玉米ZmDIR基因家族的全基因组鉴定与表达模式分析

doi:10.13560/j.cnki.biotech.bull.1985.2025-0959

摘要/Abstract

摘要：

目的 Dirigent（DIR）基因在植物生长发育及环境适应中发挥重要作用，鉴定玉米ZmDIR基因家族成员，揭示其在逆境防御中的潜在作用。方法利用生物信息学方法鉴定ZmDIR基因家族，对其保守基序、保守结构域、染色体分布、基因复制、启动子区顺式作用元件和系统发育进行系统分析，结合转录组数据阐明该家族在不同组织及生物与非生物胁迫下的表达模式。结果在玉米基因组中共鉴定出41个ZmDIR基因，分布在10条染色体上，含有0-4个内含子，78%的ZmDIR基因包含核心保守基序1、基序2和基序4。系统发育分析将ZmDIR蛋白分为6 个亚组。基因复制分析表明，片段复制和串联复制是该家族扩增的主要驱动因素。启动子分析发现，ZmDIR基因富含参与生长发育、植物激素、环境胁迫和光响应等过程的顺式作用元件。组织特异性表达分析显示，ZmDIR在根、茎、叶、叶尖、叶基、胚、胚乳、花药、雌穗和雄穗中差异表达，而且在不同发育组织中的表达模式存在多样性。转录组数据表明，ZmDIR在多种非生物胁迫（高温、盐、紫外线、低温、干旱和水涝）和生物胁迫（禾生炭疽菌）下均呈现差异表达。RT-qPCR实验验证了所选ZmDIR基因在盐（NaCl）、低温（4 ℃）、干旱（PEG）和禾生炭疽菌（Colletotrichum graminicola）胁迫下均发生特异性变化。结论在玉米基因组中鉴定出41个ZmDIR基因，该家族广泛响应生物与非生物胁迫，6个关键基因在逆境胁迫下呈显著差异表达，为解析关键成员抗逆机制及分子育种提供了靶标。

关键词: 玉米, DIR基因家族, 生物信息学分析, 逆境胁迫, 表达分析

Abstract:

Objective Dirigent (DIR) genes play important roles in plant growth, development and environmental adaptation. The objectives of this study are to identify the ZmDIR gene family in maize (Zea mays) and to preliminarily reveal its potential role in stress defense, thereby providing a theoretical basis for further research. Method Bioinformatics were used to identify the members of the ZmDIR family and systematically analyzed their conserved motifs, conserved domains, chromosomal distribution, gene duplication events, cis-regulatory elements in promoter regions and phylogenetic relationships. Transcriptome data were further employed to elucidate the expression patterns of these genes across different tissues and under both abiotic and biotic stresses. Result A total of 41 ZmDIR genes were identified in the maize genome and distributed across all 10 chromosomes and contain zero to four introns, 78% of them shared the core conserved motif 1, motif 2 and motif 4. Phylogenetic analysis indicated that DIR proteins in maize can be classified into six subgroups. Gene duplication analysis revealed that segmental and tandem duplications were the main driving forces for the expansion of this family. Promoter analysis revealed that ZmDIR genes were enriched with cis-acting elements involved in plant growth and development, phytohormone response, environmental stress and light response. Tissue-specific expression profiles revealed that ZmDIRs were differentially expressed in the roots, stems, leaves, leaf tip, leaf base, embryo, endosperm, anther, tassel and ear. The expression pattern of these genes appeared to be diverse in the different developmental tissues. Transcriptome data confirmed the differential expression of ZmDIR under abiotic (heat, salt, UV, cold, drought and WS) and biotic stress (Colletotrichum graminicola). RT-qPCR analysis validated the specific dynamic changes in selected ZmDIR genes under salt (NaCl), cold (4 ℃), drought (PEG) and Colletotrichum graminicola stresses. Conclusion This study identified 41 ZmDIR genes in the maize genome. This gene family responds extensively to both biotic and abiotic stresses. Six key genes showed significant differential expression under adverse stresses. providing targets for elucidating the stress resistance mechanisms of key members and for molecular breeding.

Key words: Zea mays, DIR gene family, bioinformatics analysis, adversity stress, expression analysis

阎晓光, 杜艳伟, 马志远, 王彬, 王国梁, 胡丹珠. 玉米ZmDIR基因家族的全基因组鉴定与表达模式分析[J]. 生物技术通报, 2026, 42(7): 126-137.

YAN Xiao-guang, DU Yan-wei, MA Zhi-yuan, WANG Bin, WANG Guo-liang, HU Dan-zhu. Genome-wide Identification and Expression Pattern Analysis of ZmDIR Gene Family in Maize[J]. Biotechnology Bulletin, 2026, 42(7): 126-137.

图/表 9

表1 ZmDIR基因家族中的重复基因对

Table 1 Duplication gene pairs in ZmDIR gene family

基因对 Gene pair		模式 Mode	Ka	Ks	Ka/Ks	分化时间/百万年 Divergence time/Mya
ZmDIR39	ZmDIR11	片段复制	0.40	0.55	0.72	42.31
ZmDIR11	ZmDIR22	片段复制	0.51	0.43	1.19	33.08
ZmDIR34	ZmDIR36	片段复制	0.73	0.84	0.86	64.62
ZmDIR25	ZmDIR33	片段复制	0.20	0.49	0.41	37.69
ZmDIR38	ZmDIR22	片段复制	0.40	0.35	1.15	26.92
ZmDIR11	ZmDIR12	串联复制	0.43	0.69	0.63	53.08
ZmDIR28	ZmDIR27	串联复制	0.14	0.40	0.36	30.77

图1 玉米DIR蛋白的保守基序和保守结构域

Fig. 1 Conserved motifs and conserved domain of DIR proteins in Zea mays L.

图2 玉米ZmDIR基因家族的染色体分布

Fig. 2 Chromosomal distribution of the ZmDIR gene family in Zea mays L.

图3 玉米ZmDIR基因的复制事件A：物种内片段复制用红线连接，串联重复基因以红色字体显示。B：不同物种间DIR基因共线性用蓝线连接，玉米与其他基因的共线性在背景中用灰线连接

Fig. 3 Duplication events of ZmDIR genes in maizeA: Intraspecies segmental duplications are connected by red lines, tandemly duplicated genes are highlighted in red. B: Syntenic DIR genes between different species are linked by blue lines, while syntenic relationships between maize and other genes in the plant genome are displayed as gray lines in the background

图4 拟南芥、水稻和玉米中DIR蛋白的系统发育树

Fig. 4 Phylogenetic tree of DIR proteins in Arabidopsis, Oryza sativa and Zea mays

图5 ZmDIR启动子区域中的顺式作用元件分析A：玉米中ZmDIR蛋白的系统发育树。B：顺式作用元件在ZmDIR启动子上的分布。C：ZmDIR启动子区顺式作用元件的类型。D：ZmDIR启动子区不同类型顺式作用元件的数量

Fig. 5 Cis-acting element analysis in ZmDIR promoter regionsA: Phylogenetic tree of ZmDIR protein in Z. mays. B: The distribution of cis-regulatory elements on the ZmDIR genes promoter. C: Types of cis-acting elements in the promoter region of ZmDIR genes. D: Numbers of different types of cis-elements in the promoter regions of ZmDIR genes

图6 玉米ZmDIR基因在不同组织中的表达模式A：不同组织中ZmDIR基因的表达水平。不同组织包括根、茎、叶、叶尖、叶基、胚、胚乳、花药、雌穗和雄穗。B-G：部分ZmDIR基因的组织特异性表达

Fig. 6 Expression pattern of ZmDIR genes in different tissues of Z. maysA: Expressions of ZmDIR genes at different tissues. The tissue-specific expressions of the ZmDIR gene including the roots, stems, leaves, leaf tip, leaf base, embryo, endosperm, anther, tassel, and ear. B-G: Tissue-specific expressions of some ZmDIR genes

图7 玉米ZmDIR基因在逆境胁迫下的表达模式A：高温、盐、紫外线和低温胁迫下ZmDIR基因的表达。B：干旱胁迫下ZmDIR基因的表达。C：水涝胁迫下ZmDIR基因的表达。D：真菌Colletotrichum graminicola感染后ZmDIR基因在玉米叶片中的表达。Hpi：接种后小时数

Fig. 7 Expression profiles of ZmDIR genes under adversity stress in Z. maysA: Expressions of ZmDIR genes under heat, salt, ultraviolet (UV) and cold stress. B: Expressions of ZmDIR genes under drought stress. C: Expressions of ZmDIR genes under waterlogging stress (WS). D: Expressions of ZmDIR genes in Z. mays leaves treated with Colletotrichum graminicola. Hpi: Hours post-inoculation

图8 逆境胁迫下叶片中ZmDIR基因的相对表达量A：200 mmol/L NaCl；B：4 ℃低温；C：20% PEG6000；D：禾生炭疽菌。*P<0.05，**P<0.01

Fig. 8 Relative expressions of ZmDIR genes in the leaves under adversity stressA: 200 mmol/L NaCl treatment. B: 4 ℃ cold treatment. C: 20% PEG6000 treatment. D: Colletotrichum graminicola treatment. *P<0.05, **P<0.01

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