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Identification, evolutionary analysis and functional diversification of RAV gene family in cotton (G. hirsutum L.)

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Abstract

Main conclusion

Genome wide analysis, expression pattern analysis, and functional characterization of RAV genes highlight their roles in roots, stem development and hormonal response.

Abstract

RAV (Related to ABI3 and VP1) gene family members have been involved in tissues/organs growth and hormone signaling in various plant species. Here, we identified 247 RAVs from 12 different species with 33 RAV genes from G. hirsutum. Phylogenetic analysis classified RAV genes into four distinct groups. Analysis of gene structure showed that most GhRAVs lack introns. Motif distribution pattern and protein sequence logos indicated that GhRAV genes were highly conserved during the process of evolution. Promotor cis-acting elements revealed that promotor regions of GhRAV genes encode numerous elements related to plant growth, abiotic stresses and phytohormones. Chromosomal location information showed uneven distribution of 33 GhRAV genes on different chromosomes. Collinearity analysis identified 628 and 52 orthologous/ paralogous gene pairs in G. hirsutum and G. barbadense, respectively. Ka/Ks values indicated that GhRAV and GbRAV genes underwent strong purifying selection pressure. Selecton model and codon model selection revealed that GhRAV amino acids were under purifying selection and adaptive evolution exists among GhRAV proteins. Three dimensional structure of GhRAVs indicated the presence of numerous alpha helix and beta-barrels. Expression level revealed that some GhRAV genes exhibited high expression in roots (GhRAV3, GhRAV4, GhRAV11, GhRAV18, GhRAV20 and GhRAV30) and stem (GhRAV3 and GhRAV18), indicating their potential role in roots and stem development. GhRAV genes can be regulated by phytohormonal stresses (BL, JA and IAA). Our study provides a reference for future studies related to the functional analysis of GhRAVs in cotton.

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Abbreviations

BL:

Brassinolide

GA:

Gibberellic acid

IAA:

Indole -3-acetic acid

3D:

3 Dimension

PEG:

Polyethylene glycol

DPA:

Days post anthesis

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Acknowledgements

We thank Huo Peng (Zhengzhou Research Center, Institute of Cotton Research of CAAS, Zhengzhou) for technical assistance.

Funding

This work was supported by the Major Research Plan of National Natural Science Foundation of China (NO.31690093), the Natural Science Foundation of Henan (No.212300410093), National Science and Technology Major Project of China (2016YFD0101006).

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Author notes

  1. Nosheen Kabir, Hai Lin and Xianhui Kong have contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China

    Nosheen Kabir, Ghulam Qanmber, YuXuan Wang & Zuoren Yang

  2. Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China

    Le Liu, Zuoren Yang & Na Zhao

  3. Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China

    Hai Lin, Xianhui Kong, Lian Zhang, Zuoren Yang & Yu Yu

  4. Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100122, China

    Zhuojing Sun

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Kabir, N., Lin, H., Kong, X. et al. Identification, evolutionary analysis and functional diversification of RAV gene family in cotton (G. hirsutum L.). Planta 255, 14 (2022). https://doi.org/10.1007/s00425-021-03782-2

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