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Phylogeny, gene structures, and expression patterns of the auxin response factor (GhARF2) in upland cotton (Gossypium hirsutum L.)

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Abstract

Background

Auxin response factors (ARFs) are a class of transcription factors that regulate the expression of auxin-responsive genes and play important functions in plant growth and development. To understand the biological functions of the auxin response factor GhARF2 gene in upland cotton, the coding sequence (CDS) of GhARF2 gene was cloned, and its protein sequence, evolutionary relationship, subcellular localization and expression pattern were analysed.

Methods

The CDS sequence of GhARF2 gene was cloned from upland cotton variety Baimian No.1, and its protein sequence was analyzed by bioinformatics method. The subcellular localization of GhARF2 protein was detected by tobacco epidermal transient transformation system, and the tissue expression and stress expression pattern of GhARF2 were analyzed by quantitative Real‑Time PCR (qRT-PCR).

Results

The full-length CDS of GhARF2 gene was 2583 bp, encoded 860 amino acids, and had a molecular weight and an isoelectric point of 95.46 KDa and 6.02, respectively. The GhARF2 protein had multiple phosphorylation sites, no transmembrane domain, and secondary structures dominated by random coils and alpha helix. The GhARF2 protein had 3 conserved typical domains of ARF gene family members, including the B3 DNA binding domain, the Auxin_resp domain, and the Aux/IAA domain. Phylogenetic analysis revealed that ARF2 proteins in different species were clustered in the Group A subgroup, in which GhARF2 was closely related to TcARF2 of Theobroma cacao L. (Malvaceae). The subcellular localization results showed that the GhARF2 protein was localized in the nucleus. Analysis of tissue expression pattern showed that the GhARF2 gene was expressed in all tested tissues, with the highest expression levels in sepal, followed by leaf, and the lowest expression levels in fiber. Further stress expression analysis showed that the GhARF2 gene was induced by drought, high-temperature, low-temperature and salt stress, and had different expression patterns under different stress conditions.

Conclusion

These results established a foundation for understanding the functions of GhARF2 and breeding varieties with high-stress tolerance in cotton.

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Acknowledgements

This work was supported in part by the National Natural Science Foundation of China (31601347), Henan Scientific and Technological Research Program (202102110014), Training Plan for University Young Key Teachers of Henan Province (2020GGJS168) and Henan Postdoctoral Science Foundation (1902042).

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Author notes

  1. Maoni Chao and Jie Dong are contributed equally to this work.

Authors and Affiliations

  1. College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China

    Maoni Chao & Jihua Tang

  2. Postdoctoral Research Base, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China

    Maoni Chao, Genhai Hu, Yanyan Li, Ling Huang, Jinbao Zhang & Qinglian Wang

  3. State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China

    Jie Dong

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Contributions

Q-LW and J-HT designed the experiments and managed the project. M-NC, JD, G-HH, Y-YL and J-BZ performed the experiments. M-NC, JD and LH performed the data analyses. M-NC, JD, Q-LW and J-HT wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Jihua Tang or Qinglian Wang.

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Chao, M., Dong, J., Hu, G. et al. Phylogeny, gene structures, and expression patterns of the auxin response factor (GhARF2) in upland cotton (Gossypium hirsutum L.). Mol Biol Rep 50, 1089–1099 (2023). https://doi.org/10.1007/s11033-022-07999-6

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