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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (4): 886-895.doi: 10.3724/SP.J.1006.2022.13026


Genetic analysis and molecular characterization of dwarf mutant gad39 in maize

LIU Lei(), ZHAN Wei-Min(), DING Wu-Si, LIU Tong, CUI Lian-Hua, JIANG Liang-Liang, ZHANG Yan-Pei*(), YANG Jian-Ping*()   

  1. College of Agriculture, Henan Agricultural University, Zhengzhou 450002, Henan, China
  • Received:2021-03-22 Accepted:2021-06-16 Online:2022-04-12 Published:2021-07-15
  • Contact: ZHANG Yan-Pei,YANG Jian-Ping E-mail:18737652119@163.com;630950832@qq.com;zhangyanpei@henau.edu.cn;jpyang@henau.edu.cn
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    National Natural Science Foundation of China(31871709);Henan Technology Innovation Guidance project(182106000050);Key Project of Beijing Natural Science Foundation(6151002)


Plant height is one of the important selection characters in maize breeding, which determines planting density and lodging resistance, and further affects yield and quality. Therefore, it is of great significance to study the genetic and molecular mechanism of related genes controlling plant height in maize. We performed phenotypic identification, cytological observation, genetic analysis, gene mapping, and gibberellin (GA3) treatment of dwarf mutant gad39, which is derived from maize inbred line Mo17. At silking stage, the plant height of gad39 was only 100.00 cm, significantly shorter than 192.60 cm of wild type Mo17, resulting in a decrease of 48.08%. Morphological identification showed that tassel length, internode number, and cell size of gad39 mutant were significantly reduced, which might be the main cause of gad39 dwarfism. In addition to plant dwarfness of gad39, the number of tillers increased, ear position decreased, stem became thinner, leaf length became shorter and ear length became shorter. Genetic analysis showed that a single recessive nuclear gene regulated the gad39 mutant phenotype, and gene controlling dwarf trait was mapped between markers td4 and td6 on the long arm of chromosome 3. The physical distance between the two markers was 15.34 kb, which contained a dwarf gene D1/ZmGA3ox2. Sequence analysis also revealed that D1 allele gene in gad39 had 10 InDels and 21 SNPs, resulting in the variations of four amino acids in exons. Mutation sites of gad39 differed from the previously reported sites of mutant dwarf1, d1-4, d1-6016, and d1-3286. In conclusion, gad39 was a novel allelic mutant of D1, which encoded GA3-oxidase (GA3ox), a key enzyme involved in the bioactive GA biosynthesis. The seedling height of gad39 was restored to the level of wild types by GA3 treatment. In this study, we detected a new dwarfing allelic mutant, which laid a foundation for further analyzing the genetic mechanism of plant height in maize.

Key words: maize, dwarf, genetic analysis, gene mapping, gibberellin

Fig. 1

Phenotypic comparison between Mo17 (WT) and gad39 mutant A, B, and C: plant phenotype of wild type (WT) and gad39 mutant at fourth-leaf, eighth-leaf, and silking stage, respectively; D: ear phenotype at mature stage. Scale bars: (A) 10 cm, (B) 15 cm, (C) 20 cm, and (D) 2 cm."

Table 1

Comparison of agronomic traits between Mo17 and mutant gad39"

株高 Plant height (cm) 192.60±8.26 100.00±14.46**
穗位 Ear height (cm) 55.00±7.53 20.22±5.36**
分蘖数 No. of tillers 1.00±0.00 2.18±1.25**
茎粗 Stem diameter (mm) 23.03±2.00 20.58±1.57*
叶长 Leaf length (cm) 81.65±2.17 50.64±5.53**
叶宽 Leaf width (cm) 10.61±0.90 10.06±1.57

Fig. 2

Histological analysis of stem internodes A: scanning electron microscope observation of stem cell; B, C: comparison of cell length and width in the stem; D: comparison of the number of aboveground internodes; E: comparison of the length of tassel and aboveground internodes at silking stage. WT: wild type Mo17. Bar: 100 µm. T: the length of tassel; 1 represents the first internode above the ear, -1 represents the first internode below the ear, and so on. **: P < 0.01; *: P < 0.05."

Table 2

Primers used in this study"

Forward primer (5°-3°)
Reverse primer (5°-3°)

Fig. 3

Fine mapping of gad39 mutant A: candidate gene was preliminarily localized between td1 and td2 molecular markers on maize chromosome 3; B: candidate gene was fine mapped to a 15.34 kb region delimited by td4 and td6 markers; C: two candidate genes in the fine-mapped region; D: the position of primer on the gene. The gray ellipse represents the centromere. The upper parts of the horizontal line are molecular markers, and the numbers beneath the horizontal line represent the numbers of recombinant plants. Chromosomal compositions of eight recombinants (plant numbers 233-1, 229-7, 229-2, 214-3, 241-2, 215-5, 233-2, 234-1, 224-11, and 225-5) are represented with their phenotypes."

Fig. 4

Sequence alignment of Zm00001d039634 gene A: genome alignment of Zm00001d039634 gene from Mo17 (WT) and gad39 mutant; B: amino acid alignment of Zm00001d039634 from Mo17 (WT) and gad39 mutant. Empty boxes represent 5' and 3' UTR, black boxes represent exons, and black solid lines represent introns and non-coding regions."

Fig. 5

Conservative analysis of gad39 mutation site in GA3ox family from different plant species ZmGA3ox2 (Zea mays, NP_001266453.1), ZmGA3ox1 (Zea mays, NP_001146525.1), AtGA3ox1 (Arabidopsis thaliana, Q39103), AtGA3ox2 (Arabidopsis thaliana, Q9ZT84), SbGA3ox2-3 (Sorghum bicolor, XP_021303725.1), BdGA3ox2 (Brachypodium distachyon, xp_014758338.1), OsGA3ox1 (Oryza sativa, Q6AT12), OsGA3ox2 (Oryza sativa, Q9FU53), PmGA3ox2 (Panicum miliaceum, RLM92489.1), SiGA3ox2 (Setaria italica, XP_004968405.1). * represents amino acid variation position."

Fig. 6

Responses of wild type Mo17 (WT) and gad39 to GA3 treatment A: the seeding phenotype of WT and gad39 after GA3 treatment; B: the plant height of WT and gad39 after GA3 treatment. Bar: 10 cm. The concentration of GA3 was 100 μg mL-1. **: P < 0.01; n.s. represents no significant difference."

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