Abstract
Poplar (Populus × xiaohei T. S. Hwang et Liang) is an excellent model plant, with a known genome sequence, for studying woody plant developmental processes, such as seed germination. Here, we report the transcriptional profiling of poplar seeds at five germination stages using RNA-Seq technology. We focused on identifying biological pathway activity changes during seed germination and transcription factors that play important roles in different stages. Among the 16 significantly changing clusters obtained using the STEM method, transcription was significantly enriched in five different clusters, 8, 21, 25, 27, and 35. The oxidative phosphorylation-related genes were only enriched in cluster 9, and expression patterns decreased in 6 and 24 HAI, while ubiquitin-dependent protein catabolic processes were only enriched in cluster 16, and expression patterns increased in 6 HAI. A weighted mean method analysis determined that most primary metabolism-associated categories, such as major carbohydrate metabolism, glycolysis, oxidative pentose phosphate, tricarboxylic acid cycle, lipid metabolism, nucleotide metabolism, amino acid metabolism, and protein metabolism, were elevated between 6 and 48 h after imbibition (HAI). ATP synthesis and C1 metabolism had highly active expression patterns between 0.75 and 48 HAI. The photosynthesis category-associated genes that were identified appeared highly active at 144 HAI. The homogenization of transcription factors in each cluster revealed that the HAP2, C3H zinc finger family, and C2C2(Zn) GATA transcription factors were present in relatively high numbers in cluster 8, while HAP5, Zn-finger (CCHC), FHA, and E2F/DP transcription factor families, as well as SNF7, were present in high numbers in cluster 25. Thus, we identified a series of biological pathway activity changes that occur, and transcription factors that are active, during poplar seed germination. Moreover, this study provides an integrated view of transcriptional regulation that can reveal the molecular events occurring during seed germination.
Highlights
Most flowering plants reproduce by seed germination
To reveal the variation among the differentially expressed genes (DEGs), a STEM tool was used to cluster and visualize RNA-Seq expression profiles of 33,338 genes differentially expressed during seed germination at any given time point in the study (Table S1)
This study revealed a more comprehensive list of transcription factor (TF) that function during the different stages of poplar seed germination
Summary
Most flowering plants reproduce by seed germination. Seed germination is a crucial phase in the life cycle of higher plants because it disseminates the genetic information necessary for the generation of plants to disperse, establish, develop and eventually reproduce to maintain the species [1,2,3].Seed germination is a very complicated process, involving a series of molecular, physiological, and morphological changes during different periods. Most flowering plants reproduce by seed germination. Seed germination is a crucial phase in the life cycle of higher plants because it disseminates the genetic information necessary for the generation of plants to disperse, establish, develop and eventually reproduce to maintain the species [1,2,3]. Seed germination is a very complicated process, involving a series of molecular, physiological, and morphological changes during different periods. Seed germination starts with imbibition, when the seed takes in water from the soil [4]. On the basis of the fresh weight pattern during seed germination, Forests 2019, 10, 664; doi:10.3390/f10080664 www.mdpi.com/journal/forests. Afterwards, seeds enter a period of post-germination until the expansion of the first true leaf
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