Comprehensive analysis of the INDETERMINATE DOMAIN (IDD) gene family and their response to abiotic stress in Zea mays

X. Feng; Q. Yu; J. Zeng; X. He; Wujun Ma; L. Ge; W. Liu

doi:10.3390/ijms24076185

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Comprehensive analysis of the INDETERMINATE DOMAIN (IDD) gene family and their response to abiotic stress in Zea mays

Journal article

Open access

Comprehensive analysis of the INDETERMINATE DOMAIN (IDD) gene family and their response to abiotic stress in Zea mays

X. Feng, Q. Yu, J. Zeng, X. He, Wujun Ma, L. Ge and W. Liu

International Journal of Molecular Sciences, Vol.24(7), Art. 6185

2023

DOI: https://doi.org/10.3390/ijms24076185

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Abstract

Transcription factors (TFs) are important regulators of numerous gene expressions due to their ability to recognize and combine cis-elements in the promoters of target genes. The INDETERMINATE DOMAIN (IDD) gene family belongs to a subfamily of C2H2 zinc finger proteins and has been identified only in terrestrial plants. Nevertheless, little study has been reported concerning the genome-wide analysis of the IDD gene family in maize. In total, 22 ZmIDD genes were identified, which can be distributed on 8 chromosomes in maize. On the basis of evolutionary relationships and conserved motif analysis, ZmIDDs were categorized into three clades (1, 2, and 3), each owning 4, 6, and 12 genes, respectively. We analyzed the characteristics of gene structure and found that 3 of the 22 ZmIDD genes do not contain an intron. Cis-element analysis of the ZmIDD promoter showed that most ZmIDD genes possessed at least one ABRE or MBS cis-element, and some ZmIDD genes owned the AuxRR-core, TCA-element, TC-rich repeats, and LTR cis-element. The Ka:Ks ratio of eight segmentally duplicated gene pairs demonstrated that the ZmIDD gene families had undergone a purifying selection. Then, the transcription levels of ZmIDDs were analyzed, and they showed great differences in diverse tissues as well as abiotic stresses. Furthermore, regulatory networks were constructed through the prediction of ZmIDD-targeted genes and miRNAs, which can inhibit the transcription of ZmIDDs. In total, 6 ZmIDDs and 22 miRNAs were discovered, which can target 180 genes and depress the expression of 9 ZmIDDs, respectively. Taken together, the results give us valuable information for studying the function of ZmIDDs involved in plant development and climate resilience in maize.

Details

Title: Comprehensive analysis of the INDETERMINATE DOMAIN (IDD) gene family and their response to abiotic stress in Zea mays
Authors/Creators: X. Feng
Q. Yu
J. Zeng
X. He
Wujun Ma - Murdoch University, Centre for Crop and Food Innovation
L. Ge
W. Liu
Publication Details: International Journal of Molecular Sciences, Vol.24(7), Art. 6185
Publisher: MDPI
Identifiers: 991005566468907891
Copyright: © 2023 by the authors.
Murdoch Affiliation: State Agricultural Biotechnology Centre; Centre for Crop and Food Innovation
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.159 Arabidopsis
Web Of Science research areas: Biochemistry & Molecular Biology; Chemistry, Multidisciplinary
ESI research areas: Chemistry