Identification of embryo proteins associated with seed germination and seedling establishment in germinating rice seeds

Unravelling the Significance of Seed Proteomics: Insights into Seed Development, Function, and Agricultural Applications

Seeds are essential for plant reproduction, ensuring species survival and dispersal while adapting to diverse environments throughout a plant's life. Proteomics has emerged as a powerful tool for deciphering the complexities of seed growth, germination, and stress responses. Advanced proteomic technologies enable the analysis of protein changes during germination, dormancy, and ageing, enhancing our understanding of seed lifespan and vitality. Recent studies have revealed detailed insights into metabolic processes and storage protein profiles across various plant species. This knowledge is crucial for improving seed storage, conserving quality, and maintaining viability. Additionally, it contributes to sustainable agriculture by identifying stress-responsive proteins and signalling pathways that can mitigate stress and enhance farming practices. This review highlights significant advancements in seed proteomics over the past decade, discussing critical discoveries related to storage proteins, protein interactions, and proteome modifications due to stress. It illustrates how these insights transform seed biology, boosting productivity, food security, and environmentally friendly practices. The review also identifies existing knowledge gaps and provides direction for future research, underscoring the need for continued interdisciplinary collaboration in this dynamic field.

A preliminary mapping of QTL qsg5.1 controlling seed germination in melon (Cucumis melo L.)

Melon (Cucumis melo L.) seed germination significantly affects its economic value. Cultivation of melon varieties with high germination ability and seedling vigor is beneficial in large-scale melon propagation. In this study, two melon genotypes differing in their germination ability, P5 with low and P10 with high germination ability, were used to identify the optimal seed germination conditions by evaluating different water immersion times and germination temperatures. The germination rate of the P5 and P10 parental genotypes and their segregating population, consisting of 358 F2:3 families, were evaluated for 2 years to identify their genetic basis. QTL analysis was performed on a high-density genetic map constructed using specific-locus amplified fragment sequencing (SLAF-seq). The germination rate of F1 and F2 populations treated with water immersion for 8 h at 28°C and measured at 48 h showed a normal distribution Genetic mapping carried out using the high-density genetic map revealed eight QTLs in chromosomes 2, 4, 5, 6, and 8 that control melon seed germination, of which 2020/2021-qsg5.1 was consistently significant in both years of experimentation. qsg5.1 explained 15.13% of the phenotypic variance with a LOD of 4.1. To fine map the candidate region of qsg5.1, eight cleaved amplified polymorphism sequence (CAPS) markers were used to construct a genetic map with another 421 F2 individual fruits. The major QTL qsg5.1 was located between SNP53 and SNP54 within a 55.96 Kb interval containing four genes. qRT-PCR gene expression analysis of the candidate genes showed that MELO3C031219.2 (Phosphorus transporter PHO-5) exhibited a significant difference in gene expression between the parental lines at 24, 32, and 48 h after germination, potentially being the underlying gene controlling melon seed germination. These results provide a theoretical basis for the molecular mechanisms controlling melon seed germination and can practically contribute to further improving germination to increase the propagation efficiency of commercial melon cultivars.

From the Outside to the Inside: New Insights on the Main Factors That Guide Seed Dormancy and Germination

The transition from a dormant to a germinating seed represents a crucial developmental switch in the life cycle of a plant. Subsequent transition from a germinating seed to an autotrophic organism also requires a robust and multi-layered control. Seed germination and seedling growth are multistep processes, involving both internal and external signals, which lead to a fine-tuning control network. In recent years, numerous studies have contributed to elucidate the molecular mechanisms underlying these processes: from light signaling and light-hormone crosstalk to the effects of abiotic stresses, from epigenetic regulation to translational control. However, there are still many open questions and molecular elements to be identified. This review will focus on the different aspects of the molecular control of seed dormancy and germination, pointing out new molecular elements and how these integrate in the signaling pathways already known.

Cellular alteration and differential protein profile explain effects of GA3 and ABA and their inhibitor on Trichocline catharinensis (Asteraceae) seed germination

Seed physiology of wild species has not been studied as deeply as that of domesticated crop species. Trichocline catharinensis (Asteraceae) is an endemic wildflower species from the high-altitude fields of southern Brazil. This species is of interest as a source of genes to improve cultivated Asteraceae because of its ornamental features, disease resistance and ability to tolerate drought and poor soil conditions. We studied the effects of abscisic acid (ABA) and gibberellic acid (GA₃ ) and their inhibitors, fluridone (FLU) and paclobutrazol (PAC), on seed germination. We individually assessed ultrastructural changes and differential protein accumulation. The principal component analysis explained 69.66% of differential accumulation for 32 proteins at phase II of seed germination in response to hormone and inhibitor treatment. GA₃ -imbibed seed germination (98.75%) resulted in increased protein accumulation to meet energy demand, redox regulation, and reserve metabolism activation. FLU-imbibed seeds showed a higher germination speed index as a consequence of metabolism activation. ABA-imbibed seeds (58.75%) showed osmotolerance and flattened cells in the hypocotyl-radicular axis, suggesting that ABA inhibits cell expansion. PAC-imbibed seeds remained at phase II for 300 h, and germination was suppressed (7.5%) because of the increased signaling proteins and halted reserve mobilization. Therefore, our findings provide insight into the behavior of Asteraceae non-dormant seed germination, which broadens our knowledge of seed germination in a wild and endemic plant species from a threatened ecosystem.

A calcium-dependent lipid binding protein, OsANN10, is a negative regulator of osmotic stress tolerance in rice

Annexin, a multi-gene family in plants, is essential for plant growth and stress responses. Recent studies demonstrated a positive effect of annexin in abiotic stress responses. Interestingly, we found OsANN10, a putative annexin gene in rice, negatively regulated plant responses to osmotic stress. Knocking down OsANN10 significantly decreased the content of H₂O₂ by increasing Peroxidase (POD) and Catalase (CAT) activities, further reducing oxidative damage in rice leaves, suggesting a negative regulation of OsANN10 in protecting cell membrane against oxidative damage via scavenging ROS under osmotic stress.

Lost in Translation: Physiological Roles of Stored mRNAs in Seed Germination

Seeds characteristics such as germination ability, dormancy, and storability/longevity are important traits in agriculture, and various genes have been identified that are involved in its regulation at the transcriptional and post-transcriptional level. A particularity of mature dry seeds is a special mechanism that allows them to accumulate more than 10,000 mRNAs during seed maturation and use them as templates to synthesize proteins during germination. Some of these stored mRNAs are also referred to as long-lived mRNAs because they remain translatable even after seeds have been exposed to long-term stressful conditions. Mature seeds can germinate even in the presence of transcriptional inhibitors, and this ability is acquired in mid-seed development. The type of mRNA that accumulates in seeds is affected by the plant hormone abscisic acid and environmental factors, and most of them accumulate in seeds in the form of monosomes. Release of seed dormancy during after-ripening involves the selective oxidation of stored mRNAs and this prevents translation of proteins that function in the suppression of germination after imbibition. Non-selective oxidation and degradation of stored mRNAs occurs during long-term storage of seeds so that the quality of stored RNAs is linked to the degree of seed deterioration. After seed imbibition, a population of stored mRNAs are selectively loaded into polysomes and the mRNAs, involved in processes such as redox, glycolysis, and protein synthesis, are actively translated for germination.

Ascorbic Acid-The Little-Known Antioxidant in Woody Plants

Reactive oxygen species (ROS) are constantly produced by metabolically active plant cells. The concentration of ROS may determine their role, e.g., they may participate in signal transduction or cause oxidative damage to various cellular components. To ensure cellular homeostasis and minimize the negative effects of excess ROS, plant cells have evolved a complex antioxidant system, which includes ascorbic acid (AsA). AsA is a multifunctional metabolite with strong reducing properties that allows the neutralization of ROS and the reduction of molecules oxidized by ROS in cooperation with glutathione in the Foyer-Halliwell-Asada cycle. Antioxidant enzymes involved in AsA oxidation and reduction switches evolved uniquely in plants. Most experiments concerning the role of AsA have been performed on herbaceous plants. In addition to extending our understanding of this role in additional taxa, fundamental knowledge of the complex life cycle stages of woody plants, including their development and response to environmental factors, will enhance their breeding and amend their protection. Thus, the role of AsA in woody plants compared to that in nonwoody plants is the focus of this paper. The role of AsA in woody plants has been studied for nearly 20 years. Studies have demonstrated that AsA is important for the growth and development of woody plants. Substantial changes in AsA levels, as well as reduction and oxidation switches, have been reported in various physiological processes and transitions described mainly in leaves, fruits, buds, and seeds. Evidently, AsA exhibits a dual role in the photoprotection of the photosynthetic apparatus in woody plants, which are the most important scavengers of ozone. AsA is associated with proper seed production and, thus, woody plant reproduction. Similarly, an important function of AsA is described under drought, salinity, temperature, light stress, and biotic stress. This report emphasizes the involvement of AsA in the ecological advantages, such as nutrition recycling due to leaf senescence, of trees and shrubs compared to nonwoody plants.

Quaternary Ammonium Salts of Iminofullerenes: Fabrication and Effect on Seed Germination

In this study, novel water-soluble quaternary ammonium salts of iminofullerenes (IFQA) were synthesized by nitrene chemistry in combination with quaternization and identified as [C₆₀(NCH₂CH₂NH₃⁺·CF₃COO^-)₄·10H₂O]_n by various spectroscopies. Maize and Arabidopsis seeds were used to test the bioactivity of IFQA in seed germination. Compared with the control, maize seed exposure to 50 mg/L IFQA (normal: 73.1% vs 58.7%; drought: 66.7% vs 50.0% at the second day) and Arabidopsis seed exposure to 20 mg/L IFQA (normal: 77.5% vs 58.8%; drought: 63.3% vs 36.7% at the second day) had higher germination rates and quicker germination. The results of two-dimensional gel electrophoresis combined with mass spectroscopy showed that the abundance of 21 proteins in embryo proteome of maize seeds was significantly changed (>1.5 fold). The downregulated six storage proteins and upregulated four proteins induced by IFQA for energy production and sugar metabolism indicated a faster metabolic activity of maize seed germination. The upregulated eight stress-related proteins and antioxidant enzymes suggested that the role of IFQA was to activate the metabolic processes in seed germination and also increase seed stress response. The results provide important information to understand the mechanism of seed germination enhancement by carbon nanomaterials.

Integrated physiology and proteome analysis of embryo and endosperm highlights complex metabolic networks involved in seed germination in wheat (Triticum aestivum L.)

The aim of this study was to investigate the physiological and proteomic changes in the embryo and endosperm during seed germination in the elite Chinese bread wheat cultivar Zhengmai 366. Upon imbibition, seed size and water content increased rapidly, followed by a series of metabolic changes including increases in soluble sugar content and α-amylase activity, a decrease in starch content, and a rapid increase in plant hormones. In total, 57 and 45 differentially accumulated proteins (DAPs) from the embryo and endosperm, respectively, were identified at five germination stages (0, 6, 12, 18, and 24 h). Principal component analysis revealed a significant proteome difference between embryo and endosperm as well as the different germination stages. The largest proteome changes occurred 24 h after seed imbibition. Embryo DAP spots were mainly involved in energy metabolism, amino acid metabolism, stress/defense, and protein metabolism; those from the endosperm were primarily related to storage protein and carbohydrate metabolism. Protein-protein interaction analysis revealed a complicated interaction network between energy-related proteins and other proteins. Metabolic pathway analysis highlighted complex regulatory networks in the embryo and endosperm that regulate wheat seed germination. These results provide new insights into the molecular mechanisms of seed germination.

Seed Dormancy Involves a Transcriptional Program That Supports Early Plastid Functionality during Imbibition

Red rice fully dormant seeds do not germinate even under favorable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and non-dormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and non-dormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 h and 8 days). Aim of the study was to highlight the differences in the transcriptome of dormant and non-dormant imbibed seeds. Transcript data suggested important differences between these seeds (at least, as inferred by expression-based metabolism reconstruction): dry-afterripening seems to impose a respiratory impairment onto non-dormant seeds, thus glycolysis is deduced to be preferentially directed to alcoholic fermentation in non-dormant seeds but to alanine production in dormant ones; phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase and alanine aminotransferase pathways appear to have an important gluconeogenetic role associated with the restoration of plastid functions in the dormant seed following imbibition; correspondingly, co-expression analysis pointed out a commitment to guarantee plastid functionality in dormant seeds. At 8 h of imbibition, as inferred by gene expression, dormant seeds appear to preferentially use carbon and nitrogen resources for biosynthetic processes in the plastid, including starch and proanthocyanidins accumulation. Chromatin modification appears to be a possible mechanism involved in the transition from dormancy to germination. Non-dormant seeds show higher expression of genes related to cell wall modification, suggesting they prepare for acrospire/radicle elongation.

Proteomic analysis reveals a role of melatonin in promoting cucumber seed germination under high salinity by regulating energy production

Seed germination is a critical and complex process in the plant life cycle. Although previous studies have found that melatonin can promote seed germination under salt stress, the involvement of melatonin in the regulation of proteomic changes remains poorly understood. In this study, a total of 157 proteins were significantly influenced (ratio ≥ 2 or ≤ -2) by melatonin during seed germination under salt stress using a label-free quantitative technique. Our GO analysis revealed that several pathways were obviously regulated by melatonin, including ribosome biosynthesis, lipid metabolism, carbohydrate metabolism, and storage protein degradation. Not only stress-tolerant proteins but also proteins that produce ATP as part of glycolysis, the citric acid cycle, and the glyoxylate cycle were upregulated by melatonin. Overall, this study provides new evidence that melatonin alleviates the inhibitory effects of NaCl stress on seed germination by promoting energy production. This study is the first to provide insights at the proteomic level into the molecular mechanism of melatonin in response to salt stress in cucumber seeds. This may be helpful to further understand the role of melatonin in cucumber seed germination under stress conditions.

Mapping the N-linked glycosites of rice (Oryza sativa L.) germinating embryos

Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered. Inspection of the motifs and sequence structures involved suggested that all the glycosites were concentrated within [NxS/T] motif, while 82.3% of them were in a coil structure. N-glycosylation preferentially occurred on proteins with glycoside hydrolase activities, which were significantly enriched in the starch and sucrose metabolism pathway, suggesting that N-glycosylation is involved in embryo germination by regulating carbohydrate metabolism. Notably, protein-protein interaction analysis revealed a network with several Brassinosteroids signaling proteins, including XIAO and other BR-responsive proteins, implying that glycosylation-mediated Brassinosteroids signaling may be a key mechanism regulating rice embryo germination. In summary, this study expanded our knowledge of protein glycosylation in rice, and provided novel insight into the PTM regulation in rice seed germination.