Transcriptomic analysis reveals somatic embryogenesis-associated signaling pathways and gene expression regulation in ma
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Transcriptomic analysis reveals somatic embryogenesis‑associated signaling pathways and gene expression regulation in maize (Zea mays L.) Meiqi Ding1 · Haixiao Dong1 · Yingjie Xue1 · Shengzhong Su1 · Ying Wu1 · Shipeng Li1 · Hongkui Liu1 · He Li1 · Junyou Han1 · Xiaohui Shan1 · Yaping Yuan1 Received: 5 September 2019 / Accepted: 31 August 2020 © Springer Nature B.V. 2020
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. Keywords Zea mays L. · Somatic embryogenesis · RNA-seq · Transcription regulation · Expression pattern
Introduction Meiqi Ding and Haixiao Dong have contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11103-020-01066-z) contains supplementary material, which is available to authorized users. * Xiaohui Shan [email protected] * Yaping Yuan [email protected] 1
College of Plant Science, Jilin University, Changchun 130062, China
Maize is one of the most important crops in international agriculture for its role in meeting global
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