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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (7): 1391-1401.doi: 10.3724/SP.J.1006.2021.02054

• RESEARCH NOTES • Previous Articles     Next Articles

Mapping QTLs for yield-related traits using chromosome segment substitution lines of Dongxiang common wild rice (Oryza rufipogon Griff.) and Nipponbare (Oryza sativa L.)

LUO Lan1, LEI Li-Xia1, LIU Jin2,3, ZHANG Rui-Hua4, JIN Gui-Xiu4, CUI Di2, LI Mao-Mao3, MA Xiao-Ding2,*(), ZHAO Zheng-Wu1,*(), HAN Long-Zhi2,*()   

  1. 1Chongqing Normal University, Chongqing 401331, China
    2National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    3Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China
    4Linyi Academy of Agricultural Sciences, Linyi 276000, Shandong, China
  • Received:2020-08-13 Accepted:2020-11-13 Online:2021-07-12 Published:2020-12-29
  • Contact: MA Xiao-Ding,ZHAO Zheng-Wu,HAN Long-Zhi E-mail:maxiaoding@caas.cn;zhaozhengwu513@sina.com;hanlongzhi@caas.cn
  • Supported by:
    This study was supported by the National Key Research and Development Program of China(2016YFD0100101);This study was supported by the National Key Research and Development Program of China(2016YFD0100301);the National Natural Science Foundation of China(31671664);the CAAS Science and Technology Innovation Program, Protective Program of Crop Germplasm of China(2018NWB036-01);the CAAS Science and Technology Innovation Program, Protective Program of Crop Germplasm of China(2018NWB036-12-2);the National Infrastructure for Crop Germplasm Resources(NICGR2018-001)


In former study, we constructed a chromosome segment substitution lines (CSSLs) of Dongxiang common wild rice (Oryza rufipogon Griff.) in the background of Nipponbare (Oryza sativa L.). In this study, in order to investigate 11 yield-related traits, such as tillering number, grains per panicle and grain shapes, the CSSLs were planted in Beijing, Linyi and Nanchang. The results of quantitative trait loci (QTLs) for yield-related traits showed that a total of 68 QTLs were detected, including 4 QTLs for plant height, 5 QTLs for panicle length, 2 QTLs for tillering number, 7 QTLs for primary branch grain number, 8 QTLs for primary branch grain number, 8 QTLs for secondary branch grain number, 10 QTLs for secondary branch grain number, 6 QTLs for grains per panicle, 7 QTLs for 1000-grain weight, 8 QTLs for grain length and 3 QTLs for grain width. LOD score of the detected QTLs ranged from 2.50 to 12.66. The phenotypic variation explained by these QTLs ranged from 4.67% to 27.79%. There were 15 QTLs with a contribution rate more than 15%, 24 QTLs overlapped with the reported loci or gene position, 44 QTLs newly detected loci. In addition, 6 QTLs were stably detected at two sites, and 1 QTL (qTGW2) as a novel QTL was detected at three sites. Finally, the reliability of the three QTLs of qPH7, qPBPP8-2 and qGW10 was verified by BSA. Our results will be helpful for the subsequent cloning of yield-related trait genes and further analysis of their genetic basis and molecular regulation mechanism.

Key words: common wild rice (Oryza rufipogon Griff.), chromosome segment substitution lines (CSSLs), yield-related traits, QTL analysis

Fig. 1

Frequency distribution of 11 yield-related traits in the CSSLs The vertical axis of each figure represents the number of CSSL individuals. The blue, red and green rectangles represent the distribution of eleven yield-related traits in the CSSLs at the Beijing, Linyi and Nanchang locations, respectively. The blue, red, and green triangles represent the positions of the means of Nipponbare in Beijing, Linyi, and Nanchang, respectively."

Table 1

Statistics of yield-related traits of Nipponbare and the CSSLs in Beijing, Linyi and Nanchang"

北京Beijing 临沂Linyi 南昌Nanchang
CV (%)
CV (%)
CV (%)
株高 PH (cm) 96.30 108.02±10.07 9.33 87.75-133.75 94.64 103.34±10.95 10.59 80.30-134.82 95.00 100.31±9.76 9.73 70.20-130.00
穗长 PL (cm) 19.68 19.97±1.53 7.68 15.07-24.94 21.59 22.29±2.03 9.10 16.64-26.96 21.74 22.32±2.01 9.01 17.78-28.03
分蘖数 TN 13.00 14.30±2.14 14.96 8.80-20.00 17.21 16.24±2.89 17.78 9.00-24.17 13.60 11.83±1.58 13.38 7.80-15.40
一次枝梗数 PBPP 10.23 10.72±1.42 13.27 7.17-15.17 10.69 10.99±1.56 14.18 8.42-19.67 9.63 10.52±1.50 14.27 6.38-15.75
一次枝梗粒数PBGN 63.42 62.50±11.28 18.04 30.50-00.17 60.60 61.79±8.65 14.00 42.50-84.83 57.38 62.79±10.57 16.84 35.38-111.75
二次枝梗数 SBPP 15.17 12.65±4.25 33.61 5.08-29.75 21.38 20.85±7.13 34.20 6.42-63.00 17.13 18.60±5.21 27.99 9.00-43.75
二次枝梗粒数 SBGN 41.79 33.97±12.04 35.46 11.08-75.17 63.02 59.58±24.91 41.80 13.92-208.17 45.75 53.05±19.48 36.72 20.75-181.63
每穗粒数 GPP 105.21 96.46±16.51 17.11 57.58-156.67 123.63 121.37±30.55 25.17 62.67-288.25 103.13 115.84±24.04 20.75 77.50-258.63
千粒重 TGW (g) 23.81 23.21±1.92 8.28 17.95-28.30 26.58 25.81±1.76 6.82 19.71-30.01 25.68 24.51±2.03 8.26 16.39-28.87
粒长 GL (mm) 6.60 6.74±0.29 4.36 6.21-7.57 6.94 7.04±0.29 4.17 6.34-7.89 6.93 7.07±0.40 5.66 6.27-8.85
粒宽 GW (mm) 3.20 3.22±0.10 3.09 2.92-3.44 3.39 3.34±0.11 3.34 2.97-3.60 3.37 3.31±0.15 4.64 2.49-3.60

Fig. 2

Mapping locations of QTLs associated with yield-related traits detected in Beijing, Linyi, and Nanchang The definitions of the abbreviations for the symbols representing the QTLs are listed in Table 2. The position of each marker is based on the physical distance shown to the left of each chromosome, and the molecular marker is shown on the right. The green characters represent the names of the QTLs detected at two sites, and the blue characters represent the name of the QTL detected at three sites."

Table 2

QTL information of yield-related traits detected in the CSSLs in Beijing, Linyi, and Nanchang"

北京Beijing 临沂Linyi 南昌Nanchang
LOD value
PVE (%)
LOD value
PVE (%)
LOD value
PVE (%)
株高PH qPH2 2 DX-C2-13 5.87 20.74 6.06 2.63 10.90 4.17
qPH5 5 DX-C5-10 3.54 11.80 6.54
qPH7 7 Indel-c7-1 2.93 9.86 5.91
qPH8 8 DX-C8-12 2.80 8.99 5.52
穗长PL qPL1 1 01-009 3.06 9.17 0.61
qPL2-1 2 DX-C2-13 5.48 17.36 0.86
qPL2-2 2 02-067 3.26 12.87 1.06 3.37 11.88 1.07
qPL5 5 05-028 3.39 10.42 2.08
qPL10 10 DX-S10-1 2.66 8.06 0.94
分蘖数TN qTN1-1 1 DX-C1-2 3.03 10.96 -1.31
qTN1-2 1 010-060 3.89 13.32 -1.70
一次枝梗数PBPP qPBPP1-1 1 DX-C1-6 2.77 9.25 1.03
qPBPP1-2 1 DX-C1-10 2.68 8.34 2.33
qPBPP3 3 DX-C3-8 3.08 9.86 -0.69
qPBPP5 5 DX-C5-3 3.48 11.23 1.05
qPBPP8-1 8 DX-C8-11 4.23 6.79 -1.41
qPBPP8-2 8 DX-C8-12 7.98 13.99 1.36
一次枝梗数PBPP qPBPP8-3 8 DX-S8-14 5.43 18.54 1.23
一次枝梗粒数PBGN qPBGN1-1 1 DX-C1-3 3.00 9.85 4.05
qPBGN1-2 1 DX-C1-10 3.74 12.29 -17.18
qPBGN1-3 1 01-046 4.10 17.32 4.94
qPBGN3 3 DX-C3-28 2.61 8.18 -5.57
qPBGN8-1 8 DX-C8-11 4.70 7.45 -10.34
qPBGN8-2 8 DX-C8-12 9.27 16.35 10.25
qPBGN8-3 8 DX-S8-14 2.90 9.33 6.36
qPBGN11 11 DX-S11-10 3.11 9.86 6.12
二次枝梗数SBPP qSBPP1 1 DX-C1-7 3.26 8.86 3.50
qSBPP2-1 2 DX-C2-1 5.52 15.83 10.49
qSBPP2-2 2 DX-C2-2 9.46 23.99 7.76
qSBPP2-3 2 02-057 5.26 12.01 2.71
qSBPP4-1 4 DX-C4-12 3.68 8.10 -1.51
qSBPP4-2 4 S4-12-2 5.50 15.75 -5.73
qSBPP6-1 6 DX-C6-2 3.17 13.08 2.93
二次枝梗数SBPP qSBPP6-2 6 S6-9-1 3.09 6.71 2.27
二次枝梗粒数SBGN qSBGN2-1 2 DX-C2-1 12.66 27.79 56.08
qSBGN2-2 2 DX-C2-2 8.56 21.39 20.58
qSBGN2-3 2 02-057 4.33 9.79 6.87
qSBGN3-1 3 DX-S3-16 3.90 6.99 20.08
qSBGN3-2 3 DX-S3-17 4.03 15.34 17.26
qSBGN4-1 4 DX-C4-2 4.93 9.03 -15.61
qSBGN4-2 4 DX-C4-8 2.68 4.67 -11.22
qSBGN4-3 4 DX-C4-12 4.64 10.55 -4.84
qSBGN6-1 6 DX-C6-2 2.85 10.56 9.59
qSBGN6-2 6 S6-9-1 4.21 9.47 7.58
每穗粒数GPP qGPP1 1 01-046 4.39 13.92 14.35
qGPP2 2 DX-C2-1 4.02 14.43 37.54
qGPP4 4 S4-12-2 3.55 12.58 -19.21
qGPP6-1 6 06-013 3.26 13.45 20.53
qGPP6-2 6 06-037 5.14 17.43 14.15
qGPP11 11 DX-S11-10 3.08 9.96 10.70
千粒重TGW qTGW2 2 02-008 4.39 14.36 -2.79 3.26 9.19 -1.98 4.21 10.96 -2.56
qTGW3 3 DX-C3-1 3.27 10.64 1.31
qTGW8-1 8 DX-C8-3 4.07 11.68 -3.14
qTGW8-2 8 DX-S8-14 3.02 8.54 -1.12 3.07 7.86 -1.27
qTGW9-1 9 DX-C9-4 2.90 8.12 1.33
qTGW9-2 9 DX-C9-10 3.02 7.81 -2.15
qTGW12 12 S12-6-3 5.28 14.11 -2.38
粒长GL qGL1 1 DX-C1-18 5.29 16.65 0.42
qGL2 2 02-067 3.13 10.71 0.13 2.86 7.12 0.15
qGL3-1 3 DX-C3-8 3.89 13.44 0.17
qGL3-2 3 indel-c3-12 3.08 9.22 0.12
qGL3-3 3 DX-S3-17 5.75 15.14 0.37
qGL3-4 3 DX-C3-23 4.78 14.90 0.17 5.69 14.95 0.25
qGL4 4 S4-12-2 3.14 10.68 0.18
qGL10 10 DX-C10-8 3.55 8.88 0.20
粒宽GW qGW3 3 DX-S3-17 2.50 10.06 -0.11
qGW8 8 DX-C8-15 4.59 17.86 -0.07 3.53 14.49 -0.07
qGW10 10 DX-C10-10 2.56 10.33 -0.08

Fig. 3

Frequency distributions of plant height, primary branches per panicle and grain width in the secondary segregated populations and Manhattan plot of ?(SNP-index) A: frequency distribution of plant height in secondary segregated population related of qPH7; B: ?(SNP-index) graph of plant height extreme mixed pools; C: frequency distribution of primary branches per panicle in secondary segregated population related of qPBPP8-2; D: ?(SNP-index) graph of primary branches per panicle extreme mixed pools; E: frequency distribution of grain width in secondary segregated population related of qGW10; F: ?(SNP-index) graph of grain width extreme mixed pools. The blue and red triangles represent the positions of the means of Nipponbare and its related CSSL, respectively."

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