Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (5): 821-837.doi: 10.3864/j.issn.0578-1752.2023.05.002

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

Candidate Gene Localization of ZmDLE1 Gene Regulating Plant Height and Ear Height in Maize

ZHOU WenQi1(), ZHANG HeTong2, HE HaiJun1, GONG DianMing2, YANG YanZhong1, LIU ZhongXiang1, LI YongSheng1, WANG XiaoJuan1, LIAN XiaoRong1, ZHOU YuQian1(), QIU FaZhan2()   

  1. 1 Crops Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070
    2 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070
  • Received:2022-10-26 Accepted:2022-12-25 Online:2023-03-01 Published:2023-03-13

Abstract:

【Objective】 Plant height is one of the important target traits in maize plant type breeding, which is closely related not only to mechanized grain harvesting and lodging resistance, but also to maize yield. Therefore, it is of great theoretical and breeding value to isolate QTL/gene of maize plant height and analyze its function. This study aims to locate a novel maize dwarf gene ZmDLE1, clarify its biological function, and provide important theoretical basis and gene resources for accelerating the improvement of maize plant type. 【Method】 A single recessive mutant was derived in maize inbred line LY8405, from Crop Research Institute of Gansu Academy of Agricultural Sciences, by chemical mutagenic agent Ethyl Methyl Sulfonate (EMS). A maize dwarf and low ear mutant was isolated from the M2 progeny, and the M3 and M4 progeny could stably inherit, which was named dwarf and low ear mutant1 (Zmdle1). The F2 population was constructed by hybridization with Mo17 and was identified by bulked segregate analysis-sequencing (BSA-seq) and target segment recombination exchange. Based on the Mo17 reference genome, the genes in the target region were obtained and functionally annotated to locate candidate genes.【Result】Phenotypic identification of Zmdle1 was carried out, and the phenotype of Zmdle1 at seedling stage was not significantly different from that of the control LY8405. The plant height and ear height of Zmdle1 at mature stage were reduced by 87.2 cm and 55.4 cm, respectively, accounting for about 35.0% and 62.9%, difference is extremely significant. Morphological observation showed that the decrease of internode number and the shortening of internode cell length were the main reasons for the significant decrease of plant height and ear height of Zmdle1. The genetic analysis of the mutant gene was conducted by using the F2:3 genetic populations. The Zmdle1 mutant is inherited in a 3﹕1 (χ2=2.854) ratio and is a single recessive gene. Therefore, according to the results of BSA-seq, the candidate gene ZmDLE1 was initially located in the 15 Mb region of Bin1.09-1.10 on chromosome 1 of maize. The polymorphism molecular markers were further developed using the re-sequencing results of Mo17 and Zmdle1, and the target gene was accurately cloned by map-based cloning. Finally, the candidate genes were mapped to the size range of 600 kb, and there were 16 candidate genes in this range. By comparing the re-sequencing data, it was found that Zm00001d033231 gene changed into A at the 2062 position G, which resulted in amino acid changing from glycine to serine, and the transcription level expression was significantly reduced compared with LY8405. Zm00001d033234 changed from T to C at the 223rd position leading to the 75th amino acid changed from serine to proline, and there was no significant difference in transcription level. Through association analysis of natural populations and the predicted genes for functional annotation, it was found that Zm00001d033231 and Zm00001d033234 were related to the growth and development of maize. 【Conclusion】 The candidate gene ZmDLE1 in the Bin1.09 region at the end of chromosome 1, was identified to effectively regulate maize plant height and ear height, and the target region was reduced to 600 kb by fine localization. Association analysis showed that Zm00001d033231 was genetic locus significantly associated with plant height within the target region.

Key words: maize, plant height, ear height, BSA-seq, fine mapping, association analysis

Table 1

Part of the primers used in this study"

引物名称Primer name 正向引物 Forward primer (5′-3′) 反向引物 Reverse primer (5′-3′)
Umc2047 GACAGACATTCCTCGCTACCTGAT CTGCTAGCTACCAAACATTCCGAT
Umc1914 CAACATGAGCGTGCTAAATACTCG ACAGGAACACATGAGGTCATCAAA
TIDP6556 TCAAGGAGGTCATCCTCACC ATCACATATCTTGACGCGAGG
Umc1968 CTTCCCCTCCGCTACTGCTC GTACTTGGTGTTGTCGCTCTTCTTC
Umc2612 AACTCAGGTACTTCAATCCCACCC TGTTGCCATCAACAGGTTAAAGAA
Umc2510 TCTGCGAATAGAACTTAAACAGGTTG AGAGGTCCGGGAAGAACAAGTAGT
BKN2-8 GTGTCTGCGCTCGATCTGT TGTGTGATGGTGGCCTGTTA
1.10-14 AGACGTAAGACGATGCGACA TCATGGGTTGCAATGGTAAA
MJD-52 AGAACCACCACTGCCAAAAA GCTCTCATCTTGCCAAAACC
MJD-64 GCCGCTTGTTTCTTTTCCTT TTCCTTCATGGCTCACCTGT
InDel-1 GTTGAGTTGAGTGGAAGGTG GACCAGAGGAGAAAGCACCC
InDel-2 CGCTTCTCGTCGGCTGTCTG CAGCCCTCGACCACGGTAA
InDel-3 CGAATGGAGATGGAGGCGACAG GGAAAACCGCCCGGATCGCTT
InDel-5 TCCCAATCTGTTCCGAGCCAG CACCTCCGCCGAAAGCCCCT
InDel-9 GGACCAATTACACGTAGCCG CTTCTGGACGGTTCTGTTGC
InDel-13 TTAGTCCTATTTAGAACCTC CAAACTCACCCAATCCACAT
InDel-22 CCCGACATCCTCTGCTCACG TAGAGCACCTCCGATAGTTC
InDel-25 ACTTCTTGGGTTGTTGTGC ATCTGGCACGAGTCTGAGAGG
InDel-26 CCTCTGATCCTATCTCGTGCTT CATTGCGTTTGTTCCTTTG

Fig. 1

Seedling traits of Zmdle1 and LY8405 A: Plants 3 days (d) after germination, showed no significant difference in plant height and root length, bars=5 cm; B-F: Indicated the plant phenotypes of 7 d, 14 d, 21 d, 28 d and 35 d after seed germination, respectively; G: Plant height at seedling stage, there were no significant difference. Bars=10 cm"

Table 2

Analysis of agronomic character data of Zmdle1 and LY8405"

类型Type 性状Trait LY8405 Zmdle1 PP-value n
株型
Plant type
株高Plant height (cm) 248.9±21.8 161.7±23.8** 1.40931E-08 100
穗位高Ear height (cm) 88.1±16.5 32.7±11.4** 1.82449E-09 100
雄穗
Tassel
雄穗分枝数Number of tassel branches 11.1±3.1 8.1±1.8** 0.001072267 30
雄穗长Tassel length (cm) 50.4±2.6 50.3±2.3 0.545429534 30
雌穗
Ear
穗长Ear length (cm) 13.2±1.8 12.3±2.3 0.164088327 30
穗粗Ear diameter (cm) 4.2±0.2 4.4±0.4 0.156854806 30
轴粗Corncob thickness (cm) 2.6±0.2 3.2±0.2* 0.116425574 30
穗行数Number of rows per ear 16.7±1.7 16.0±2.0 0.543525975 30
行粒数Row number 18.8±2.3 16.9±3.4 0.173632692 30
叶型
Blade profile
倒3叶长The third top leaf length (cm) 38.1±6.0 45.0±3.8* 0.032741731 30
倒3叶宽The third top leaf width (cm) 8.2±0.9 6.7±0.4** 0.002881444 30
剑叶长Flag leaf length (cm) 25.2±3.7 30.0±5.6 0.119644254 30
剑叶宽Flag leaf width (cm) 4.4±0.4 4.5±0.9 0.938315361 30
粒型
Grain dimension
粒长Grain length (cm) 1.13±0.30 1.04±0.20** 4.07025E-05 100
粒宽Grain width (cm) 0.78±0.03 0.84±0.04* 0.01070802 100
千粒重Thousand seed weight (g) 289.5±15.6 305.1±22.7 0.55039481 1000

Fig. 2

Camparison of phenotypes between the Zmdle1 and LY8405 A, B: Zmdle1 mutant was shorter and had lower ear position than LY8405. C: LY8405×Mo17, F2 isolated Zmdle1 homozygous phenotype, low spike position; D: PH and EH statistics; E: The number of internodes and the length of each node of LY8405 and Zmdle1, a total of 15 nodes, the panicle level nodes, the three upper panicle nodes (orange) and the three lower panicle nodes (blue) were significantly different. Bars=30 cm. ** mean very significant difference (P<0.01)"

Fig. 3

Phenotypes of stem nodes and roots of LY8405 and Zmdle1 A: The internode diagram of Zmdle1 and LY8405 shows that Zmdle1 is shorter than LY8405 in the lower and upper panicle segments; B: Zmdle1 has smaller roots than LY8405; C, D: Electron scanning morphogram of stem cells under ear in LY8405 and Zmdle1; E: Cell length in longitudinal section. A, B: Bars=5 cm; C, D: Bars=200 μm"

Fig. 4

Ear and grain characteristics of LY8405 and Zmdle1 A: Zmdle1 and LY8405 ears with good fruit bearing; B: From left to right, they are sword blade, inverted 2 blade and inverted 3 blade respectively. The inverted 3 blade of Zmdle1 becomes longer and narrower. C, E: Ear and grain traits; D: Zmdle1 and LY8405 young panicle development is normal, there is no difference; F: The tassels of LY8405 and Zmdle1 developed normally, the number of branches of Zmdle1 decreased significantly by 2-4, and the flowering period was one week earlier. G, H: Zmdle1 grains had shorter grain length and wider grain width than LY8405 grains (n=20). A, B, D-H: Bars=5 cm; C: Bar=2 cm"

Table 3

Genetic separation ratio test between normal and dwarf plants in F2 population"

群体
Population
总株数
Total plant number
正常表型
Normal phenotype
矮化表型
Dwarfing phenotype
分离比
Segregation ratio
P
P value
χ2
(LY8405×Zmdle1) F2 538 400 138 2.9﹕1 0.73 1.975
(Mo17×Zmdle1) F2 2381 1821 560 3.2﹕1 0.102 2.854

Fig. 5

Plots the probability of complete linkage disequilibrium between each SNP marker and related gene (y-axis) corresponding to the physical location of each SNP marker (x-axis) Black boxes indicate possible candidate gene intervals"

Fig. 6

Linkage map of ZmDLE1 candidate genes ΔSNP-index is the linkage map of this population. The black boxes mark possible candidate gene intervals. The green and blue dots are SNP-index or ΔSNP-index; The red line is the SNP-index or ΔSNP-index windowing fitting line; The purple line is the 95% confidence line; The orange-yellow line is 99% confidence line; SNP-index (highbulk) was the linkage location map of mutant progeny; SNP-index (lowbulk) was the linkage location map of wild progeny"

Table 4

Crossing-over value of preliminary localization markers and phenotypes"

标记名称
Molecular markers
umc 1914 umc2047 umc1968 BKN2-8 umc2510 umc2612 1.10-14 MJD-52 MJD-64
交换频率
Crossing- over value
0.39 0.24 0.19 0.15 0.14 0.18 0.32 0.38 0.45

Fig. 7

Fine mapping of ZmDLE1 candidate genes"

Table 5

Candidate genes within the segment"

候选基因
Candidate gene
蛋白类型
Protein type and putative function
基因位置
Position (bp)
表达差异(P值)
Differential expression (P value)
Zm00001d033229 假设蛋白Hypothetical protein 255233719—255234639 0.620542
Zm00001d033230 类受体蛋白29 Receptor like protein 29 255243582—255245348 0.505878
Zm00001d033231 扩张蛋白B4 Expansin B4 255266246—255275500 0.001218**
Zm00001d033232 花粉Ole e1过敏原和扩展蛋白家族蛋白
Pollen Ole e1 allergen and extensin family protein
255276609—255280338 0.974205
Zm00001d033233 类水解酶蛋白质Hydrolase-like protein 255287266—255290302 0.008914**
Zm00001d033234 蛋白激酶PINOID Protein kinase PINOID 255293638—255295053 0.1486
Zm00001d033235 未知蛋白Unknown 255315224—255316506 0.48863
Zm00001d033236 未知蛋白Unknown 255319161—255321117 0.373901
Zm00001d033237 L型植物凝集素类受体蛋白激酶
L-type lectin-domain containing receptor kinase
255361226—255391452 0.466955
Zm00001d033238 未知功能Unknown 255391827—255391899 #DIV/0!
Zm00001d033239 未知功能Unknown 255392565—255392637 #DIV/0!
Zm00001d033240 感光性NPH3家族蛋白Phototropic-responsive NPH3 family protein 255510009—255515376 0.125879
Zm00001d033241 阳离子氨基酸转运体4 Cationic amino acid transporter 4 255565519—255569235 0.139972
Zm00001d033244 转导蛋白/WD40重复样超家族蛋白
Transducin/WD40 repeat-like superfamily protein
255748790—255757682 0.698459
Zm00001d033246 HD-Zip蛋白Class Ⅲ HD-Zip protein Ⅲ 255864303—255869980 0.770706
Zm00001d033247 转导蛋白/WD40类重复超家族蛋白
Transducin/WD40 repeat-like superfamily protein
255988480—256003180 0.137846

Fig. 8

Association analyses of plant height traits The gene associated with plant height trait was Zm00001d033231"

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