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Transcriptomic analysis reveals somatic embryogenesis-associated signaling pathways and gene expression regulation in maize (Zea mays L.)

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Abstract

Key message

Transcriptome analysis of maize embryogenic callus and somatic embryos reveals associated genes reprogramming, hormone signaling pathways and transcriptional regulation involved in somatic embryogenesis in maize.

Abstract

Somatic embryos are widely utilized in propagation and genetic engineering of crop plants. In our laboratory, an elite maize inbred line Y423 that could generate intact somatic embryos was obtained and applied to genetic transformation. To enhance our understanding of regulatory mechanisms during maize somatic embryogenesis, we used RNA-based sequencing (RNA-seq) to characterize the transcriptome of immature embryo (IE), embryogenic callus (EC) and somatic embryo (SE) from maize inbred line Y423. The number of differentially expressed genes (DEGs) in three pairwise comparisons (IE-vs-EC, IE-vs-SE and EC-vs-SE) was 5767, 7084 and 1065, respectively. The expression patterns of DEGs were separated into eight major clusters. Somatic embryogenesis associated genes were mainly grouped into cluster A or B with an expression trend toward up-regulation during dedifferentiation. GO annotation and KEGG pathway analysis revealed that DEGs were implicated in plant hormone signal transduction, stress response and metabolic process. Among the differentially expressed transcription factors, the most frequently represented families were associated with the common stress response or related to cell differentiation, embryogenic patterning and embryonic maturation processes. Genes include hormone response/transduction and stress response, as well as several transcription factors were discussed in this study, which may be potential candidates for further analyses regarding their roles in somatic embryogenesis. Furthermore, the temporal expression patterns of candidate genes were analyzed to reveal their roles in somatic embryogenesis. This transcriptomic data provide insights into future functional studies, which will facilitate further dissections of the molecular mechanisms that control maize somatic embryogenesis.

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Data Availability

The raw RNA-Seq data was available at NCBI-SRA (PRJNA645628) in fastq format.

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Acknowledgements

This work was supported by the National Key Research and Development Program of China (2016YFD0101203); The National Transgenic Crops of New Varieties Breeding Major Project-New Germplasm Combination Breeding of Cold Tolerance Transgenic Maize (20142X0800305B).

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  1. Meiqi Ding and Haixiao Dong have contributed equally to this work.

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  1. College of Plant Science, Jilin University, Changchun, 130062, China

    Meiqi Ding, Haixiao Dong, Yingjie Xue, Shengzhong Su, Ying Wu, Shipeng Li, Hongkui Liu, He Li, Junyou Han, Xiaohui Shan & Yaping Yuan

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Contributions

MD, XS and YY conceived and designed the experiments. MD, XS and HD performed the experiments; MD, XS, HD and YY analyzed the data. Others supply reagents/materials/analysis tools. MD and HD wrote the paper. All authors read and approved the manuscript.

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Correspondence to Xiaohui Shan or Yaping Yuan.

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Ding, M., Dong, H., Xue, Y. et al. Transcriptomic analysis reveals somatic embryogenesis-associated signaling pathways and gene expression regulation in maize (Zea mays L.). Plant Mol Biol 104, 647–663 (2020). https://doi.org/10.1007/s11103-020-01066-z

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