Abstract
Soybean (Glycine max) is a major legume crop worldwide, providing a critical source of protein and oil. The release of the soybean genome fuelled several transcriptome projects comprising multiple developmental stages and environmental conditions. Nevertheless, the global transcriptional patterns of embryonic axes during germination remain unknown. Here we report the analysis of ~1.58 billion RNA-Seq reads from soybean embryonic axes at five germination stages. Our results support the early activation of processes that are critical for germination, such as glycolysis, Krebs cycle and cell wall remodelling. Strikingly, only 3 hours after imbibition there is a preferential up-regulation of protein kinases and transcription factors, particularly from the LOB domain family, implying that transcriptional and post-transcriptional regulation play major roles early after imbibition. Lipid mobilization and glyoxylate pathways are also transcriptionally active in the embryonic axes, indicating that the local catabolism of oil reserves in the embryonic axes contributes to energy production during germination. We also present evidence supporting abscisic acid inactivation and the up-regulation of gibberellin, ethylene and brassinosteroid pathways. Further, there is a remarkable differential activation of paralogous genes in these hormone signalling pathways. Taken together, our results provide insights on the regulation and biochemistry of soybean germination.
Highlights
Several large-scale transcriptomic studies were conducted for a variety of dicot species, such as Arabidopsis thaliana[15] and chickpea[16]
Total mapped reads acid (ABA) and gibberellic acid (GA), respectively[8,10,11]; further, key genes involved in the GA/ABA interplay have been characterized [e.g. 9-cis epoxycarotenoid dioxygenase (NCED), gibberellin 2-oxidase (GA2ox), gibberellin insensitive dwarf 1 (GID1) and phytochrome-interacting factors (PIF’s)], which helped elucidate underlying aspects of ABA and GA regulation[12,13,14]
Among our main results are: i) a strong preferential activation of transcription factors (TFs) and protein kinases in the onset of germination; ii) an important carbohydrate partitioning system underlying cell wall metabolism and ATP production; iii) an early activation of primary catabolic pathways; iv) a strong up-regulation of genes involved in hormone biosynthesis, catabolism and signalling; iv) transcriptional divergence and potential sub-functionalization of paralogous genes with critical roles in hormone signalling, (e.g. GID1, DELLA and CYP707A)
Summary
Acid (ABA) and gibberellic acid (GA), respectively[8,10,11]; further, key genes involved in the GA/ABA interplay have been characterized [e.g. 9-cis epoxycarotenoid dioxygenase (NCED), gibberellin 2-oxidase (GA2ox), gibberellin insensitive dwarf 1 (GID1) and phytochrome-interacting factors (PIF’s)], which helped elucidate underlying aspects of ABA and GA regulation[12,13,14]. Soybean transcriptomic studies allowed the discovery of important genes involved in the determination of floral organs and maintenance of shoot apical meristem[17]; seed filling[18]; response against drought stress[19] and regulation of seed development[20]. The transcriptomic changes of soybean embryonic axes during germination remain unexplored, in spite of the essential nature of this stage in plant growth. Among our main results are: i) a strong preferential activation of transcription factors (TFs) and protein kinases in the onset of germination; ii) an important carbohydrate partitioning system underlying cell wall metabolism and ATP production; iii) an early activation of primary catabolic pathways; iv) a strong up-regulation of genes involved in hormone biosynthesis, catabolism and signalling; iv) transcriptional divergence and potential sub-functionalization of paralogous genes with critical roles in hormone signalling, (e.g. GID1, DELLA and CYP707A)
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