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

• Published in: The Plant journal : for cell and molecular biology 2019-07, Vol.99 (1), p.163-175
• Main Authors: Ponnaiah, Maharajah, Gilard, Françoise, Gakière, Bertrand, El‐Maarouf‐Bouteau, Hayat, Bailly, Christophe
• Format: Article
• Language: English
• Subjects: Arabidopsis; Arabidopsis - metabolism; Arabidopsis - physiology; Arabidopsis thaliana; Clustering; Datasets; Deregulation; Dormancy; Gene expression; Gene Expression Regulation, Plant - genetics; Gene Expression Regulation, Plant - physiology; Germination; Germination - genetics; Germination - physiology; Imbibition; Life Sciences; Metabolic pathways; Metabolism; Metabolomics; Plant Dormancy - genetics; Plant Dormancy - physiology; plant pathways; Regulators; RNA transport; seed; Seed germination; Seeds; Seeds - metabolism; Seeds - physiology; Signal transduction; Transcription; Transcriptome - genetics; transcriptomics; Vegetal Biology; Vitamin B6
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.14311

Summary 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. Significance Statement Actual models of seed transcriptome analysis do not provide a comprehensive view of the germination process because they do not catch additive effects of small variations of gene expression in a signalling or in a metabolic pathway. Here, we provide a pathway‐based analysis that allows us to reveal the involvement of alternative pathways in seed germination and which demonstrates that the route to completing this process differs according to the genetic background.