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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (5): 1124-1135.doi: 10.3724/SP.J.1006.2024.33044

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Identification and gene cloning of leafy dwarf mutant lyd1 in maize

SU Shuai(), LIU Xiao-Wei, NIU Qun-Kai, SHI Zi-Wen, HOU Yu-Wei, FENG Kai-Jie, RONG Ting-Zhao, CAO Mo-Ju*()   

  1. Maize Research Institute, Sichuan Agricultural University / Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture and Rural Affairs, Chengdu 611130, Sichuan, China
  • Received:2023-07-31 Accepted:2024-01-12 Online:2024-05-12 Published:2024-02-08
  • Contact: E-mail: caomj@sicau.edu.cn
  • Supported by:
    Sichuan Science and Technology Program(2021YFYZ0011);Sichuan Science and Technology Program(2021YFYZ0017);Sichuan Science and Technology Program(MZGC20230108);Specific Research Supporting Program for Discipline Construction at Sichuan Agricultural University.

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Abstract:

The decrease of plant height in maize is usually caused by the decrease in the number of internodes, the shortening of internodes or the combination of both. However, in this study, the mutant leafy dwarf1 (lyd1) found in the progeny of gene editing, exhibited more leaves and shorter stature. Quantitative measurements indicated the plant height of mutant lyd1 was only 93.10 cm, the plant height of wild-type KN5585 was 159.95 cm. The plant height was significantly reduced by 41.79% in mutant lyd1 compared with the wild type KN5585. The wild type KN5585 produced an average of 17.8 leaves at maturity stage, whereas mutants lyd1 produced 27.8 leaves. The number of leaves were significantly increased by 56.18% in mutant lyd1 compared with the wild type. Genetic analysis showed that the mutation phenotype of lyd1 was controlled by a pair of recessive nuclear genes. We applied a map-based cloning strategy to identify the gene responsible for the lyd1 phenotype. The gene was located between Indel10 and Indel11 on maize chromosome 3, and the physical distance was 0.74 Mb. Gene sequencing analysis of 13 genes (excluding pseudogenes) within the interval revealed that one base A was substituted in the fourth exon of ZmTE1, and there was no significant difference in other genes. ZmTE1 encoded an RNA-binding protein. The amino acid substitution was in the third RNA binding domain (RRM3), resulting in the conversion of aspartic acid to valine. The mutation sites of the mutant lyd1 were different from te1-mum1, te1-mum2, te1-mum3, and zm66 in previously reported. The discovery of lyd1 provides valuable materials for further analysis of the genetic mechanism of the balance between leaves and internodes development in maize.

Key words: maize, the number of leaves, the length of internodes, gene mapping

Fig. 1

Comparison of characters between wild type KN5585 and mutant lyd1 A, B, and C: represent the 5th leaf stage, 10th leaf stage, and mature stage of wild type KN5585 and mutant lyd1, respectively. D: leaves phenotypes of wild type KN5585 and mutant lyd1 at maturity. E: the tassel phenotype of wild type KN5585 and mutant lyd1. F, G: phenotypes of ear and kernel of wild types KN5585 and mutant lyd1. Bar: A 15 cm; B, C, D 30 cm; E 5 cm; F 2 cm."

Fig. 2

Comparison of internodes and leaves development between wild type KN5585 and mutant lyd1 A: the comparison of internodes length between the wild type KN5585 and mutant lyd1, 0 represents the internode of the ear, -1 represents the first internode below the ear, +1 represents the first internode above the ear, and so on. B: the comparison of leaves development between wild type KN5585 and mutant lyd1. The vertical axis shows the average number of leaves in the surveyed population. The horizontal axis indicates the survey date."

Table 1

Agronomic characters of lyd1 and KN5585"

农艺性状
Agronomic trait		 野生型
KN5585		 突变体
lyd1		 相比KN5585
Compared with KN5585 (%)
株高 Plant height (cm) 159.95±6.37 93.10±6.78 -41.79**
穗位高 Ear height (cm) 64.37±5.50 43.48±2.96 -32.45**
完全叶数量 Number of the complete leaves 17.80±0.96 27.80±1.18 56.18**
雄穗分支数 Number of the tassel branches 12.07±1.38 9.59±1.53 -20.55**
叶长(穗位叶) Length of leaf (cm) 63.60±2.76 43.65±1.29 -31.37**
叶长(穗位叶下第一叶) Length of leaf (cm) 63.30±3.62 43.51±1.76 -31.26**
叶长(穗位叶下第二叶) Length of leaf (cm) 63.30±2.11 39.60±2.19 -37.44**
叶宽(穗位叶) Width of leaf (cm) 6.81±0.23 6.24±0.32 -8.37*
叶宽(穗位叶下第一叶) Width of leaf (cm) 7.72±0.20 6.58±0.57 -14.77**
叶宽(穗位叶下第二叶) Width of leaf (cm) 8.17±0.25 6.89±0.33 -15.67**
穗长 Ear length (mm) 137.5±3.94 75.93±4.54 -44.78**
穗粗 Ear width (mm) 41.66±1.51 35.61±1.35 -14.52**
穗行数 Ear rows 14.53±0.88 14.70±1.24 1.17
行粒数 Kernels per row 28.47±2.31 14.40±2.73 -49.42**
穗粒重 Grain weight per ear (g) 88.75±3.83 27.78±3.09 -68.70**
百粒重 100-kernel weight (g) 23.56±1.31 16.80±2.35 -25.70**
播种至群体内50%植株散粉的天数
Time to sow until 50% of the plant is powdered (d)		 89.03±2.10
 88.64±1.79
 0.44

Fig. 3

Paraffin sections of wild type KN5585 and mutant lyd1 in the second internode of ear after loose powder were observed A: the observation of longest intersegmental (the internode where the 11th leaf is located.) cells of wild type KN5585 after loose powder; B: the observation of longest intersegmental (the internode where the 19th leaf is located.) cells of mutant lyd1 after loose powder; C, D: the comparison of longest intersegmental cell length and number between wild type KN5585 and mutant lyd1. Bar: 5 μm; **: P < 0.01."

Table 2

Gene location-related marker information of mutant lyd1"

引物
Primer name		 正向引物物理位置
Physical location of the forward sequences in Chr.3		 正向引物
Forward sequence (5'-3')		 反向引物
Reverse sequence (5'-3')
Bnlg1019 26,363,937 ACCATAGTTGGACGGACCAC ACCACAACACAGACGAGCAC
Indel1 119,614,380 GTCTCCTCAGGCTCAGCG TCCAGTGGTGGTGTAGCAGA
Indel2 151,632,100 CGCATTTGAACACAGACAATG TTGTTTGTCAGATTGGACCG
Indel3 153,748,760 CGCATTTGAACACAGACAATG TTGTTTGTCAGATTGGACCG
Indel4 158,344,977 AATTCTTGCAGAAGTAGAGAGCC ACTTCATCACCACCTCCACC
Indel5 159,813,116 CTTTTGCCTCTGGCGTTTG GCAGTCAATGGGGATGGA
Indel6 160,577,046 ATTGGGAGGCACAGCCTAAC CTGAGCCTCTGTACCTTGGG
Indel7 164,148,097 CCCTCCACATCATCACCAGT GATGATCCGACGCTGTCTTT
Inde18 175,087,860 TGAACGAACGATTAACGATGA GAGGATTTCGTCTTGGTTCG
Indel9 176,089,140 GACATGTCCGTCGGTTCC CACGTACATGGTTCGCATTC
Indel10 169,660,810 GAACGCGACACGGAGGTC TGACTGACACATGCTTGCAC
Indel11 170,400,425 CGGCCGAATAATTAGAGTTCC GAGCATCTTTTTGGACCAGC
Indel12 170,529,987 TCTGAGCACCAGATCAAATCA GCACTCGAGGGAATGAAATC
Indel13 171,483,961 CACTGGCAGCAGCAGACTAA AAATATTCCGAGAACGAGCG
SNP1 169,869,794 GCTAGTAACGCCATAGCCCA TCTCGCCTGGTTCTTGATCG

Fig. 4

Fine mapping of lyd1 mutant A: the candidate gene was preliminarily located between the Indel7 and Indel8 molecular markers on chromosome 3; B: the candidate gene was finely positioned between the Indel10 and Indel11 molecular markers on chromosome 3; C: there are 14 candidate genes in the fine localization interval. Above the horizontal line is the molecular marker, below the horizontal line is the number of recombinant individual plants."

Table 3

Information of candidate genes within the localization interval"

基因ID
B73_V5_gene ID		 功能注释
Function annotation		 位置
Location
Zm00001eb144240 Ald1-aldolase 170,387,546-170,390,313
Zm00001eb144160 Ccp33-cysteine protease 170,125,038-170,126,144
Zm00001eb144140 RNA blind protein 169,867,979-169,872,110
Zm00001eb144180 JmjC domain—containing histone demethylase 170,134,182-170,134,702
Zm00001eb144170 JmjC domain—containing histone demethylase 170,128,075-170,133,903
Zm00001eb144220 Protein_coding 170,296,791-170,307,581
Zm00001eb144250 Protein_coding 170,390,315-170,392,581
Zm00001eb144260 Protein_coding 170,393,357-170,396,464
Zm00001eb144210 Protein_coding 170,142,920-170,157,964
Zm00001eb144200 Non_coding 170,140,528-170,140,860
Zm00001eb144190 Non_coding 170,140,015-170,140,550
Zm00001eb144150 Non_coding 170,124,627-170,126,302
Zm00001eb144230 Non_coding 170,332,480-170,333,214
Zm00001eb144130 Pseudogene 169,694,106-169,706,660

Fig. 5

lyd1 mutation site and conservative analysis of mutation site A: the comparison of CDS difference sequence of ZmTE1 in mutant lyd1 and wild type KN5585; B, C: the conservative analysis of amino acid residues mutated in ZmTE1 protein sequence."

Fig. 6

Population verification of ZmTE1 sequence difference sites between wild type KN5585 and mutant lyd1"

Fig. 7

Tissue expression analysis of ZmTE1 A: the relative expression level of ZmTE1 genes in different tissues of wild type KN5585; B: the comparison of ZmTE1 expression in wild type KN5585 and mutant lyd1. V3, V7, V11, and V17 represent the stage when the maize has 3, 7, 11, and 17 fully unfolded leaves, respectively."

Fig. 8

Subcellular localization of ZmTE1 PC2300-eGFP-ZmTE1 are colocalized with NLS (nuclear marker) and mCherry (cell membrane marker). Bar: 50 μm."

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