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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Bioinformatics
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1506853
This article is part of the Research Topic Exploring Structural Variants in Plant Pangenomics: Innovations and Applications View all 3 articles

Pan-genome analysis and expression verification of the maize ARF gene family

Provisionally accepted
Quan-cai Man Quan-cai Man 1Yan-qun Wang Yan-qun Wang 2*Shun-juan Gao Shun-juan Gao 1*Zhi-chang Gao Zhi-chang Gao 1*Zhengping Peng Zhengping Peng 2Jiang-hui Cui Jiang-hui Cui 1*
  • 1 College of Agronomy, Hebei Agricultural University, Baoding, China
  • 2 College of Resources and Environmental Sciences, Hebei Agriculture University, Baoding, Hebei Province, China

The final, formatted version of the article will be published soon.

    Auxin transcription factors regulate auxin responses and play crucial roles in plant growth, development, and responses to abiotic stress. Utilizing the maize pangenome data, this study identified 35 ARF family members in maize, comprising 21 core genes, 10 near-core genes, and 4 non-essential genes; no private genes were detected. The construction of a phylogenetic tree using Arabidopsis thaliana revealed that the G3 subfamily comprises the highest number of core genes, with a total of 10, and exhibits relative stability throughout the evolution of maize. The calculation of the Ka/Ks ratios for ARF family members across 26 genomes indicated that, aside from ARF8 and ARF11, which were subjected to positive selection, the remaining genes underwent purifying selection. Analysis of structural variation revealed that the expression level of the ARF4 gene significantly differed as a result of this variation.Simultaneously, the structural variation also influenced the conserved domain and cisacting elements of the gene. Further combining the transcriptome data and RT-qPCR found that, The expression levels of ARF family members in maize were higher at the early stage of embryo and grain development, and the expression levels of each member in embryo and grain were complementary, and the ARF4 plays an important role in abiotic stress. In summary, this study utilizes the maize pan-genome and bioinformatics methods to investigate the evolutionary relationships and functional roles of ARF family members in maize, thereby providing a novel theoretical framework for further research on the maize ARF family.

    Keywords: maize pan-genome, Auxin transcription factors, Structure variation, Selection pressure, transcriptome data analysis

    Received: 06 Oct 2024; Accepted: 23 Dec 2024.

    Copyright: © 2024 Man, Wang, Gao, Gao, Peng and Cui. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Yan-qun Wang, College of Resources and Environmental Sciences, Hebei Agriculture University, Baoding, Hebei Province, China
    Shun-juan Gao, College of Agronomy, Hebei Agricultural University, Baoding, China
    Zhi-chang Gao, College of Agronomy, Hebei Agricultural University, Baoding, China
    Jiang-hui Cui, College of Agronomy, Hebei Agricultural University, Baoding, China

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