Crops ›› 2023, Vol. 39 ›› Issue (4): 31-37.doi: 10.16035/j.issn.1001-7283.2023.04.005

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Transcriptomic Analysis to Reveal Lodging Resistance Genes and Metabolism Pathways in Maize (Zea mays L.)

Liu Songtao1(), Tian Zaimin1, Liu Zigang1, Gao Zhijia2, Zhang Jing2, He Donggang3, Huang Zhihong1, Lan Xin1   

  1. 1Hebei North University/Key Laboratory of Hebei Province Agricultural Products Food Quality and Safety Analysis and Testing, Zhangjiakou 075000, Hebei, China
    2Hebei Universe Agricultural Science and Technology Co., Ltd., Zhangjiakou 075000, Hebei, China
    3Hebei Zhaoyu Seed Industry Group Co., Ltd., Shijiazhuang 050000, Hebei, China
  • Received:2022-01-02 Revised:2022-04-02 Online:2023-08-15 Published:2023-08-15

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Abstract:

Lodging is one of the important factors affecting maize production. In this study, three maize varieties with different lodging resistance [Jingnongke 728 with high lodging resistance (H), Jinnong 738 with medium lodging resistance (M) and Xianyu 335 with low lodging resistance (L)] were used for transcriptome analysis to explore the genes related to maize lodging resistance. The results showed that a total of 10093 differentially expressed genes (DEGs) were identified in the three comparison groups, and the most DEGs of 7779 were identified in Xianyu 335 and Jingnongke 728 groups. GO functional enrichment analysis showed that the different lodging resistance of the three maize varieties may be related to the different number of DEGs enriched into the same GO terms. Metabolic pathway enrichment analysis showed that L-vs-H, M-vs-H were significantly enriched in phenylpropanoid biosynthesis, secondary metabolite biosynthesis and flavonoid biosynthesis, while L-vs-M was significantly enriched in photosynthesis antenna protein and plant-pathogen interaction pathways. The stem microstructure showed that Xianyu 335 had the smallest single vascular bundle area and the thinnest stem epidermal cell thickness, while Jingnongke 728 had the largest single vascular bundle area and the thickest epidermal cell thickness. The results of this study further clarified the genes and metabolic pathways related to lodging resistance in maize, which laid a foundation for directional cloning, and also provided a foundation for molecular design breeding of new lodging resistant varieties.

Key words: Maize, RNA-seq, Microscopic structure, Differentially expressed genes, Lodging-resistant

Table1

The primer sequence of RT-qPCR"

基因名称Gene name 前引物Forward primer 后引物Reverse primer 产物长度Product size (bp)
LOC100281532 GGAGGAGATGATGGGCAGC CTCGATCTTCACCAGGGGC 79
LOC100273579 AGAAGTCGCTGAGCCTGAAC TCTGCATCAGCGGGTAGTTG 141
LOC100272756 AGGAGGACAAGTCCGTGGAG TATCGATCTTGTCGAGGCCG 174
LOC541914 CCGTTAACCTGTCGAGGCTT GTCTCCAACCTTCCAGCTCC 123
LOC100272970 ATCAGCGTACATCGCGTCC AACTGAGGTGGGCTCTGTGT 94
LOC100194371 CGGTTCTGCTTCAAGACGAT CGGTAGTAGCTCCTTGGGTG 113
LOC100281042 TGGTGGAGGAGTACAGGAGG GTGCCGTTCATCATGCTGTC 172
LOC100282047 GTCGAACAGCGAGGAGTACC GTCGAACCAGAGGTGGAACC 163
LOC100283318 CTACTTCATCTCGGAGGGGC GAGTAGGTGTGGAAGTCGGC 177
LOC100284765 CCACCATCAGTAGCGGTCG GCCCGTGATGTTGCTGGA 168

Table 2

The summary of RNA-Seq data"

样品名称
Sample name		 原始数据
Raw read		 有效数据
Clean read		 碱基所占百分比
Q30(%)		 GC含量
GC content(%)		 单一比对率
Unique mapped		 多比对率
Multi mapped
JNK728-1 46743554 44778802 94.64 53.21 38131199(85.15%) 2833048(3.58%)
JNK728-2 42213792 40278042 93.90 53.24 34173234(84.84%) 2543399(3.56%)
JNK728-3 45140086 42175780 94.60 53.16 35820137(84.93%) 2740012(3.64%)
JN738-1 45628206 43858376 94.36 53.69 38079538(86.82%) 2519952(3.37%)
JN738-2 49113472 46927518 94.46 53.78 40671536(86.67%) 2782255(3.41%)
JN738-3 47537856 45732776 93.90 53.72 39628836(86.65%) 2690579(3.43%)
XY335-1 45920308 44134008 94.30 54.57 38518679(87.28%) 2222552(3.04%)
XY335-2 44670476 42529790 94.55 54.84 37079717(87.19%) 2186084(3.04%)
XY335-3 46723572 44596496 94.02 55.08 38796470(86.99%) 2319389(3.06%)

Fig.1

Principal componentanalysis of samples used for transcriptome sequencing"

Table 3

Statistics of differentially expressed genes"

分组
Group		 DEGs数量
DEGs number		 下调
Down-regulated		 上调
Up-regulated
L-vs-H 7779 4411 3368
L-vs-M 5373 2896 2477
M-vs-H 4905 2831 2074

Fig.2

Venn diagram analysis of DEGs observed in comparison groups"

Fig.3

Gene ontology (GO) enrichment analysis of DEGs The colorgradient (orange to red)corresponds to the level of significance (lower to higher; P<0.05) of enrichment of the corresponding GO terms"

Fig.4

Metabolic pathway enrichment analysis of DEGs"

Fig.5

Microstructure of the stems of the three maize varieties (a) number of stem vascular bundles within the microscope visual scope; (b)single vascular bundle area; (c)stem epidermal cell thickness"

Fig.6

Microstructures of the stalk of the three maize varieties Different letters indicate significant difference (P<0.05)"

Fig.7

The qRT-PCR validation of the RNA-seq data for the ten DEGs"

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