This work represents the first systematic integration of transcriptomic and lipidomic data focusing on dynamic changes during the germination stage in B. napus, systematically illustrating the global molecular and lipid metabolic features of rapeseed seeds across sequential imbibition stages.
Abstract
Background
Lipids represent the major storage reserve in Brassica napus seeds. During germination, lipid mobilization delivers indispensable energy to support seedling establishment, thereby profoundly influencing germination vigor and subsequent seedling growth capacity. Although lipid mobilization is fundamentally required for successful rapeseed germination, the temporal coordination between transcriptional reprogramming and lipid metabolic conversion remains largely elusive, and the underlying molecular regulatory network remains to be systematically deciphered.
Results
We conducted an integrated transcriptomic and lipidomic analysis on dry B. napus seeds and germinating seeds at 6, 12, 24, and 48 h after imbibition. The results revealed distinct stage-specific characteristics of gene expression and lipid metabolism during germination. In the early imbibition stage, differentially expressed genes (DEGs) were primarily enriched in biological processes related to water transport, stress response, and signal transduction, whereas significant changes in lipid metabolism were observed to be relatively delayed. During the initiation of germination, triacylglycerols (TGs) underwent rapid degradation, accompanied by a significant up-regulation of genes involved in the β-oxidation and gluconeogenesis pathways. In the late germination stage, genes responsible for membrane lipid synthesis were sharply up-regulated, which induced extensive membrane lipid remodeling.
Conclusion
This work represents the first systematic integration of transcriptomic and lipidomic data focusing on dynamic changes during the germination stage in B. napus, systematically illustrating the global molecular and lipid metabolic features of rapeseed seeds across sequential imbibition stages. It further delineates stage-specific expression patterns of key functional genes and lipid metabolites throughout germination. Collectively, these results advance our comprehensive understanding of the regulatory networks controlling rapeseed seed germination, and offer reliable theoretical references and candidate gene resources for breeding high-yield and high-quality B. napus varieties.
Seed germination of Paris polyphylla var. yunnanensis is intrinsically low, severely restricting its artificial propagation. Despite the known roles of ABA and GAs, the regulatory functions of other phytohormones in this process remain largely unexplored. In this study, we integrated transcriptomic and targeted metabolomic profiling to systematically investigate the dynamics of 34 phytohormones and global gene expression patterns across five germination stages of P. polyphylla seeds. Seven hormones showed significant changes during germination, including auxins, melatonin, cytokinins, and jasmonate, which exhibited distinct accumulation patterns. Integrative correlation analysis further uncovered candidate genes potentially involved in hormone biosynthesis and signaling. Collectively, our findings provide new insights into the hormonal regulation of seed germination in P. polyphylla, establish a foundational framework for understanding its germination mechanisms, and offer candidate molecular targets for improving seed propagation efficiency.
Xunge Zhu, Zong-Liang Xu, Jichao Li et al.· Horticulturae· 0 citations
Sesame is an important oilseed crop, and floral development is a key biological process that lays the foundation for pollination, fertilization, and seed formation, which are closely associated with final yield potential. However, the dynamic transcriptional and metabolic regulatory mechanisms during floral development remain unclear. Here, we performed an integrated transcriptomic and metabolomic analysis across five key developmental stages (T1–T5) of sesame flowers to systematically dissect the multi‑omics regulatory network. KEGG enrichment analysis revealed distinct stage‑specific metabolic characteristics: early stages (T1–T2) were enriched in primary energy metabolism (glycolysis and starch/sucrose metabolism); the middle stage (T3) showed enrichment in DNA replication and phenylpropanoid biosynthesis; and late stages (T4–T5) were associated with plant hormone signaling and α‑linolenic acid metabolism. WGCNA identified two modules correlated with development: a positive module involved in phenylpropanoid biosynthesis, and a negative module related to DNA replication and repair. Genes in the phenylpropanoid/flavonoid pathway displayed a clear sequential expression pattern, promoting flavonoid and anthocyanin accumulation. Collectively, this study provides a comprehensive multi‑omics resource and a descriptive framework for understanding transcriptional and metabolic dynamics during sesame floral development, and identifies candidate pathways and genes that may serve as targets for future functional validation and molecular breeding.
Qiyuan An, Hongsen Cheng, Huijie Sun et al.· Frontiers in Plant Science· 0 citations
A molecular map of chloroplast development is established, elucidating how transcriptional, post-transcriptional, and post-translational layers may contribute to efficient plastid maturation.
Findings demonstrate that dormancy release in P. sibiricum is governed by coordinated hormonal reprogramming, metabolic mobilization, and transcription factor-mediated regulation, providing a theoretical foundation for improving seed germination in this medicinal plant.
Xiaoyu Su, Chunming Li, Lei Li et al.· International Journal of Mol...· 0 citations
Lipids play a crucial role in the initiation and establishment of plant defense responses, however, the mechanisms underlying the links between lipid dynamics and downstream transcriptional events against pathogens remain largely unclear. Here, we conducted a lipidomic analysis to investigate the lipid profile of Arabidopsis seedlings in response to Verticillium dahliae. Our results revealed that V. dahliae infection triggered profound lipid metabolism and transcriptional reprogramming in Arabidopsis. Comprehensive profiling showed extensive remodeling of lipid-associated metabolic pathways, characterized by the significant accumulation of lysophospholipids (LysoPLs) in infected seedlings. This lipid perturbation was mechanistically linked to the transcriptional activation of phospholipase A (PLA) coding genes such as PLA2A, PLA-Iβ2 and PLP5. Genetic evidence has demonstrated that these PLAs are required for disease resistance because their loss-of-function mutants exhibit incresed susceptibility to V. dahliae and compromise the expression of defense-related genes. Furthermore, the PLAs acted as the central regulatory nodes in modulating multiple defense-related signal axes, including SA, JA and ROS, as well as differentially regulating the expression of defense-related genes in response to LysoPLs signal. Together, these findings uncovered an integrated lipid-based and transcription regulatory network, wherein PLA-mediated LysoPLs dynamics served as a critical determinant of plant immunity against V. dahliae.
Fengning Wang, Minying Xie, Xueping Xu et al.· Journal of Experimental Bota...· 0 citations
Seed dormancy is a critical agronomic trait that affects uniform germination and seedling establishment in Luffa cylindrica. In this study, we performed phenotypic, transcriptomic, and metabolomic analyses on two contrasting Luffa cylindrica materials: Z-184 and Z-114. Phenotypic evaluation revealed that compared with Z-114 seeds, Z-184 seeds exhibited significantly lower germination potentials and germination rates. Transcriptomic analysis revealed that the DEGs were predominantly associated with plant hormone signal transduction, MAPK signaling, and metabolic pathways. Metabolomic profiling revealed 2,469 metabolites, with 728 showing significant changes during dormancy release. Integrated transcriptomic and metabolomic analyses highlighted coordinated changes in hormone-, energy-, and secondary metabolism-related pathways. Hormone quantification further demonstrated that the differential accumulation of GA₄, trans-zeatin and trans-zeatin riboside (tZ + tZR), and 2- cis-4-trans- (+) abscisic acid (an isomer of abscisic acid, ABA) was closely associated with the contrasting dormancy phenotypes. These findings provide reference data for the study of the dormancy mechanism of seeds in Luffa cylindrica and lay the foundation for the breeding of weakly dormant Luffa cylindrica.
Luyao Gao, Wenqi Dong, Yu-jie Shi et al.· Plant Science· 0 citations
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