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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (01): 140-146.doi: 10.3724/SP.J.1006.2020.92022

• RESEARCH NOTES • Previous Articles     Next Articles

Identification of rice chromosome segment substitution Line Z747 with increased grain number and QTL mapping for related traits

WANG Da-Chuan,WANG Hui,MA Fu-Ying,DU Jie,ZHANG Jia-Yu,XU Guang-Yi,HE Guang-Hua,LI Yun-Feng,LING Ying-Hua,ZHAO Fang-Ming()   

  1. Rice Research Institute, Southwest University/Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
  • Received:2019-04-15 Accepted:2019-08-09 Online:2020-01-12 Published:2019-09-11
  • Contact: Fang-Ming ZHAO E-mail:zhaofangming2004@163.com
  • Supported by:
    This study was supported by the National Key Research and Development Program of China(2017YFD0100202);Project of Chongqing Science & Technology Commission(CSTC, 2016shms-ztzx0017);Fundamental Research Funds for the Central Universities(XDJK2017A004)


Increasing grain number per panicle is important for rice breeding for high yield. Its inheritance is very complex and controlled by many genes. Chromosome segment substitution lines can dissect complex traits controlled by many genes, and thus are ideal genetic research materials. Here, an excellent rice chromosome segment substitution line Z747 with increased grain number was identified from recipient Nipponbare and donor Xihui 18 through advanced backcrossing and inbreeding combined SSR marker-assisted selection. Z747 carried fifteen substitution segments with 4.49 Mb of average length. Compared with Nipponbare, Z747 had significantly increased spikelet number per panicle, number of primary branches, number of secondary branches, panicle length and grain length, and decreased grain width and seed setting rate. However, the seed setting rate in Z747 was still up to 81%. Furthermore, secondary F2 population from crosses between Nipponbare and Z747 was used to map QTL for related traits. A total of 46 QTLs distributed on chromosomes 1, 2, 3, 5, 6, 9, 11, and 12 were detected. Among them, 12 QTLs such as qGPP12, qPH-3-1, and qPH-3-2 etc. might be alleles of cloned genes, and the remaining 34 QTLs such as qSPP9 etc. might not be identified in the past. The spikelet number per panicle of Z747 was mainly controlled by two QTLs (qSPP3 and qSPP5) with effects of increasing spikelet number and one (qSPP9) with decreasing effects. These results are important for fine mapping and cloning of major QTL, and developing single-segment substitution lines carrying favorable QTLs.

Key words: rice, chromosome segment substitution lines, grain number, QTL mapping

Fig. 1

Substitution segments and detected QTL of Z747 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. PH: plant height; PL: panicle length; NPB: number of primary branches; NSB: number of secondary branches; GPP: grain number per panicle; SPP: spikelet number per panicle; SSR: seed setting rate; GL: grain length; GW: grain width; RLW: rate of length to width; GWT: 1000-grains weight. Partial QTL noted superscript [20]-[30] indicate that these QTLs are possible alleles with the cloned genes. [20]: OsRLCK102; [21]: HTD2; [22]: pbr2; [23]: JMJ703; [24]: ND1; [25]: DFO1; [26]: OsMCA1, [27]: OsFRDL1; [28]: PTB1; [29]: DCM1; [30]: OsVPE3."

Fig. 2

Phenotype of Nipponbare and Z747"

Table 1

Statistical parameters of different traits in Nipponbare, Z747, and the F2 population"

Mean±SD (parents)
F2 population
Z747 平均值±标准差
株高 Plant height (cm) 88.1±3.4 91.8±6.9 91.9±8.2 68.0-130.8 0.39 0.31
穗长Panicle length (cm) 19.7±1.2 23.3±1.3** 19.3±1.6 14.8-27.3 -0.18 0.57
有效穗数Panicle number 19.3±5.1 15.5±6.4 15.6±5.5 3.0-36.0 0.40 -0.03
一次枝梗数Number of primary branch 7.4±0.5 12.2±1.3** 8.5±1.1 6.9-13.4 -0.15 0.27
二次枝梗数Number of secondary branch 14.3±1.7 40.5±1.2** 15.1±4.3 7.4-45.6 0.03 0.71
每穗总粒数Spikelet number per panicle 110.7±16.4 173.0±49.6** 94.3±19.9 21.9-221.7 -0.19 0.39
每穗实粒数Grain number per panicle 101.4±16.5 139.8±41.2 79.4±15.6 10.1-142.5 -0.23 0.65
结实率Seed setting rate (%) 91.0±2.0 81.0±0.7** 85.1±12.9 10.9-96.3 -2.17 10.44
粒长Grain length (mm) 7.17±0.24 7.93±0.04** 7.45±0.47 6.61-10.05 0.36 1.81
粒宽Grain width (mm) 3.40±0.08 3.23±0.05* 3.34±0.13 2.38-3.52 -0.38 0.26
千粒重1000-grain weight (g) 24.6±1.6 25.5±0.7 25.5±1.8 21.0-32.3 0.28 1.27
单株产量Yield per plant (g) 38.6±9.8 40.9±5.3 31.7±12.4 2.4-72.5 0.45 0.20

Table 2

QTL for rice agronomically important traits detected in Z747"

QTL 染色体
Linked marker
Additive effect
Var. (%)
Possible alleles
株高 qPH-3-1 3 RM5474 -7.79 9.45 0.0004 OsRLCK102[20]
Plant height qPH-3-2 3 RM3417 5.74 5.15 0.0003 HTD2 [21]
qPH-3-3 3 RM6266 5.03 10.30 <0.0001
qPH5 5 RM5874 13.67 27.54 0.0003
qPH11 11 RM7120 5.31 4.39 0.0090
穗长 qPL3 3 RM6266 0.51 2.70 0.0020
Panicle length qPL11 11 RM7120 1.28 6.61 0.0012
一次枝梗数 qNPB2 2 RM1385 0.59 6.07 0.0002 Pbr2[22]
Number of primary branch qNPB3 3 RM3766 0.83 7.45 0.0012
qNPB9 9 RM24537 1.79 9.96 <0.0001
qNPB12 12 RM247 -1.07 8.14 0.0049
二次枝梗数 qNSB2 2 RM6378 2.33 1.65 0.0004
Number of secondary branch qNSB3 3 RM3766 3.86 7.83 0.0005
qNSB5 5 RM18067 3.59 5.92 0.0036 JMJ703[23]
qNSB6 6 RM494 -2.46 7.10 0.0004
qNSB-9-1 9 RM7048 -7.39 20.71 0.0007
qNSB-9-2 9 RM24537 6.29 6.05 0.0001
实粒数 qGPP2 2 RM1385 8.89 4.53 0.0014
Grain number per panicle qGPP-9-1 9 RM7048 -28.08 19.83 0.0008
qGPP-9-2 9 RM24537 18.49 3.66 0.0038
qGPP12 12 RM3331 -18.64 8.21 <0.0001 ND1[24]
总粒数 qSPP3 3 RM3766 20.73 9.66 0.0002
Spikelet number per panicle qSPP5 5 RM18067 20.07 7.90 0.0015
qSPP9 9 RM7048 -29.51 14.15 0.0044
结实率 qSSR1 1 RM259 -24.38 11.97 0.0001 DFO1[25]
Seed setting rate qSSR2 2 RM1385 4.65 1.19 0.0069
qSSR-3-1 3 RM5474 18.66 9.82 <0.0001 OsMCA1[26]
qSSR-3-2 3 RM3766 -10.38 3.58 0.0014 OsFRDL1[27]
qSSR5 5 RM5874 42.72 46.67 <0.0001 PTB1[28]
qSSR6 6 RM5371 -17.59 6.48 0.0013 DCM1[29]
qSSR-9-1 9 RM7048 -20.74 10.33 0.0004
qSSR-9-2 9 RM24537 23.28 5.24 <0.0001
qSSR12 12 RM3331 -14.58 4.80 <0.0001
粒长 qGL3 3 RM6266 0.40 63.73 <0.0001
Grain length qGL5 5 RM18067 0.24 9.29 0.0007
qGL12 12 RM3331 0.16 3.21 0.0047
粒宽 qGW2 2 RM1385 -0.07 5.59 0.0080 OsVPE3[30]
Grain width qGW5 5 RM18148 -0.08 6.05 0.0029
长宽比 qRLW2 2 RM1385 0.08 5.35 0.0004
Rate of length to width qRLW-3-1 3 RM3766 0.10 5.42 0.0047
qRLW-3-2 3 RM6266 0.13 19.74 <0.0001
qRLW5 5 RM18148 0.13 10.17 0.0002
qRLW6 6 RM494 -0.09 10.31 <0.0001
qRLW12 12 RM3331 0.15 7.70 <0.0001
千粒重 qGWT2 2 RM1385 -0.80 4.01 0.0048 OsVPE3[30]
1000-kernel weight qGWT3 3 RM6266 1.82 28.67 <0.0001
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