Genome-wide Identification and Expression Pattern Analysis of ZmDIR Gene Family in Maize

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

Abstract

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

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.

Figures/Tables 9

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

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

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

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

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

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

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

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

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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