 6 qPH6-1 109.31±2.00 9.36 1.35E-09
S7 RM103--RM494--long arm end 0.20 6 qPH6-2 104.95±1.73 9.36 4.67E-08
S8 RM5371--RM7412-RM103-RM494--long arm end 2.57 6 qPH6 106.20±2.29 7.80 2.93E-08
N a 穗长
Panicle length (cm)
S1 RM2770--RM6378--RM1075 1.04 2 qPL2 22.70±1.29 1.84 8.53E-07
S4 RM5928--RM6266--RM157 1.43 3 qPL3 24.60±2.19 2.79 1.69E-05
S5 RM5688--RM1155--RM17078 2.95 4 qPL4 21.64±1.62 1.31 0.001
S7 RM103--RM494--long arm end 0.20 6 qPL6 26.02±1.92 3.50 4.63E-08
N a 一次枝梗数
Number of primary branch
S2 RM6378--RM1075--RM5699 2.58 2 qNPB2 12.80±1.60 1.67 1.57E-05
S8 RM5371--RM7412-RM103-RM494--long arm end 2.57 6 qNPB6 10.27±0.96 0.40 0.02
N a 二次枝梗数
Number of secondary branch
S1 RM2770--RM6378--RM1075 1.04 2 qNSB2-1 18.82±2.75 1.40 0.03
S2 RM6378--RM1075--RM5699 2.58 2 qNSB2-2 25.78±2.97 4.88 1.38E-06
N a 粒长
Grain length (mm)
S4 RM5928--RM6266--RM157 1.43 3 qGL3 7.71±0.23 0.23 0.0002
S7 RM103--RM494--long arm end 0.20 6 qGL 6 7.55±0.21 0.15 0.002
N a 长宽比
Ratio of length to width
S4 RM5928--RM6266--RM157 1.43 3 qRLW3 2.31±0.07 0.07 0.0003
S5 RM5688--RM1155--RM17078 2.95 4 qRLW4 2.33±0.11 0.08 0.0007
S7 RM103--RM494--long arm end 0.20 6 qRLW6 2.50±0.12 0.16 9.94E-07
N a 结实率
Seed-setting rate (%)
S5 RM5688--RM1155--RM119 2.95 4 qSSR4 81.24±4.32 -5.75 0.0002
N a 每穗总粒数
Spikelets per panicle
S5 RM5688--RM1155--RM17078 2.95 4 qSP4 104.00±9.37 6.12 0.006
S7 RM103--RM494--long arm end 0.20 6 qSP6 117.6±10.12 12.92 1.30E-05
N a 千粒重
1000-grain weight (g)
S4 RM5928--RM6266--RM157 1.43 3 qGWT3 27.56±0.47 1.75 7.11E-10
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