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Weighted gene co-expression network analysis unveils gene networks regulating folate biosynthesis in maize endosperm

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Abstract

Folates are essential elements for human growth and development, and their deficiency can lead to serious disorders. Waxy maize is a rich source of folates; however, the regulatory mechanism underlying folate biosynthesis in the endosperm remains unclear. Here, we examined changes in the folate content of maize endosperm collected at 15, 18, 21, 24, and 27 days after pollination (DAP) using liquid chromatograph-mass spectrometry and identified genes related to folate biosynthesis using transcriptome sequencing data. The results showed that 5-methyl-tetrahydrofolate and 5,10-methylene tetrahydrofolate were the main storage forms of folates in the endosperm, and their contents were relatively high at 21–24 days. We also identified 569, 3183, 4365, and 5513 differentially expressed genes (DEGs) in different days around milk stage. Functional annotation revealed 518 transcription factors (TFs) belonging to 33 families exhibiting specific expression in at least one sampling time. The key hub genes involved in folate biosynthesis were identified by weighted gene co-expression network analysis. In total, 24,976 genes were used to construct a co-expression network with 29 co-expression modules, among which the brown and purple modules were highly related to folate biosynthesis. Further, 187 transcription factors in the brown and purple modules were considered potential transcription factors related to endosperm folate biosynthesis. These results may improve the understanding of the molecular mechanism underlying folate biosynthesis in waxy maize and lead to the development of nutritionally fortified varieties.

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Data accessibility

Raw sequencing data were deposited in the NCBI SRA database (accession number: PRJNA660527).

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Acknowledgements

The authors are grateful to our colleagues who have shared their knowledge and reagents, at the State Shanghai Key Laboratory of Agricultural Genetics and Breeding (Shanghai Academy of Agricultural Sciences). They also thank the editor and reviewers for critical comments and thoughtful suggestions.

Funding

The project was supported by the funding of Shanghai Agriculture Applied Technology Development Program (Z20180103), Shanghai Agricultural Science Committee Youth Talents Development Plan No. 2018 (1-34), Shanghai Academy of Agricultural Sciences Youth Talent Program (ZP21211), Shanghai Engineering Technology Research Center of Specialty Maize (20DZ2255300), and Shanghai Science and Technology Commission of the belt and road project (20310750500).

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Author notes

  1. Lili Song and Diansi Yu have contributed equally to this work.

Authors and Affiliations

  1. Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Supervision and Test Center for Ecological Environment Safety of Crops of MOA, Shanghai, China

    Lili Song, Guogan Wu, Yu Sun, Peng Li, Jinbin Wang, Cui Wang, Beibei Lv & Xueming Tang

  2. Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106, China

    Lili Song, Diansi Yu, Hongjian Zheng, Guogan Wu, Yu Sun, Peng Li, Jinbin Wang, Cui Wang, Beibei Lv & Xueming Tang

  3. Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, CIMMYT-China Specialty Maize Research Center, Shanghai, 201403, China

    Diansi Yu & Hongjian Zheng

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  1. Lili Song
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  2. Diansi Yu
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Contributions

XT and LS designed the experiments. LS, DY, GW, and CW performed the experiments. DY, PL, and YS analyzed the data. JW and BL contributed to the RNA-seq data accessibility via the FileZilla. LS and DY wrote the article. HZ provided the seeds. All the authors have read and agreed to the published version of the manuscript.

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Correspondence to Xueming Tang.

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Song, L., Yu, D., Zheng, H. et al. Weighted gene co-expression network analysis unveils gene networks regulating folate biosynthesis in maize endosperm. 3 Biotech 11, 441 (2021). https://doi.org/10.1007/s13205-021-02974-7

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