Regulatory actors and alternative routes for Arabidopsis seed germination are revealed using a pathway‐based analysis of transcriptomic datasets

First author: Maharajah Ponnaiah; Affiliations: Sorbonne Université (索邦大学): Paris, France

Corresponding author: Christophe Bailly

Regulation of seed germination by dormancy relies on a complex network of transcriptional and post‐transcriptional modifications during seed imbibition that controls seed adaptive responses to environmental cues. High‐throughput technologies have brought significant progress in the understanding of this phenomenon and have led to identify major regulators of seed germination, mostly by studying the behaviour of highly differentially expressed genes. However, the actual models of transcriptome analysis cannot catch additive effects of small variations of gene expression in individual signalling or metabolic pathways, which are also likely to control germination. Therefore, the comprehension of the molecular mechanism regulating germination is still incomplete and to gain knowledge about this process we have developed a pathway‐based analysis of transcriptomic Arabidopsis datasets, to identify regulatory actors of seed germination. The method allowed quantifying the level of deregulation of a wide range of pathways in dormant versus non‐dormant seeds. Clustering pathway deregulation scores of germinating and dormant seed samples permitted the identification of mechanisms involved in seed germination such as RNA transport or vitamin B6 metabolism, for example. Using this method, which was validated by metabolomics analysis, we also demonstrated that Col and Cvi seeds follow different metabolic routes for completing germination, demonstrating the genetic plasticity of this process. We finally provided an extensive basis of analysed transcriptomic datasets that will allow further identification of mechanisms controlling seed germination.

休眠调控植物种子萌发依赖于种子吸胀期一个十分复杂的转录和转录后修饰网络，该调控网络控制种子对于外界环境信号的适应性反应。高通量测序技术加速了我们对于该过程的理解，并通过基因的显著差异表达鉴定了种子萌发过程的主要调控子。然而，现有的转录组分析手段并不能够捕获单个信号或代谢通路上基因表达微弱变异的加性效应，而这些很有可能在种子萌发过程中也发挥着重要作用。因此，调控种子萌发的分子机制仍然还不完整，为了深入研究该过程的分子机制，作者开发了一套基于通路的转录组分析方法用来鉴定种子萌发过程的调控因子。该方法能够定量休眠种子相对于非休眠种子在各通路上的去调控水平。对于萌发和休眠种子样本的去调控通路聚类打分能够鉴定出参与种子萌发的分子机制，比如说RNA转运或是维生素B6代谢。利用这种方法，作者还揭示了Col和Cvi种子会采取不同的代谢途径来完成发芽，并进一步通过代谢组学的分析验证了这一结果，说明了该过程的遗传可塑性。最终，作者在本文中开发了一套新的转录组分析方法，该方法能够进一步鉴定控制种子萌发的分子机制。

doi: https://doi.org/10.1111/tpj.14311

Journal: the plant journal

First Published: March 14, 2019