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Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (10): 1477-1484.doi: 10.3724/SP.J.1006.2018.01477


Identification of Rice Chromosome Segment Substitution Line Z1377 with Increased Plant Height and QTL Mapping for Agronomic Important Traits

Guo-Qing CUI1,Shi-Ming WANG1,Fu-Ying MA1,Hui WANG1,Chao-Zhong XIANG2,Yun-Feng LI1,Guang-Hua HE1,Chang-Wei ZHANG1,Zheng-Lin YANG1,Ying-Hua LING1,Fang-Ming ZHAO1,*()   

  1. 1 Rice Research Institute, Southwest University / Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
    2 Center of Agricultural Serve at Longkong Town, Fengdu County, Chongqing 408200, China
  • Received:2018-01-05 Accepted:2018-06-12 Online:2018-10-10 Published:2018-06-20
  • 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);the Project of Chongqing Science & Technology Commission(CSTC, 2016shms-ztzx0017);the Fundamental Research Funds for the Central Universities(XDJK2017A004)


Plant height is an important agronomic trait in rice, usually relating to yield-related traits. Here, a novel rice chromosome segment substitution line Z1377 with increased plant height was identified from recipient Nipponbare and donor Jinhui 35 through selection of both phenotype and molecular marker. Z1377 carried 18 substitution segments with average substitution length of 2.95 Mb. Compared with Nipponbare, Z1377 had significantly increased plant height, length of the 1st, 2nd, 3rd, and 4th internode, panicle length, number of primary and secondary branches and grain length, and decreased grain width, number of panicles per plant and seed setting ratio. However, the seed setting ratio was still 86.75%. Furthermore, F2 population from crosses between Nipponbare and Z1377 was used to map QTLs for plant height and other important agronomic traits. A total of 16 QTLs were detected, of which eight had been reported with the cloned genes such as GW2, EUI1, ZFP185, and the other eight were still not reported, such as qPH3. The plant height of Z1377 was mainly controlled by a major QTL (qPH3) with the explained phenotypic variance of 28.59% and a minor QTL (qPH5). Moreover, the high and dwarf plants basically displayed a bimodal distribution in the F2 population, and fitted to 3:1 segregation ratio by Chi-square test, indicating that high plant is dominant to dwarf plants and mainly conferred by qPH3. These results lay a foundation for fine mapping and cloning qPH3, meanwhile, also provide good bases for developing excellent chromosome segment substitution lines with moderate height plant carrying 2-3 substitution segments to be used in breeding.

Key words: rice, chromosome segment substitution lines, plant height, yield-related traits, QTL mapping

Fig. 1

Substitution segments of Z1377 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."

Table 1

Statistical parameters of different traits in Nipponbare, Z1377, and the F2 population"

Mean±SD (parents)
F2 群体
F2 population
Z1377 平均值±标准差
株高Plant height (cm) 89.68±2.65** 171.39±3.87** 130.07±21.39 81.60-169.50 -0.62 -0.58
有效穗数Panicle number 13.65±3.30** 5.20±1.17** 8.70±4.17 1.00-27.00 1.24 3.97
倒一节Length of the first internode (cm) 39.02±2.16** 56.02±1.81** 45.69±6.23 32.00-59.80 -0.17 -0.65
倒二节Length of the second internode (cm) 18.32±1.37** 26.58±1.27** 22.45±4.71 10.50-32.30 -0.36 -0.03
倒三节Length of the third internode (cm) 10.19±1.67** 22.45±1.64** 15.96±4.60 3.80-26.20 -0.21 -0.12
倒四节Length of the fourth internode (cm) 1.84±0.75** 17.46±1.05** 11.96±3.54 1.80-19.50 -0.89 1.05
倒五节Length of the fifth internode (cm) 11.08±2.78 7.03±3.20 1.70-13.70 0.20 -0.88
倒六节Length of the sixth internode (cm) 4.00±1.29 5.21±3.00 1.30-10.10 0.15 -1.52
穗长Panicle length (cm) 20.09±2.17** 33.49±3.17** 27.86±5.39 18.00-42.77 0.22 -0.32
一次枝梗数Number of primary branch 8.43±1.73** 15.33±1.91** 12.12±2.63 7.21-18.10 -0.03 -0.56
二次枝梗数Number of secondary branch 26.47±7.51** 71.69±22.46** 49.85±17.90 21.13-98.90 0.32 -0.29
粒长Grain length (mm) 7.01±0.10** 10.02±0.16** 8.45±0.75 7.00-9.87 -0.35 -0.85
粒宽Grain width (mm) 3.42±0.07** 2.92±0.08** 3.14±0.25 2.50-3.60 -0.41 -0.62
实粒数Grains per panicle 96.99±8.62** 233.06±55.96** 91.69±53.23 2.00-224.00 0.28 -0.44
总粒数Spikelets per panicle 103.04±8.82** 272.65±69.96** 187.18±71.76 42.00-370.00 0.39 -0.25
结实率Seed setting ratio (%) 94.13±0.01** 86.75±2.97** 0.54±0.31 0.02-0.95 -0.29 -1.42
千粒重1000-grain weight (g) 25.60±0.56 25.37±0.66 24.61±3.21 16.60-31.40 -0.26 -0.44
单株产量Yield per plant (g) 33.82±7.15 30.77±7.43 22.42±17.71 0.27-82.4 1.16 1.62

Fig. 2

Phenotype of Nipponbare and Z1377"

Fig. 3

Distribution of plant height in F2 population from the cross between Nipponbare and Z1377"

Table 2

QTLs for agronomic important traits in rice"

QTL 染色体
Linked marker
Estimated effect
Var. (%)
株高Plant height (cm) qPH3 3 RM14412 7.52 28.59 0.0008
株高Plant height (cm) qPH5 5 RM3321 4.65 10.96 0.0305
倒一节Length of the first internode (cm) qLFI2 2 RM6378 1.15 3.65 0.0474
倒三节Length of the third internode (cm) qLTI4 4 RM7187 1.19 8.50 0.0367
倒三节长Length of the third internode (cm) qLTI6-1 6 RM3183 1.80 19.41 0.0031
倒三节长Length of the third internode (cm) qLTI6-2 6 RM103 1.13 7.59 0.0484
倒四节长Length of the fourth internode (cm) qLFOI3 3 RM14412 1.31 16.44 0.0043
穗长Panicle length (cm) qPL2 2 RM6378 1.30 11.00 0.0124
一次枝梗数Number of primary branch qNPB2 2 RM6378 0.54 8.09 0.0188
二次枝梗数Number of secondary branch qNSB2 2 RM6378 4.57 11.09 0.0082
粒长Grain length (mm) qGL3 3 RM14412 0.18 12.38 0.0220
粒长Grain width (mm) qGW2 2 RM6378 -0.06 7.43 0.0210
实粒数Grains per panicle qGPP6 6 RM3183 38.86 0.50 0.0062
实粒数Grains per panicle qGPP9 9 RM7048 90.26 2.71 0.0025
总粒数Spikelets per panicle qSPP2 2 RM6378 14.68 5.82 0.0433
有效穗数Panicle number qPN7 7 RM5481 -2.53 3.90 0.0293
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