, 215:27 | Cite as

Systematic identification and characterization of candidate genes for the regulation of plant height in maize

  • Hengsheng Wang
  • Xingen Zhang
  • Fangxiu Hu
  • Mingli Liu
  • Yang Zhao
  • Yan Wang
  • Longjiang GuEmail author
  • Qing MaEmail author


Plant height, which is an important trait for maize breeding because of its relationship with lodging resistance and yield production, is reportedly determined by multiple qualitative and quantitative genes. However, only a few plant height-related genes have been cloned or characterized in maize. In the present study, previously characterized genes involved in the regulation of plant height were collected from maize, Arabidopsis thaliana, Oryza sativa and sorghum. A collinearity analysis was subsequently performed to identify homologs in the maize genome. A total of 82 new homologous genes were identified as possibly influencing plant height in maize. Interestingly, most of the candidates were involved in the synthesis or signaling of various phytohormones, particularly gibberellin (GA), implying that phytohormones are critical for regulating plant height. Moreover, in a comprehensive analysis of the expression patterns for these genes, substantial variability was observed across tissues and developmental stages, and each tissue exhibited diverse gene expression patterns. An RNA-sequencing analysis of tall and dwarf inbred lines revealed that 15 candidates were differentially expressed, among which six (40.0%) genes were functionally characterized as affecting various phytohormone pathways. Furthermore, the expression of candidate genes potentially involved in the GA signaling pathway was strongly induced by an exogenous GA treatment. This increased expression may have contributed to the observed faster growth rate of the GA-treated plants compared with the mock controls. Our results indicate that the spatial or temporal expression of genes involved in various phytohormone pathways may be associated with the regulation of plant height in maize.


Plant height Maize Collinearity analysis Phytohormone RNA-seq analysis 



This study was supported by Grants from the National Natural Science Foundation of China (91435110, 31540042, 31701436) and the National Program on Key Basic Research Project (973 Program, No. 2014CB138204). We are grateful to Professor Beijiu Cheng for his helpful discussions and dedicated technical assistance.

Authors’ contributions

Longjiang Gu and Yang Zhao designed the research, collected the samples, and wrote the paper; Hengsheng Wang, Xingen Zhang and Mingli Liu, performed the experiments, analyzed the data, and drafted the manuscript; Fangxiu Hu and Yan Wang designed qRT-PCR primers and finished the qRT-PCR experiment, Qing Ma provided some constructive suggestions to clarify the questions raised by the reviewers and also made careful modifications on the original manuscript. All authors have read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

NGS accession numbers

The data generated in this study have been deposited in the NCBI Gene Expression Omnibus database ( and are accessible through accession number GSE116366.

Supplementary material

10681_2019_2345_MOESM1_ESM.tif (5.9 mb)
Fig. S1 Distribution of Ka and Ks values of collinear genes among species. (a), (b), (c), and (h) represent the collinear genes of maize and Arabidopsis thaliana, maize and maize, maize and Sorghum bicolor, and maize and rice, respectively. (d), (e), and (g) represent the collinear genes of rice and A. thaliana, rice and rice, and rice and S. bicolor. (f) and (i) represent the collinear genes of A. thaliana and S. bicolor, and A. thaliana and A. thaliana. Collinear gene pairs with a Ka/Ks ratio > 1 are above the black line, and pairs with a Ka/Ks ratio of 0.5–1 are between the black and dotted lines (TIF) (TIFF 6024 kb)
10681_2019_2345_MOESM2_ESM.tif (8.6 mb)
Fig. S2 Steroid biosynthesis pathway, which is related to brassinosteroid biosynthesis (TIF) (TIFF 8775 kb)
10681_2019_2345_MOESM3_ESM.tif (10.3 mb)
Fig. S3 Carotenoid biosynthesis pathway, which is related to abscisic acid and strigolactone syntheses (TIF) (TIFF 10539 kb)
10681_2019_2345_MOESM4_ESM.tif (7.1 mb)
Fig. S4 Diterpenoid biosynthesis pathway, which is related to gibberellin biosynthesis (TIF) (TIFF 7229 kb)
10681_2019_2345_MOESM5_ESM.tif (6.5 mb)
Fig. S5 RNA-seq results for two maize inbred lines and effects of a GA treatment of ‘Chuan29’ (TIF) (TIFF 6672 kb)
10681_2019_2345_MOESM6_ESM.xlsx (43 kb)
Table S1 Sources of all plant height-related genes (XLSX 42 kb)
10681_2019_2345_MOESM7_ESM.xlsx (47 kb)
Table S2 Collinear pairs of plant height-related genes among four species (XLSX 47 kb)
10681_2019_2345_MOESM8_ESM.xlsx (33 kb)
Table S3 Genetic information for the plant height-related genes in maize (XLSX 32 kb)
10681_2019_2345_MOESM9_ESM.xlsx (12 kb)
Table S4 Microsyntenic pairs of plant height-related genes in maize (XLSX 12 kb)
10681_2019_2345_MOESM10_ESM.xlsx (12 kb)
Table S5 Gene ontology (GO) annotation of plant height-related genes (XLSX 12 kb)
10681_2019_2345_MOESM11_ESM.xlsx (10 kb)
Table S6 KEGG annotation of maize genes (P-value < 0.05) (XLSX 10 kb)
10681_2019_2345_MOESM12_ESM.xlsx (55 kb)
Table S7 Original expression profiles of maize plant height-related genes during different developmental stages (XLSX 55 kb)
10681_2019_2345_MOESM13_ESM.xlsx (40 kb)
Table S8 Differential expression of plant height-related genes in maize based on an RNA-seq analysis of tall and dwarf inbred lines (XLSX 40 kb)
10681_2019_2345_MOESM14_ESM.xlsx (15 kb)
Table S9 Distribution of KEGG pathways for the upregulated DEGs (P-value < 0.05) (XLSX 15 kb)
10681_2019_2345_MOESM15_ESM.xlsx (13 kb)
Table S10 Primers used for the quantitative real-time PCR analysis (XLSX 13 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Hengsheng Wang
    • 1
  • Xingen Zhang
    • 1
  • Fangxiu Hu
    • 1
  • Mingli Liu
    • 1
  • Yang Zhao
    • 1
  • Yan Wang
    • 1
  • Longjiang Gu
    • 1
    Email author
  • Qing Ma
    • 1
    Email author
  1. 1.National Engineering Laboratory of Crop Stress Resistance BreedingAnhui Agricultural UniversityHefeiChina

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