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Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (9): 1357-1366.doi: 10.3724/SP.J.1006.2018.01357

• RESEARCH PAPERS • Previous Articles     Next Articles

Fine Mapping and Genetic Effect Analysis of a Major QTL qPH3.2 Associated with Plant Height in Maize (Zea mays L.)

Zhong-Xiang LIU1,*(),Mei YANG2,*(),Peng-Cheng YIN2,Yu-Qian ZHOU1,Hai-Jun HE1,Fa-Zhan QIU2,*()   

  1. 1 Crops Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, Gansu, China
    2 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
  • Received:2018-01-08 Accepted:2018-04-11 Online:2018-09-10 Published:2018-05-14
  • Contact: Zhong-Xiang LIU,Mei YANG,Fa-Zhan QIU E-mail:lzhxiang@sina.com;1186322965@qq.com;qiufazhan@mail.hzau.edu.cn
  • Supported by:
    This study was supported by the National Natural Science Foundation of China (31760390)


Plant height is one of the most important factors affecting maize yield, which is determined by the number and the length of internode in maize. In this research, two advanced-backcross recombinant inbred lines (W1 and W2) with significant difference in plant height were used. They have the same number of internodes. We found that the different cell lengths of the internode in upper spike were the main reason causing the difference in plant height. The results of exogenous GA test showed that the QTL/genes controlling plant height were not included in GA pathway. The F2 and F2:3 populations derived from W1 and W2 were used to map the QTLs associated with plant height, showing that one major named qPH3.2 was commonly identified under three different environments in two years which was located on chromosome 3 between markers C42 and P17 with 20 Mb and could explain 22.22% of phenotypic variation. On the basis of the primary mapping results, QTL qPH3.2 was divided into two major QTLs qPH3.2.1 and qPH3.2.2 via recombinant exchange individuals and its self-cross progeny. Furthermore, we did the fine mapping work for qPH3.2.1 and qPH3.2.2 using substitution lines. The qPH3.2.1 was fine-mapped to the region of about 2 Mb between markers YH305 and Y72, and qPH3.2.2 was fine-mapped to the region of about 1.6 Mb between markers YH112 and Y150, which all showed the positive additive effects. The results of this research provide reliable genetic loci for the genetic improvement of plant height in maize, and a good foundation for cloning QTLs for plant height in the future.

Key words: plant height, genetic analysis, fine mapping, recombinant exchange, Zea mays L.

Fig. 1

Comparison of plant height (PH) between W1 and W2 A: The plant height (PH) between W1 and W2; B: The difference analysis of W1 and W2 in Wuhan of Hubei (15WH), Huanggang of Hubei (16HG), and Weifang of Shandong (16SD), respectively."

Fig. 2

Comparison of internode length between W1 and W2*, **, *** indicate significant difference at the 0.05, 0.01, and 0.001 probability levels, respectively. Error bars represent the SD of the mean (nW1=30, nW2=49). The internodes above the ear are labeled as 1, 2, 3, 4, 5, and 6. The internodes below the ear are labeled as -1, -2, -3, -4, -5, and -6. The tassel is labeled as T."

Fig. 3

Cell morphological observation of stemA and B are hand-cut longitudinal section of W1 and W2 (scale bar: 500 μm); C: the length of internode cells in W1 and W2."

Table 1

Plant height in exogenous GA treatment (cm)"

W1 149.33±3.39 161.83±6.99***
W2 143.78±3.60 156.41±6.49***

Fig. 4

Effect of exogenous GA on the plant height of W1 and W2A and B are the treatment and control of W1, respectively; C and D are the treatment and control of W2, respectively."

Table 2

Descriptive statistics of phenotype and normality test for plant height and ear height in F2:3 mapping population"

Average (cm)
Range (cm)
CV (%)
偏度Skewness 峰度
株高PH 2013WH 165.47 116.50-191.00 6.76 -0.379 0.527 0.19ns
2014HG 127.60 104.92-160.57 6.23 0.163 0.335 0.32ns
2014SD 162.71 128.41-192.81 5.44 0.042 0.337 0.92ns
穗位高EH 2014HG 42.77 22.96-65.79 12.50 0.319 0.844 0.85ns
2014SD 60.94 42.86-78.59 8.80 0.168 0.113 0.98ns

Table 3

Analysis of heritability for plant height and ear height of F2:3 families"

Genetic variance
Residual variance
Heritability (%)
2014HG 100.08*** 38.03 83.04
2014SD 157.54*** 46.49 87.14
2014HG 44.53*** 15.74 84.98
2014SD 55.84*** 22.10 80.84

Table 4

Putative major QTLs (qPH3.2) detected for maize plant height (PH, cm) across three environments"

Range (cM)
Flanking markers
Peak position (cM)
bin LOD 加性效应
D/A 基因作用
2013WH 59.09-81.46 bnlg602-SSR5 73.51 3.04-3.05 4.98 4.42 0.35 0.08 A 8.47
2014HG 59.09-81.46 bnlg602-SSR5 75.51 3.04-3.05 13.85 4.29 1.11 0.26 PD 22.22
2014SD 71.46-102.9 SSR4-umc2266 87.01 3.05-3.06 12.15 4.37 1.76 0.40 PD 14.21

Table 5

Single marker analysis of RHL (Y36)"

AA qPH3.2 aaW2
Size of population
Number of individual
C42 6E-04 154.2±4.2 20 147.1±4.8 24
Y45 4E-09 155.8±5.1 19 141.9±6.1 21
Y72 1E-09 155.3±6.0 23 141.5±6.3 25
YH196 4E-10 155.4±5.6 25 141.4±5.9 22
Y91 2E-06 152.7±5.7 22 141.7±6.6 20

Table 6

Single marker analysis of RHL (Y113)"

AA qPH3.2 aaW2
Size of population
Number of individual
YH55 0.03 152.1±3.5 12 149.0±2.8 13
YH61 0.03 153.5±4.4 24 150.8±4.4 26
P17 4E-05 155.1±3.2 14 147.7±4.0 13
YH112 0.04 155.5±3.2 14 151.8±3.2 12
YH121 3E-05 157.2±3.1 21 151.4±3.5 22

Fig. 5

Fine mapping of qPH3.2.1A: the pre-mapping result of qPH3.2 located on red bar, green and blue bars indicate the remapping results of qPH3.2.1 and qPH3.2.2, respectively; B: the mapping results of qPH3.2.1 using N1, N2, and N3 three overlapping lines; C: the fine mapping results of qPH3.2.1. N indicates the number of the evaluated individuals in each line. AA means the allele derived from qPH3.2.1; aa indicates the allele derived from genetic background W2."

Fig. 6

Fine mapping of qPH3.2.2 A: the pre-mapping result of qPH3.2 located on red bar, green and blue bars indicate the remapping results of qPH3.2.1 and qPH3.2.2, respectively; B: the mapping results of qPH3.2.2 using N4 and N5 overlapping lines; C: the fine mapping results of qPH3.2.2; N indicates the number of the evaluated individuals in each line. AA means the allele derived from qPH3.2.2; aa indicates the allele derived from genetic background W2."

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