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Identification and co-expression network analysis of plumule-preferentially expressed genes in Oryza sativa

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Abstract

Background

The seedling establishment is controlled by the programmed expression of sets of genes at the specific tissues of seed, abundance and environment. Plumule is an important part of the seed embryo and expresses the suits of genes to exert distinct functions during seed germination. Although rice genomic resources are available and developed rapidly, thousands of transcripts have not previously been located in the plumule of rice.

Objective

This study was performed to identify plumule-preferentially expressed (OsPluP) genes in rice and determine the expression profiles and functions of OsPluP genes.

Methods

We identified the OsPluP genes through Affymetrix microarray data. Meanwhile, qRT-PCR was performed to validate the expression pattern, also found that OsPluP genes were regulated by dark/light treatment. The cis-acting regulatory elements were analyzed in the promoters’ regions of OsPluP genes. The T-DNA mutant of the OsPluP seed was used to reveal the function in seed germination.

Results

In this study, a genomic survey of OsPluP genes was performed, and we identified 88 OsPluP genes based on Affymetrix microarray data. The expression profiles of 88 OsPluP members in 24 representative tissues covering rice whole life cycle can be roughly classified into three major groups, suggesting functional divergence of OsPluP genes in seed germination. The microarray data, qRT-PCR, and promoter analysis results demonstrated that transcripts of more than half OsPluPs (54 genes) could be enhanced in the darkness and respond to phytohormone. Gene Ontology (GO)and Kyoto encyclopedia of genes and genomes (KEGG) analysis demonstrated that OsPluP and their co-expressed genes were highly enriched in fatty acid metabolism. Moreover, OsPluP82 T-DNA mutant seeds displayed short plumule length and storage lipid accumulation.

Conclusion

This study would enable the functions of OsPluP genes during seed germination and contribute to the goal of molecular regulatory networks that lay the foundation for further studies of seedling growth.

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Data availability

The expression profile of the OsPluP genes in various tissues of cultivar Minghui 63 was extracted from NCBI Gene Expression Omnibus GSE19024.

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (Grant no. 32160699, 32060587 and 31660046), Guizhou Province Natural Science Foundation [QKHJC-ZK[2022]ZD032]. The Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou province (Grant no. U1812401). Guizhou Educational project Qianjiaohe ([2021]309).

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Author notes

  1. Huiqing Yan

    Present address: Huaxi District, Guiyang City, Guizhou Province, China

  2. Guilian Sun and Zongmin Wu contributed equally to the work and should be regarded as co-first authors.

Authors and Affiliations

  1. School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China

    Guilian Sun, Zongmin Wu, Lisheng Zhai, Yin Yi, Huiqing Yan & Xiaolong Huang

  2. Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China

    Guilian Sun, Zongmin Wu, Lisheng Zhai, Yin Yi & Xiaolong Huang

  3. Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, 550001, China

    Guilian Sun, Zongmin Wu & Xiaolong Huang

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Sun, G., Wu, Z., Zhai, L. et al. Identification and co-expression network analysis of plumule-preferentially expressed genes in Oryza sativa. Genes Genom 45, 319–336 (2023). https://doi.org/10.1007/s13258-023-01366-w

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  • DOI: https://doi.org/10.1007/s13258-023-01366-w

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