Studies on the molecular mechanisms of seed germination

Physiology and transcriptome of Eucommia ulmoides seeds at different germination stages

E. ulmoides (Eucommia ulmoides) has significant industrial and medicinal value and high market demand. E. ulmoides grows seedlings through sowing. According to previous studies, plant hormones have been shown to regulate seed germination. To understand the relationship between hormones and E. ulmoides seed germination, we focused on examining the changes in various indicators during the germination stage of E. ulmoides seeds. We measured the levels of physiological and hormone indicators in E. ulmoides seeds at different germination stages and found that the levels of abscisic acid (ABA), gibberellin (GA), and indole acetic acid (IAA) significantly varied as the seeds germinated. Furthermore, we confirmed that ABA, GA, and IAA are essential hormones in the germination of E. ulmoides seeds using Gene Ontology and Kyoto Encyclopedia of Genes and Genomics enrichment analyses of the transcriptome. The discovery of hormone-related synthesis pathways in the control group of Eucommia seeds at different germination stages further confirmed this conclusion. This study provides a basis for further research into the regulatory mechanisms of E. ulmoides seeds at different germination stages and the relationship between other seed germination and plant hormones.

Selection of adjunct cultures for the ripening of plant cheese analogues

Fermentation contributes to the taste and odor of plant cheeses. The selection of functional cultures for the fermentation of plant cheeses, however, is in its infancy. This study aimed to select lactic acid bacteria for ripening of soy and lupin cheese analogues. Bacillus velezensis and B. amyloliquefaciens were used for germination of seeds to produce proteolytic enzymes; Lactococcus lactis and Lactiplantibacillus plantarum served as primary acidifying cultures. Levilactobacillus hammesii, Furfurilactobacillus milii, or Lentilactobacillus buchneri were assessed as adjunct cultures for the ripening of plant cheese. Growth of bacilli was inhibited at low pH. Both Lc. lactis and Lp. plantarum were inactived during plant cheese ripening. Cell counts of Lv. hammesii remained stable over 45 d of ripening while Ff. milii and Lt. buchneri grew slowly. Sequencing of full length 16S rRNA genes confirmed that the inocula the plant cheeses accounted for more than 98% of the bacterial communities. HPLC analysis revealed that Lt. buchneri metabolized lactate to acetate and 1,2-propanediol during ripening. Bacilli enhanced proteolysis as measured by quantification of free amino nitrogen, and the release of glutamate. LC-MS/MS analysis quantified kokumi-active dipeptides. The concentrations of γ-Glu-Leu, γ-Glu-Ile, and γ-Glu-Ala, γ-Glu-Cys in unripened cheeses were increased by seed germination but γ-Glu-Phe was degraded. Lt. buchneri but not Lv. hammesii or Ff. milii accumulated γ-Glu-Val, γ-Glu-Ile or γ-Glu-Leu during ripening, indicating strain-specific differences. In conclusion, a consortium of bacilli, acidification cultures and adjunct cultures accumulates taste- and kokumi-active compounds during ripening of plant cheeses.

Selective penetration of fullerenol through pea seed coats mitigates osmosis-repressed germination via chromatin remodeling and transcriptional reprograming

BACKGROUND

The alteration of chromatin accessibility plays an important role in plant responses to abiotic stress. Carbon-based nanomaterials (CBNMs) have attracted increasing interest in agriculture due to their potential impact on crop productivity, showcasing effects on plant biological processes at transcriptional levels; however, their impact on chromatin accessibility remains unknown.

RESULTS

This study found that fullerenol can penetrate the seed coat of pea to mitigate the reduction of seed germination caused by osmotic stress. RNA sequencing (RNA-seq) revealed that the application of fullerenol caused the high expression of genes related to oxidoreduction to return to a normal level. Assay for transposase accessible chromatin sequencing (ATAC-seq) confirmed that fullerenol application reduced the overall levels of chromatin accessibility of numerous genes, including those related to environmental signaling, transcriptional regulation, and metabolism.

CONCLUSION

This study suggests that fullerenol alleviates osmotic stress on various fronts, encompassing antioxidant, transcriptional, and epigenetic levels. This advances knowledge of the working mechanism of this nanomaterial within plant cells. © 2024 Society of Chemical Industry.

Enhancing Sugarcane Seedling Resilience to Water Stress through Exogenous Abscisic Acid: A Study on Antioxidant Enzymes and Phytohormone Dynamics

Exogenous hormones play a crucial role in regulating plant growth, development, and stress tolerance. However, the effects of exogenous abscisic acid (ABA) on sugarcane seedlings under water stress remain poorly understood. Here, in this study, a pot experiment was conducted on sugarcane seedlings 4 weeks after transplanting, employing three treatments: control (normal growth), drought (water stress), and drought + ABA (foliar application of 100 μM ABA before water stress). The main objectives of this research are to understand the effects of exogenous ABA on sugarcane seedlings under water stress conditions and to assess the changes in antioxidant enzyme activity and phytohormone levels in response to exogenous ABA. Water stress was induced in the solution culture by adding 25% (w/v) polyethylene glycol (PEG) 6000 to the Hoagland solution. Leaf samples were collected at 3, 6, and 9 days after treatment, and the photosynthetic and biochemical responses of ABA-treated plants to drought stress were investigated. The indole acetic acid (IAA) activity of the ABA-treated drought plants is compared to that of drought plants. Moreover, the endogenous ABA levels of the ABA-treated drought plants were significantly enhanced by 42.2, 39.9, and 42.3% at 3, 6, and 9 days, respectively, compared to those of drought plants. Additionally, the proline content of the ABA-treated drought plants significantly increased by 45 and 80% at 6 and 9 days, respectively, compared to that of drought plants. The expression of the catalase 1 (CAT1) gene was increased in the ABA-treated drought plants by 2.1-fold, 0.7-fold, and 1.37-fold at 3, 6, and 9 days, respectively, compared to that in drought plants. Similarly, the expression of superoxide dismutase, peroxidase, and ascorbate peroxidase genes of the ABA-treated drought plants also increased compared to those of the drought plants. In conclusion, foliar application of ABA mitigated the negative effects of water shortage of sugarcane plants under water stress. Applying ABA improved the antioxidant defense system of sugarcane plants under drought stress, thereby enhancing their photosynthetic activities and productivity.

Sweet corn association panel and genome-wide association analysis reveal loci for chilling-tolerant germination

Sweet corn is highly susceptible to the deleterious effects of low temperatures during the initial stages of growth and development. Employing a 56K chip, high-throughput single-nucleotide polymorphism (SNP) sequencing was conducted on 100 sweet corn inbred lines. Subsequently, six germination indicators-germination rate, germination index, germination time, relative germination rate, relative germination index, and relative germination time-were utilized for genome-wide association analysis. Candidate genes were identified via comparative analysis of homologous genes in Arabidopsis and rice, and their functions were validated using quantitative real-time polymerase chain reaction (qRT-PCR). The results revealed 35,430 high-quality SNPs, 16 of which were significantly correlated. Within 50 kb upstream and downstream of the identified SNPs, 46 associated genes were identified, of which six were confirmed as candidate genes. Their expression patterns indicated that Zm11ΒHSDL5 and Zm2OGO likely play negative and positive regulatory roles, respectively, in the low-temperature germination of sweet corn. Thus, we determined that these two genes are responsible for regulating the low-temperature germination of sweet corn. This study contributes valuable theoretical support for improving sweet corn breeding and may aid in the creation of specific germplasm resources geared toward enhancing low-temperature tolerance in sweet corn.

Carbon nanotubes in plant dynamics: Unravelling multifaceted roles and phytotoxic implications

Carbon nanotubes (CNTs) have emerged as a promising frontier in plant science owing to their unique physicochemical properties and versatile applications. CNTs enhance stress tolerance by improving water dynamics and nutrient uptake and activating defence mechanisms against abiotic and biotic stresses. They can be taken up by roots and translocated within the plant, impacting water retention, nutrient assimilation, and photosynthesis. CNTs have shown promise in modulating plant-microbe interactions, influencing symbiotic relationships and mitigating the detrimental effects of phytopathogens. CNTs have demonstrated the ability to modulate gene expression in plants, offering a powerful tool for targeted genetic modifications. The integration of CNTs as sensing elements in plants has opened new avenues for real-time monitoring of environmental conditions and early detection of stress-induced changes. In the realm of agrochemicals, CNTs have been explored for their potential as carriers for targeted delivery of nutrients, pesticides, and other bioactive compounds. CNTs have the potential to demonstrate phytotoxic effects, detrimentally influencing both the growth and developmental processes of plants. Phytotoxicity is characterized by induction of oxidative stress, impairment of cellular integrity, disruption of photosynthetic processes, perturbation of nutrient homeostasis, and alterations in gene expression. This review aims to provide a comprehensive overview of the current state of knowledge regarding the multifaceted roles of CNTs in plant physiology, emphasizing their potential applications and addressing the existing challenges in translating this knowledge into sustainable agricultural practices.

Combined Analysis of Untargeted Metabolomics and Transcriptomics Revealed Seed Germination and Seedling Establishment in Zelkova schneideriana

Zelkova schneideriana Hand.-Mazz is a valuable ornamental tree and timber source, whose seedling breeding and large-scale cultivation are restricted by low seed germination and seedling rates. The regulatory mechanisms underlying seed germination and seedling establishment in Z. schneideriana remain unknown. This study conducted metabolomic and transcriptomic analyses of seed germination and seedling establishment in Z. schneideriana. Regular expression of genes and metabolite levels has been observed in plant hormone signal transduction, starch and sucrose metabolism, linoleic acid metabolism, and phenylpropanoid biosynthesis. The reduction in abscisic acid during seed germination may lead to seed release from dormancy. After the seed is released from dormancy, the metabolic levels of auxin, cytokinins, brassinolide, and various sugars are elevated, and they are consumed in large quantities during the seedling establishment stage. Linoleic acid metabolism is gradually activated during seedling establishment. Transcriptome analysis showed that a large number of genes in different metabolic pathways are upregulated during plant establishment, and material metabolism may be accelerated during seedling establishment. Genes regulating carbohydrate metabolism are altered during seed germination and seedling establishment, which may have altered the efficiency of carbohydrate utilization. In addition, the syntheses of lignin monomers and cellulose have different characteristics at different stages. These results provide new insights into the complex mechanisms underlying seed germination and seedling establishment in Z. schneideriana and other woody plants.

The impact of chemical and hormonal treatments to improve seed germination and seedling growth of Juniperus procera Hochst. ex Endi

Purpose

Juniper (Juniperus procera) is a common forest tree species in Saudi Arabia. The decline in many populations of J. procera in Saudi Arabia is mainly due to seed dormancy and loss of natural regeneration. This study assessed the effects of chemical and hormonal treatments on seed germination and seedling growth in juniper plants.

Methods

The seeds were subjected to either chemical scarification with 90% sulfuric acid and 20% acetic acid for 6 min or hormonal treatment by seed soaking in two concentrations (50 and 100 ppm) of three growth regulators, namely, indole acetic acid (IAA), gibberellins (GA3), and kinetin, for 72 h. A control group without any seed treatment was also prepared. The experiments were performed in an incubator maintained at room temperature and under a light and dark period of 12 h for 6 w. The germinated seeds for each treatment were counted and removed from the dishes. The selected germinated seeds from different treatments were planted in a greenhouse and irrigated with tap water for another 6 weeks. The hormone-treated seedlings were sprayed with their corresponding hormone concentrations 1 w after planting.

Results

The highest percentage of seed germination was significantly recorded after seed soaking in 50 ppm GA3, whereas treatment with IAA (100 ppm) resulted in the best seedling growth. Seedlings treated with the three phytohormones showed a significant increase in photosynthetic pigments, total soluble sugars, proteins, percentage of oil, IAA, GA3, and kinetin contents of juniper seedlings compared with the control value, whereas abscisic acid content was decreased compared with chemical treatments.

Conclusion

The investigated different treatments had an effective role in breaking seed dormancy and improving seedling growth of J. procera, which is facing a notable decline in its population worldwide. Moreover, such an effect was more pronounced in the three phytohormones that succeeded in breaking dormancy and growth of the Juniperus plant than in the other treatments.

Molecular mechanisms underlying the signal perception and transduction during seed germination

QuerySeed germination is a vital step in the life cycle of a plant, playing a significant role in seedling establishment and crop yield potential. It is also an important factor in the conservation of plant germplasm resources. This complex process is influenced by a myriad of factors, including environmental conditions, the genetic makeup of the seed, and endogenous hormones. The perception of these environmental signals triggers a cascade of intricate signal transduction events that determine whether a seed germinates or remains dormant. Despite considerable progress in uncovering the molecular mechanisms governing these processes, many questions remain unanswered. In this review, we summarize the current progress in the molecular mechanisms underlying the perception of environmental signals and consequent signal transduction during seed germination, and discuss questions that need to be addressed to better understand the process of seed germination and develop novel strategies for germplasm improvement.

Comparative regulatory network of transcripts behind radicle emergence and seedling stage of maize (Zea mays L.)

The transition from radicle emergence to seedling growth in maize is a crucial phase in the plant's life cycle, where rapid physiological and biochemical changes occur to facilitate successful development. In this study, we conducted a comparative transcriptomic analysis to gain a deeper understanding of the molecular processes driving this critical transition. The early divergence in gene expression patterns highlighted the upregulation of a substantial number of genes during radicle emergence. During radicle emergence, gene ontology (GO) term enrichment analysis unveiled active participation in biological processes such as chromatin assembly, cellular response to abiotic stress, and hormone signaling. This indicates that the initial stages of growth are marked by cellular expansion and adaptation to environmental stimuli. Conversely, in the seedling growth stage, GO analysis demonstrated a shift toward processes such as photosynthesis, nitrogen metabolism, and secondary metabolite biosynthesis, reflecting a transition to energy production and enhanced growth. In contrast, seedling growth was characterized by pathways related to photosynthesis and the production of gibberellins, crucial for robust seedling development. Hormonal regulation and starch metabolism were also prominent during radicle emergence, with various hormones, including auxins, diterpenoids, and brassinosteroids, driving processes like cell enlargement and stem growth. Moreover, starch and sucrose metabolism genes were expressed to mobilize stored reserves for energy during this stage. These findings offer valuable insights into the dynamic regulation of genes and pathways during this critical phase of maize development.

The Impact of Water Potential and Temperature on Native Species' Capability for Seed Germination in the Loess Plateau Region, China

Global warming is increasing the frequency and intensity of heat waves and droughts. One important phase in the life cycle of plants is seed germination. To date, the association of the temperature and water potential thresholds of germination with seed traits has not been explored in much detail. Therefore, we set up different temperature gradients (5-35 °C), water potential gradients (-1.2-0 MPa), and temperature × water potential combinations for nine native plants in the Loess Plateau region to clarify the temperature and water combinations suitable for their germination. Meanwhile, we elucidated the temperature and water potential thresholds of the plants and their correlations with the mean seed mass and flatness index by using the thermal time and hydrotime models. According to our findings, the germination rate was positively correlated with the germination percentage and water potential, with the former rising and the latter decreasing as the temperature increased. Using the thermal time and hydrotime models, the seed germination thresholds could be predicted accurately, and the germination thresholds of the studied species varied with an increase in germination percentage. Moreover, temperature altered the impact of water potential on the germination rate. Overall, the base water potential for germination, but not the temperature threshold, was negatively correlated with mean seed mass and was lower for rounder seeds than for longer seeds. This study contributes to improving our understanding of the seed germination characteristics of typical plants and has important implications for the management and vegetation restoration of degraded grasslands.

Genotype-specific germination behavior induced by sustainable priming techniques in response to water deprivation stress in rice

Water stress brought about by climate change is among the major global concerns threatening food security. Rice is an important staple food which requires high water resources. Being a semi-aquatic plant, rice is particularly susceptible to drought. The aim of this work was to develop techniques directed to promote rice resilience to water deprivation stress during germination by implementing specific seed priming treatments. Five popular Italian rice varieties were subjected to priming treatments using novel, sustainable solutions, like poly-gamma-glutamic acid (γ-PGA), denatured γ-PGA (dPGA), and iron (Fe) pulsing, alone or in combination. The effect of the developed priming methods was tested under optimal conditions as well as under water deprivation stress imposed by polyethylene glycol (PEG) treatments. The priming efficacy was phenotypically determined in terms of germination behavior by measuring a series of parameters (germinability, germination index, mean germination time, seed vigor index, root and shoot length, germination stress tolerance index). Biochemical analyses were carried out to measure the levels of iron uptake and accumulation of reactive oxygen species (ROS). Integrative data analyses revealed that the rice varieties exhibited a strong genotype- and treatment-specific germination behavior. PEG strongly inhibited germination while most of the priming treatments were able to rescue it in all varieties tested except for Unico, which can be defined as highly stress sensitive. Molecular events (DNA repair, antioxidant response, iron homeostasis) associated with the transition from seed to seedling were monitored in terms of changes in gene expression profiles in two varieties sensitive to water deprivation stress with different responses to priming. The investigated genes appeared to be differentially expressed in a genotype-, priming treatment-, stress- and stage-dependent manner. The proposed seed priming treatments can be envisioned as sustainable and versatile agricultural practices that could help in addressing the impact of climate challenges on the agri-food system.

The Effects of Exogenous 2,4-Epibrassinolide on the Germination of Cucumber Seeds under NaHCO3 Stress

This investigation focused on the suppressive impact of varying NaHCO3 concentrations on cucumber seed germination and the ameliorative effects of 2,4-Epibrassinolide (EBR). The findings revealed a negative correlation between NaHCO3 concentration and cucumber seed germination, with increased NaHCO3 concentrations leading to a notable decline in germination. Crucially, the application of exogenous EBR significantly counteracted this inhibition, effectively enhancing germination rates and seed vigor. Exogenous EBR was observed to substantially elevate the activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD), thereby mitigating oxidative damage triggered under NaHCO3 stress conditions. Additionally, EBR improved enzyme activity under alkaline stress conditions and reduced starch content in the seeds. Pertinently, EBR upregulated genes that were associated with gibberellin (GA) synthesis (GA20ox and GA3ox), and downregulated genes that were linked to abscisic acid (ABA) synthesis (NCED1 and NCED2). This led to an elevation in GA3 concentration and a reduction in ABA concentration within the cucumber seeds. Therefore, this study elucidates that alleviating oxidative stress, promoting starch catabolism, and regulating the GA and ABA balance are key mechanisms through which exogenous EBR mitigates the suppression of cucumber seed germination resulting from alkaline stress.

Gibberellin-Producing Bacteria Isolated from Coastal Soil Enhance Seed Germination of Mallow and Broccoli Plants under Saline Conditions

Salinity hinders plant growth, posing a substantial challenge to sustainable agricultural yield maintenance. The application of plant growth-promoting rhizobacteria (PGPR) offers an emerging strategy to mitigate the detrimental effects of high salinity levels. This study aimed to isolate and identify gibberellin-producing bacteria and their impact on the seed germination of Malva verticillata (mallow) and Brassica oleracea var. italica (broccoli) under salt stress. In this study, seven bacterial isolates (KW01, KW02, KW03, KW04, KW05, KW06, and KW07) were used to assess their capacity for producing various growth-promoting traits and their tolerance to varying amounts of salinity (100 mM and 150 Mm NaCl). The findings revealed that KW05 and KW07 isolates outperformed other isolates in synthesizing indole-3-acetic acid, siderophores, and exopolysaccharides and in solubilizing phosphates. These isolates also enhanced phosphatase activity and antioxidant levels, including superoxide dismutase and catalase. Both KW05 and KW07 isolate highlight the growth-promoting effects of gibberellin by enhancing of growth parameters of Waito-C rice. Further, gas chromatography-mass spectrometry validation confirmed the ability of KW05 and KW07 to produce gibberellins (GAs), including GA1, GA3, GA4, and GA7. Seed germination metrics were enhanced due to the inoculation of KW05 and KW07. Moreover, inoculation with KW05 increased the fresh weight (FW) (7.82%) and total length (38.61%) of mallow under salt stress. Inoculation with KW07 increased the FW (32.04%) and shoot length of mallow under salt stress. A single inoculation of these two isolates increased broccoli plants' FW and shoot length under salt stress. Gibberellin-producing bacteria helps in plant growth promotion by improving salt tolerance by stimulating root elongation and facilitating enhanced absorption of water and nutrient uptake in salty environments. Based on these findings, they can play a role in boosting agricultural yield in salt-affected areas, which would help to ensure the long-term viability of agriculture in coastal regions.

NACs, generalist in plant life

Plant-specific NAC proteins constitute a major transcription factor family that is well-known for its roles in plant growth, development, and responses to abiotic and biotic stresses. In recent years, there has been significant progress in understanding the functions of NAC proteins. NAC proteins have a highly conserved DNA-binding domain; however, their functions are diverse. Previous understanding of the structure of NAC transcription factors can be used as the basis for their functional diversity. NAC transcription factors consist of a target-binding domain at the N-terminus and a highly versatile C-terminal domain that interacts with other proteins. A growing body of research on NAC transcription factors helps us comprehend the intricate signalling network and transcriptional reprogramming facilitated by NAC-mediated complexes. However, most studies of NAC proteins have been limited to a single function. Here, we discuss the upstream regulators, regulatory components and targets of NAC in the context of their prospective roles in plant improvement strategies via biotechnology intervention, highlighting the importance of the NAC transcription factor family in plants and the need for further research.

Application of Methionine Increases the Germination Rate of Maize Seeds by Triggering Multiple Phenylpropanoid Biosynthetic Genes at Transcript Levels

Methionine is an essential amino acid that initiates protein synthesis and serves as a substrate for various chemical reactions. Methionine metabolism plays an important role in Arabidopsis seed germination, but how methionine works in seed germination of maize has not been elucidated. We compared the changes in germination rate, the contents of methionine and folates, and transcriptional levels using transcriptome analysis under water or exogenous methionine treatment. The results indicate that the application of methionine increases seed germination rate (95% versus 70%), leading to significant differences in the content of methionine at 36 h, which brought the rapid increase forward by 12 h in the embryo and endosperm. Transcriptome analysis shows that methionine mainly affects the proliferation and differentiation of cells in the embryo, and the degradation of storage substances and signal transduction in the endosperm. In particular, multiple phenylpropanoid biosynthetic genes were triggered upon methionine treatment during germination. These results provide a theoretical foundation for promoting maize seed germination and serve as a valuable theoretical resource for seed priming strategies.

Transcriptome profiling reveals ethylene formation in rice seeds by trichloroisocyanuric acid

KEY MESSAGE

Ethylene formation via methionine reacting with trichloroisocyanuric acid under FeSO4 condition in a non-enzymatical manner provides one economically and efficiently novel ethylene-forming approach in planta. Rice seed germination can be stimulated by trichloroisocyanuric acid (TCICA). However, the molecular basis of TCICA in stimulating rice seed germination remains unclear. In this study, the molecular mechanism on how TCICA stimulated rice seed germination was examined via comparative transcriptome. Results showed that clustering of transcripts of TCICA-treated seeds, water-treated seeds, and dry seeds was clearly separated. Twenty-two and three hundred differentially expressed genes were identified as TCICA treatment responsive genes and TCICA treatment potentially responsive genes, respectively. Two and one TCICA treatment responsive genes were involved in ethylene signal transduction and iron homeostasis, respectively. Seventeen of the three hundred TCICA treatment potentially responsive genes were significantly annotated to iron ion binding. Meanwhile, level of methionine (ethylene precursor) showed a 73.9% decrease in response to TCICA treatment. Ethylene was then proved to produce via methionine reacting with TCICA under FeSO4 condition in vitro. Revealing ethylene formation by TCICA not only may bring novel insights into crosstalk between ethylene and other phytohormones during rice seed germination, but also may provide one economically and efficiently novel approach to producing ethylene in planta independently of the ethylene biosynthesis in plants and thereby may broaden its applications in investigational and applied purposes.

A study about factors influencing rice palatability based on changes in sensory and physicochemical properties under different postharvest conditions

Postharvest management plays a key role in determining the end-use quality of rice; therefore, a practical approach to inhibit quality deterioration is necessary. In this study, the effects of postharvest management-drying delay time (DDT) and moisture content after drying (DM) immediately after harvesting, and storage temperatures (ST) and periods (SP) of dried paddy rice-on the physicochemical, quality, and sensory properties of rice were comprehensively analyzed. Germination rate, seed viability, fat acidity, and sensory quality tended to significantly deteriorate with increasing DDT, DM, ST, and SP. The highest correlation (r = 0.8289) was observed between germination rate and sensory quality, indicating that germination rate can reliably predict sensory quality. Degradation of germination rate and overall sensory quality were analyzed: sensory quality exhibited a more gradual change than germination rate. Lastly, the effects of the postharvest conditions on overall sensory quality were predicted using a regression equation model. DDT, DM, and ST exhibited different patterns of change, which can be used to predict the sensory quality during storage. Germination rate was successfully applied as an influencing factor for the development of a rice-palatability prediction model. The results of this study are useful for maintaining fresh-rice palatability by preventing aging during postharvest storage.

Metabolic pathways modulated by coumarin to inhibit seed germination and early seedling growth in Eleusine indica

Coumarin is an allelochemical that is widely present in the plant kingdom and has great potential for weed control. However, its mechanisms of action remain largely unknown. This study employed metabolomic and transcriptomic analyses along with evaluations of amino acid profiles and related physiological indicators to investigate how coumarin inhibits the germination and seedling growth of Eleusine indica by modifying metabolic pathways. At 72 h of germination at 50 and 100 mg L-1 coumarin, E. indica had lower levels of soluble sugar and activities of amylases and higher levels of starch, O2-, H2O2, auxin (IAA) and abscisic acid (ABA) compared to the control. Metabolomic analysis demonstrated that coumarin treatments had a significant impact on the pathways associated with amino acid metabolism and transport and aminoacyl-tRNA biosynthesis. Exposure to coumarin induced significant alterations in the levels of 19 amino acids, with a decrease in 15 of them, including Met, Leu and γ-aminobutyric acid (GABA). Additionally, transcriptomic analysis showed that coumarin significantly disrupted several essential biological processes, including protein translation, secondary metabolite synthesis, and hormone signal transduction. The decrease in TCA cycle metabolite (cis-aconitate, 2-oxoglutarate, and malate) contents was associated with the suppression of transcription for related enzymes. Our findings indicate that the inhibition of germination and growth in E. indica by coumarin involves the suppression of starch conversion to sugars, modification of the amino acid profile, interference of hormone signalling and the induction of oxidative stress. The TCA cycle appears to be one of the most essential pathways affected by coumarin.

The Role of Silica Nanoparticles in Promoting the Germination of Tomato (Solanum lycopersicum) Seeds

The addition of nanoparticles has been reported to be an effective strategy for enhancing seed germination, but the underlying mechanisms whereby this occurs are unclear. In the present study, we added silica nanoparticles (SiNPs) to an aqueous growth medium in which tomato seeds were germinated. We examined the effects of SiNPs on growth and possible mechanisms of action. SiNPs had a diameter of 10-17 nm and 110-120 nm. SiNPs shortened the mean germination time from 5.24 ± 0.29 days to 4.64 ± 0.29 days. Seedling vigor, measured by criteria including length and weight, was also improved compared to the control condition. The presence of SiNPs in the seedlings was assessed using an X-ray fluorescence spectrometer. The nanoparticles may have promoted germination by enhancing water imbibition by the seeds or altering the external microenvironment. Scanning electron microscopy revealed changes in the seed coat during germination, many of which were only observed in the presence of nanoparticles. Soil bacteria affect germination; specifically, Bacillus sp. may promote germination. The number of Bacillus sp. changed in the germination medium with SiNPs compared to the control. This suggested that these bacteria could interact with SiNPs to promote germination.

SMAX1 interacts with DELLA protein to inhibit seed germination under weak light conditions via gibberellin biosynthesis in Arabidopsis

Karrikins (KARs) were first identified as a class of small-molecule chemicals derived from smoke that promote seed germination. However, the implied mechanism is still not well understood. Here, we find that KAR signaling mutants have a lower germination percentage than that of wild type under weak light conditions, and KARs promote seed germination through transcriptional activation of gibberellin (GA) biosynthesis via SMAX1. SMAX1 interacts with the DELLA proteins REPRESSOR of ga1-3-LIKE 1 (RGL1) and RGL3. The interaction enhances the transcriptional activity of SMAX1 and inhibits GIBBERELLIN 3-oxidase 2 (GA3ox2) gene expression. The KAR signaling mutant seed germination defect under weak light is partially rescued by exogenous application of GA₃ or by GA3ox2 overexpression, and the rgl1 rgl3 smax1 triple mutant exhibits higher germination rates under weak light than the smax1 mutant. Thus, we show a crosstalk between KAR and GA signaling pathways via a SMAX1-DELLA module in regulating seed germination in Arabidopsis.

PROTEIN PHOSPHATASE 2C08, a Negative Regulator of Abscisic Acid Signaling, Promotes Internode Elongation in Rice

Clade A protein phosphatase 2Cs (PP2CAs) negatively regulate abscisic acid (ABA) signaling. Here, we investigated the functions of OsPP2CAs and their crosstalk with ABA and gibberellic acid (GA) signaling pathways in rice (Oryza sativa). Among the nine OsPP2CAs, OsPP2C08 had the highest amino acid sequence similarity with OsPP2C51, which positively regulates GA signaling in rice seed germination. However, OsPP2C08 was expressed in different tissues (internodes, sheaths, and flowers) compared to OsPP2C51, which was specifically expressed in seeds, and showed much stronger induction under abiotic stress than OsPP2C51. Transgenic rice lines overexpressing OsPP2C08 (OsPP2C08-OX) had a typical ABA-insensitive phenotype in a post-germination assay, indicating that OsPP2C08, as with other OsPP2CAs, negatively regulates ABA signaling. Furthermore, OsPP2C08-OX lines had longer stems than wild-type (WT) plants due to longer internodes, especially between the second and third nodes. Internode cells were also longer in OsPP2C08-OX lines than in the WT. As GA positively regulates plant growth, these results suggest that OsPP2C08 might positively regulate GA biosynthesis. Indeed, the expression levels of GA biosynthetic genes including gibberellin 20-oxidase (OsGA20ox4) and Ent-kaurenoic acid oxidase (OsKAO) were increased in OsPP2C08-OX lines, and we observed that GIBBERELLIN 2-OXIDASE 4 (OsGA2ox4), encoding an oxidase that catalyzes the 2-beta-hydroxylation of several biologically active GAs, was repressed in the OsPP2C08-OX lines based on a transcriptome deep sequencing and RT-qPCR analysis. Furthermore, we compared the accumulation of SLENDER RICE 1 (SLR1), a DELLA protein involved in GA signaling, in OsPP2C08-OX and WT plants, and observed lower levels of SLR1 in the OsPP2C08-OX lines than in the WT. Taken together, our results reveal that OsPP2C08 negatively regulates ABA signaling and positively regulates GA signaling in rice. Our study provides valuable insight into the molecular mechanisms underlying the crosstalk between GA and ABA signaling in rice.

Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination

Seed germination is a complex, multistage developmental process that is an important step in plant development. In this study, RNA-Seq was conducted in the embryo and endosperm of unshelled germinating rice seeds. A total of 14,391 differentially expressed genes (DEGs) were identified between the dry seeds and the germinating seeds. Of these DEGs, 7109 were identified in both the embryo and endosperm, 3953 were embryo specific, and 3329 were endosperm specific. The embryo-specific DEGs were enriched in the plant-hormone signal-transduction pathway, while the endosperm-specific DEGs were enriched in phenylalanine, tyrosine, and tryptophan biosynthesis. We categorized these DEGs into early-, intermediate-, and late-stage genes, as well as consistently responsive genes, which can be enriched in various pathways related to seed germination. Transcription-factor (TF) analysis showed that 643 TFs from 48 families were differentially expressed during seed germination. Moreover, 12 unfolded protein response (UPR) pathway genes were induced by seed germination, and the knockout of OsBiP2 resulted in reduced germination rates compared to the wild type. This study enhances our understanding of gene responses in the embryo and endosperm during seed germination and provides insight into the effects of UPR on seed germination in rice.

Isolation and Genome-Based Characterization of Biocontrol Potential of Bacillus siamensis YB-1631 against Wheat Crown Rot Caused by Fusarium pseudograminearum

Fusarium crown rot (FCR) caused by Fusarium pseudograminearum is one of the most serious soil-borne diseases of wheat. Among 58 bacterial isolates from the rhizosphere soil of winter wheat seedlings, strain YB-1631 was found to have the highest in vitro antagonism to F. pseudograminearum growth. LB cell-free culture filtrates inhibited mycelial growth and conidia germination of F. pseudograminearum by 84.14% and 92.23%, respectively. The culture filtrate caused distortion and disruption of the cells. Using a face-to-face plate assay, volatile substances produced by YB-1631 inhibited F. pseudograminearum growth by 68.16%. In the greenhouse, YB-1631 reduced the incidence of FCR on wheat seedlings by 84.02% and increased root and shoot fresh weights by 20.94% and 9.63%, respectively. YB-1631 was identified as Bacillus siamensis based on the gyrB sequence and average nucleotide identity of the complete genome. The complete genome was 4,090,312 bp with 4357 genes and 45.92% GC content. In the genome, genes were identified for root colonization, including those for chemotaxis and biofilm production, genes for plant growth promotion, including those for phytohormones and nutrient assimilation, and genes for biocontrol activity, including those for siderophores, extracellular hydrolase, volatiles, nonribosomal peptides, polyketide antibiotics, and elicitors of induced systemic resistance. In vitro production of siderophore, β-1, 3-glucanase, amylase, protease, cellulase, phosphorus solubilization, and indole acetic acid were detected. Bacillus siamensis YB-1631 appears to have significant potential in promoting wheat growth and controlling wheat FCR caused by F. pseudograminearum.

Imbibitional redox and hormonal priming revealed regulation of oxidative window as a key factor for progression of germination of indica rice cultivars

In the present investigation we have manipulated seeds of two indica rice cultivars, differing in sensitivity towards salinity stress (Oryza sativa L. cv. IR29 and Pokkali), with different combination of germination influencing hormones and redox modulating agents [500 µM Gibberellic acid (GA) + 20 mM H2O2, 500 µM GA + 100 µM Diphenyleneiodonium chloride (DPI), 500 µM GA + 500 µM N,N-dimethylthiourea (DMTU), 30 µM Triadimefon (TDM) + 100 µM DPI, 30 µM TDM + 500 µM DMTU] during early imbibition for exploring significance of regulation of oxidative window during germination. Reactive oxygen species (ROS)-antioxidant (AOX) interaction dynamics, assessed through redox metabolic fingerprints revealed significant changes in oxidative window of germinating tissue under redox and hormonal priming. GA (500 µM) + H2O2 (20 mM) priming formed favorable redox cue and opened the oxidative window for germination, whereas GA (500 µM) + DPI (100 µM), GA (500 µM) + DMTU (500 µM) and TDM (30 µM) + DPI (100 µM) combination failed to generate redox cue for opening the oxidative window at metabolic interface. Assessment of transcript abundance of genes of enzymes of central redox hub (RBOH-SOD-ASC-GSH/CAT pathway) further confirmed the transcriptional reprogramming of genes (Osrboh, OsSodCc2, OsCatA, OsAPx2, OsGRase) necessary for antioxidant-coupled origin of redox cue for germination. Assessment of pool of gibberellic acid, abscisic acid and jasmonic acid revealed a close connection between the hormonal homeostasis and internal redox cue. Role of oxidative window generated during metabolic reactivation phase for successful progression of germination is suggested.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01303-x.

Metabolomics and chemometrics depict the changes in the chemical profile of white lupine (Lupinus albus L.) bioactive metabolites during seed germination

The current study attempts to illustrate how the chemical and biological profile of white lupine seeds varies throughout the course of various germination days using UHPLC-QqQ-MS combined to chemometrics. Abscisic acid showed maximum level in the un-germinated seeds and started to decline with seed germination accompanied by an increase in the levels of gibberellins which were undetectable in un-germinated seeds. Coumaronochromones were the most prevalent constituents detected in un-germinated seeds while day 2 sprouts showed significant accumulation of flavones. The levels of alkaloids showed significant increase upon germination of the seeds reaching its maximum in day 14 sprouts. The OPLS model coefficients plot indicated that lupinalbin D and F, apigenin hexoside, kaempferol hexoside, albine, and hydoxylupanine showed strong positive correlation to the alpha amylase inhibitory activity of the tested samples while lupinalbin A, lupinisoflavone, lupinic acid and multiflorine were positively correlated to the inhibition of alpha glycosidase activity. The results obtained indicated that seed germination has a profound effect on the chemical profile as well as the in-vitro antidiabetic activity of lupine seeds.

Establishment of a novel experimental system for studying the photoperiodic response of short-day dicots using soybean 'cotyledon-only plant' as material

Soybean is an important model crop for photoperiodic response studies in plants and contributes significantly to the study of plant development and physiology in the past century. Because soybean plant is much bigger in size and longer in life cycle than Arabidopsis, it needs much more space for growth and time for investigation, which significantly hamper the efficiency of research. In the current study, we tested the photoperiodic response of a distinctive artificially-made cotyledon-only plant (COP) using a photoperiod-sensitive soybean variety Zigongdongdou (ZGDD) and other varieties with diverse sensitivity to photoperiod. ZGDD COPs flowered 39.4 ± 2.5 d after emergence under short-day conditions but maintained vegetative growth under long-day and night break conditions, which is similar to the case in the intact ZGDD plants. The COPs of early-maturing and medium-maturing soybean varieties also grew and flowered normally under natural day-length conditions. At the molecular level, the key genes in the photoperiodic pathway such as E1, GmFT1a, GmFT2a, and GmFT5a in the COPs also showed the same photoperiod sensitivity as in the intact plants. In addition, a simpler material of COP with only one cotyledon and root was generated and found to be sensitive to photoperiod as well. Notably, the COPs are only one-fifth the height of intact plants and one-third the maximum diameter of the intact plants grown in chambers 30 d after emergence. Based on COPs, we established a novel experimental system characterized by an entire photoperiodic response and longer longevity of cotyledons in addition to small plant size, ensuring the consistency, reliability, and stability of plant materials. COPs have the potential to be a novel model material for studies of the developmental biology of soybean and other dicots.

Study of macronutrients in hemp seeds during short-term germination

At present, hemp seeds are becoming increasingly popular as a source of nutrients. This work addressed the dynamics of macronutrients in the process of short-term germination of hempseeds by chemical and spectroscopic methods. Lyudmila 2021 cultivated hemp seeds along with hemp sprouts were used as objects of research. The germination of hemp seeds was carried out under laboratory conditions using special trays at 18–20 °C with the water added at a ratio of 2:1 for 5 days with periodic moistening. The obtained experimental data on the protein complex suggested that, in the studied interval of the germination of hemp seeds, the key hydrolytic decomposition of proteins occurs along with changes in structural components, including through the synthesis of new proteins accompanying the sprouting. The variations in such parameters as fat content, acid number and peak intensity of functional groups in the lipid fingerprint region (1745, 1157 and 1140 cm-1) indicated the accumulation of fatty acids as a result of the hydrolysis of triglycerides. The analysis of the IR spectra of hemp sprouts and the intensity of the bands of the corresponding functional groups in the carbohydrate region (1200–680 cm-1) suggested the intensive hydrolytic decomposition of polysaccharides. The variation in the content of extractive matter in the aqueous solutions of hemp sprouts indicated the accumulation and utilisation of water-soluble substances at the early stages of germination. The data on the predominance of water- and salt-soluble protein fractions indicated an increase in the biological value of hemp seeds during short-term germination.

Analysis of QTL mapping for germination and seedling response to drought stress in sunflower (Helianthus annuus L.)

Sunflower is an important oilseed crop across the world. It is considered as a moderately drought tolerant plant, however, its yield is still negatively affected by drought stress. Improving drought tolerance is of the outmost important for breeding. Although several studies have documented the relationship between the sunflower phenotype and genotype under drought stress, but relatively few studies have simultaneously investigated the molecular mechanisms of drought tolerance in the sunflower at different growth stages. In this study, we conducted quantitative trait locus (QTL) analysis for different sunflower traits during the germination and seedling stages. Eighteen phenotypic traits were evaluated under well-watered and drought stress conditions. We determined that the germination rate, germination potential, germination index, and root-to-shoot ratio can be used as effective indexes for drought tolerance selection and breeding. A total of 33 QTLs were identified on eight chromosomes (PVE: 0.016%-10.712% with LOD: 2.017-7.439). Within the confidence interval of the QTL, we identified 60 putative drought-related genes. Four genes located on chromosome 13 may function in both germination and seedling stages for drought response. Genes LOC110898128, LOC110898092, LOC110898071, and LOC110898072 were annotated as aquaporin SIP1-2-like, cytochrome P450 94C1, GABA transporter 1-like, and GABA transporter 1-like isoform X2, respectively. These genes will be used for further functional validation. This study provides insight into the molecular mechanisms of the sunflower's in response to drought stress. At the same time, it lays a foundation for sunflower drought tolerance breeding and genetic improvement.

Citric Acid in Rice Root Exudates Enhanced the Colonization and Plant Growth-Promoting Ability of Bacillus altitudinis LZP02

Exploration of the underlying mechanisms of plant-microbe interactions is very important. In the present study, citric acid in the root exudates of rice significantly enhanced the colonization of Bacillus altitudinis LZP02 in the rhizosphere. According to the results of transcriptome and reverse transcription-quantitative PCR or analyses, citric acid increased the expression of several genes involved in bacterial chemotaxis and biofilm formation in B. altitudinis LZP02. In addition, citric acid also increased the expression of several genes associated with S-adenosylmethionine biosynthesis and metabolism. Interestingly, the secretion of citric acid by rice roots could be increased by inoculation with B. altitudinis LZP02. The result indicated that citric acid might be a vital signal in the interaction between rice and B. altitudinis LZP02. Further verification showed that citric acid enhanced the plant growth-promoting ability of B. altitudinis LZP02. IMPORTANCE In a previous study, the mechanism by which citric acid in rice root exudates enhanced the colonization of Bacillus altitudinis LZP02 was discovered. The present study verified that citric acid increased the recruitment and rice growth-promoting ability of B. altitudinis LZP02. These findings serve as an interesting case for explaining the underlying mechanisms of plant-microbe interactions. Henceforth, citric acid and B. altitudinis LZP02 could be exploited for the development of sustainable agronomy.

Cell Membrane Features as Potential Breeding Targets to Improve Cold Germination Ability of Seeds

Cold stress breeding that focuses on the improvement of chilling tolerance at the germination stage is constrained by the complexities of the trait which involves integrated cellular, biochemical, hormonal and molecular responses. Biological membrane serves as the first line of plant defense under stress. Membranes receive cold stress signals and transduce them into intracellular responses. Low temperature stress, in particular, primarily and effectively affects the structure, composition and properties of cell membranes, which ultimately disturbs cellular homeostasis. Under cold stress, maintenance of membrane integrity through the alteration of membrane lipid composition is of prime importance to cope with the stress. This review describes the critical role of cell membranes in cold stress responses as well as the physiological and biochemical manifestations of cold stress in plants. The potential of cell membrane properties as breeding targets in developing strategies to improve cold germination ability is discussed using cotton (Gossypium hirsutum L.) as a model.

Quantitative Acetylome Analysis of Soft Wheat Seeds during Artificial Ageing

Lysine acetylation (Kac) is a protein post-translational modification (PTM) widely found in plants that plays vital roles in metabolic pathways. Although seed germination and development are regulated by Kac, its potential function in seed ageing remains to be investigated. Our preliminary study demonstrated that Kac levels were altered during wheat seed artificial ageing. However, its specific role in this process still needs to be elucidated. Here, we performed quantitative acetylation proteomics analysis of soft wheat seeds with different germination rates during artificial ageing. A total of 175 acetylation proteins and 255 acetylation modification sites were remarkably changed. The differentially acetylated proteins were enriched in metabolism; response to harsh intracellular environment, such as ROS; protein storage and processing. Notably, expression, point mutation to mimic Kac by K to Q mutation at K80 and K138, protein purification and enzyme activity detection revealed that the Kac of ROS-scavenging glutathione transferase attenuated its activity, indicating that the defense ability of wheat seeds to stress gradually diminished, and the ageing process was inevitable. Collectively, our data provide a basis for further understanding the roles of Kac in seed ageing and might aid in the development of new techniques to prolong seed viability and food quality.

Dynamic RNA-Seq Study Reveals the Potential Regulators of Seed Germination in Paris polyphylla var. yunnanensis

Paris polyphylla var. yunnanensis is an important traditional Chinese medicine, but poor seed germination limits its large-scale artificial cultivation. Thus, it is crucial to understand the regulators of seed germination to obtain clues about how to improve the artificial cultivation of Paris polyphylla. In this study, the seeds at three germination stages, including ungerminated seeds (stage 1), germinated seeds with a 0.5 cm radicel length (stage 2), and germinated seeds with a 2.0 cm radicel length (stage 3) after warm stratification (20 °C) for 90 days were used for RNA sequencing. Approximately 220 million clean reads and 447,314 annotated unigenes were obtained during seed germination, of which a total of 4454, 5150, and 1770 differentially expressed genes (DEGs) were identified at stage 1 to stage 2, stage 1 to stage 3, and stage 2 to stage 3, respectively. Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the DEGs were significantly enriched in carbohydrate metabolism, lipid metabolism, signal transduction, and translation. Of them, several genes encoding the glutamate decarboxylase, glutamine synthetase, alpha-galactosidase, auxin-responsive protein IAA30, abscisic-acid-responsive element binding factor, mitogen-activated protein kinase kinase 9/18, and small and large subunit ribosomal proteins were identified as potentially involved in seed germination. The identified genes provide a valuable resource to study the molecular basis of seed germination in Paris polyphylla var. yunnanensis.

Effect of Exogenous Glycine Betaine on the Germination of Tomato Seeds under Cold Stress

Cold stress is known to influence tomato growth, development, and yield. In this study, we analyzed the germination of tomato seeds treated with exogenous glycine betaine (GB) at a low temperature (14 °C). The results showed that cold stress inhibited tomato seed germination, and pretreatment with exogenous GB reduced this inhibition and enhanced the germination rate (GR), germination index (GI), and viability of tomato seeds at low temperatures. Analysis of gene expression and metabolism revealed that GB positively regulated endogenous hormone gibberellin (GA) content and negatively regulated abscisic acid (ABA) content, while GB reduced the starch content in the seeds by up-regulating the amylase gene expression. Gene expression analysis showed that the key genes (SlSOD, SlPOD, and SlchlAPX) involved in reactive oxygen species (ROS) scavenging systems were up-regulated in GB-pretreated tomato seeds compared with the control. At the same time, levels of malondialdehyde and hydrogen peroxide were significantly lower, while the proline content and peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) levels were elevated compared with those in the control. These results demonstrate that exogenous GB as a positive regulator effectively alleviated the inhibition of tomato seed germination under cold stress by different signal pathways.

A Long Noncoding RNA Derived from lncRNA-mRNA Networks Modulates Seed Vigor

The discovery of long noncoding RNAs (lncRNAs) has filled a great gap in our understanding of posttranscriptional gene regulation in a variety of biological processes related to plant stress responses. However, systematic analyses of the lncRNAs expressed in rice seeds that germinate under cold stress have been elusive. In this study, we performed strand-specific whole transcriptome sequencing in germinated rice seeds under cold stress and normal temperature. A total of 6258 putative lncRNAs were identified and expressed in a stage-specific manner compared to mRNA. By investigating the targets of differentially expressed (DE) lncRNAs of LT-I (phase I of low temperature)/NT-I (phase I of normal temperature), it was shown that the auxin-activated signaling pathway was significantly enriched, and twenty-three protein-coding genes with most of the members of the SAUR family located in chromosome 9 were identified as the candidate target genes that may interact with five lncRNAs. A seed vigor-related lncRNA, SVR, which interplays with the members of the SAUR gene family in cis was eventually identified. The CRISPR/Cas 9 engineered mutations in SVR cause delay of germination. The findings provided new insights into the connection between lncRNAs and the auxin-activated signaling pathway in the regulation of rice seed vigor.

Maturation and Post-Harvest Resting of Fruits Affect the Macronutrients and Protein Content in Sweet Pepper Seeds

There are few studies about the influence of fruit maturation and post-harvest resting on seed composition, which can be necessary for seedling development and future establishment. Thus, the objective of this study was to evaluate the effect of maturation and post-harvest resting of fruits on the macronutrient and protein content of sweet pepper seeds. The experimental design was a randomized block, with eight treatments, in a 4 × 2 factorial arrangement. The first factor was fruit maturation stages (35, 50, 65 and 80 days after anthesis), and the second, with and without post-harvest resting of the fruits for 7 days. The characteristics evaluated in seeds were the dry weight of one thousand seeds, macronutrient content, and content of albumin, globulin, prolamin and glutelin proteins. There were reductions in K, Ca and Mg content, and an increase in seed content of albumin, globulin and prolamins as a function of the fruit maturation stage. Post-harvest resting of the fruits provided higher Ca content and protein albumin in seeds. The decreasing order of macronutrients and protein content in seeds, independent of fruit maturation and resting stage of the fruits, was N > K > P > Mg > S > Ca, and albumin > globulin ≈ glutelin > prolamine, respectively.

Meta-analysis of QTLs and candidate genes associated with seed germination in rice (Oryza sativa L.)

Seed germination is one of the critical stages of plant life, and many quantitative trait loci (QTLs) control this complex trait. Meta-analysis of QTLs is a powerful computational technique for estimating the most stable QTLs regardless of the population's genetic background. Besides, this analysis effectively narrows down the confidence interval (CI) to identify candidate genes (CGs) and marker development. In the current study, a comprehensive genome-wide meta-analysis was performed on QTLs associated with germination in rice. This analysis was conducted based on the data reported over the last two decades. In this case, various analyses were performed, including seed germination rate, plumule length, radicle length, germination percentage, coleoptile length, coleorhiza length, radicle fresh weight, germination potential, and germination index. A total of 67 QTLs were projected onto a reference map for these traits and then integrated into 32 meta-QTLs (MQTLs) to provide a genetic framework for seed germination. The average CI of MQTLs was considerably reduced from 15.125 to 8.73 cM compared to the initial QTLs. This situation identified 728 well-known functionally characterized genes and novel putative CGs for investigated traits. The fold change calculation demonstrated that 155 CGs had significant changes in expression analysis. In this case, 112 and 43 CGs were up-regulated and down-regulated during germination, respectively. This study provides an overview and compares genetic loci controlling traits related to seed germination in rice. The findings can bridge the gap between QTLs and CGs for seed germination.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01232-1.

BcWRKY1 confers salt sensitivity via inhibiting Reactive oxygen species scavenging

WRKY transcription factors play important roles in abiotic stress by directly regulating stress-related genes. However, the molecular mechanism of its involvement in salt stress in pak-choi is still poorly understood. In this study, we elucidated the function of BcWRKY1 from pak-choi (Brassica rapa ssp. chinensis) in salt stress. The expression level of BcWRKY1 showed the highest in rosette leaves among different tissues and was induced by salt and ABA treatment in pak-choi. Subcellular localization showed that BcWRKY1 was located in nucleus. The transgenic Arabidopsis overexpressing BcWRKY1 exhibited enhanced salt sensitivity and higher H₂O₂ contents, which were further confirmed by silencing BcWRKY1 in pak-choi. In addition, the expression of ZAT12 was negatively regulated with BcWRKY1 under salt stress both in pak-choi and Arabidopsis. Yeast one-hybrid and dual luciferase reporter assay showed that BcWRKY1 could bind to the promoter of BcZAT12, and BcsAPX expression was activated by BcZAT12. To sum up, we propose a BcWRKY1-BcZAT12-BcsAPX regulatory model that involves in pak-choi salt stress response.

Understanding of Hormonal Regulation in Rice Seed Germination

Seed germination is a critical stage during the life cycle of plants. It is well known that germination is regulated by a series of internal and external factors, especially plant hormones. In Arabidopsis, many germination-related factors have been identified, while in rice, the important crop and monocot model species and the further molecular mechanisms and regulatory networks controlling germination still need to be elucidated. Hormonal signals, especially those of abscisic acid (ABA) and gibberellin (GA), play a dominant role in determining whether a seed germinates or not. The balance between the content and sensitivity of these two hormones is the key to the regulation of germination. In this review, we present the foundational knowledge of ABA and GA pathways obtained from germination research in Arabidopsis. Then, we highlight the current advances in the identification of the regulatory genes involved in ABA- or GA-mediated germination in rice. Furthermore, other plant hormones regulate seed germination, most likely by participating in the ABA or GA pathways. Finally, the results from some regulatory layers, including transcription factors, post-transcriptional regulations, and reactive oxygen species, are also discussed. This review aims to summarize our current understanding of the complex molecular networks involving the key roles of plant hormones in regulating the seed germination of rice.

Metabolome profiling of stratified seeds provides insight into the regulation of dormancy in Davidia involucrata

Dove tree (Davidia involucrata), a tertiary vestige species, is well-adapted to cool conditions. Dormancy in D. involucrata seed lasts for an extremely long period of time, typically between 3 and 4 years, and this characteristic makes the species an excellent model for studying the mechanisms of seed dormancy. The molecular mechanisms governing germination control in D. involucrata are still unknown. Seed stratification have been reported to enhance germination in recalcitrant seeds. We performed a widely targeted metabolome profiling to identify metabolites and associated pathways in D. involucrata seeds from six different moist sand stratification durations (0-30 months) using the ultra-high-performance liquid chromatography-Q Exactive Orbitrap-Mass spectrometry. There was an increasing germination rate with prolonged stratification durations (12-30 months). Furthermore, we detected 10,008 metabolites in the stratified seeds. We also detected 48 differentially accumulated metabolites (DAMs) between all stratification periods in the seeds, with 10 highly conserved metabolites. Most of the differentially accumulated metabolites between unstratified and stratified seeds were enriched in purine metabolism, pyrimidine metabolism, flavone and flavonol biosynthesis, phenylpropanoid biosynthesis, and arginine biosynthesis pathways. Key phytohormones, abscisic acid, indole-3 acetic acid, and sinapic acid were differentially accumulated in the seeds and are predicted to regulate dormancy in D. involucrata. We have provided extensive metabolic information useful for future works on dove tree germination study.

Effects of Four-Week Exposure to Salt Treatments on Germination and Growth of Two Amaranthus Species

Soil salinity represents one of the most restrictive environmental factors for agriculture worldwide. In the present study, the salt tolerance of two weeds of the genus Amaranthus, A. albus and A. hybridus, the latter cultivated as green vegetable in Africa, were analysed. Both species showed a remarkable salt tolerance phenotype during germination and vegetative growth. To evaluate the percentage and rate of germination, seeds were germinated in Petri dishes in a germination chamber under increasing concentrations up to 300 mM NaCl. Higher concentrations of salt ranging from 150 to 600 mM NaCl were applied for one month to plants grown in individual pots in the greenhouse. All seeds of A. albus germinated in the control and almost half of the seeds under 200 mM NaCl, but only 4% of the seeds under 250 mM NaCl. In A. hybridus, germination was considerably lower in all treatments and was completely prevented at 250 mM NaCl. The plant growth of both species was severely affected by high salt concentrations of 450 and 600 mM NaCl, but not under lower concentrations. At this stage of the biological cycle, A. hybridus showed a higher salt tolerance, as indicated by the smaller reduction in its growth parameters. The dry weight of leaves and roots of plants receiving 600 mM NaCl decreased in comparison to control: less than 60% in A. hybridus but more than 70% in A. albus. The salt tolerance of the two species contributes to their invasive potential, but on the other hand represents a useful trait when considering them as potential crops for the future.

Gene expression variation explains maize seed germination heterosis

BACKGROUND

Heterosis has been extensively utilized in plant breeding, however, the underlying molecular mechanism remains largely elusive. Maize (Zea mays), which exhibits strong heterosis, is an ideal material for studying heterosis.

RESULTS

In this study, there is faster imbibition and development in reciprocal crossing Zhengdan958 hybrids than in their parent lines during seed germination. To investigate the mechanism of heterosis of maize germination, comparative transcriptomic analyses were conducted. The gene expression patterns showed that 1324 (47.27%) and 1592 (66.44%) of the differential expression genes between hybrids and either parental line display parental dominance up or higher levels in the reciprocal cross of Zhengdan958, respectively. Notably, these genes were mainly enriched in metabolic pathways, including carbon metabolism, glycolysis/gluconeogenesis, protein processing in endoplasmic reticulum, etc. CONCLUSION: Our results provide evidence for the higher expression level genes in hybrid involved in metabolic pathways acting as main contributors to maize seed germinating heterosis. These findings provide new insights into the gene expression variation of maize embryos and improve the understanding of maize seed germination heterosis.

SALT AND ABA RESPONSE ERF1 improves seed germination and salt tolerance by repressing ABA signaling in rice

Rice (Oryza sativa) germination and seedling establishment, particularly in increasingly saline soils, are critical to ensure successful crop yields. Seed vigor, which determines germination and seedling growth, is a complex trait affected by exogenous (environmental) and endogenous (hormonal) factors. Here, we used genetic and biochemical analyses to uncover the role of an APETALA2-type transcription factor, SALT AND ABA RESPONSE ERF1 (OsSAE1), as a positive regulator of seed germination and salt tolerance in rice by repressing the expression of ABSCISIC ACID-INSENSITIVE5 (OsABI5). ossae1 knockout lines exhibited delayed seed germination, enhanced sensitivity to abscisic acid (ABA) during germination and in early seedling growth, and reduced seedling salt tolerance. OsSAE1 overexpression lines exhibited the converse phenotype, with increased seed germination and salt tolerance. In vivo and in vitro assays indicated that OsSAE1 binds directly to the promoter of OsABI5, a major downstream component of the ABA signaling pathway and acts as a major regulator of seed germination and stress response. Genetic analyses revealed that OsABI5-mediated ABA signaling functions downstream of OsSAE1. This study provides important insights into OsSAE1 regulation of seed vigor and salt tolerance and facilitates the practical use of OsSAE1 in breeding salt-tolerant varieties suitable for direct seeding cultivation.

Nutrients Regulate the Effects of Arbuscular Mycorrhizal Fungi on the Growth and Reproduction of Cherry Tomato

Arbuscular mycorrhizal fungi (AMF) colonize the rhizosphere of plants and form a symbiotic association with plants. Mycorrhizal symbionts have diversified ecological roles and functions which are affected by soil conditions. Understanding the effects of different AMF inoculation on plants under varied nutritional conditions is of great significance for further understanding the effects of the external environment regulating mycorrhizal symbiosis on plant phenotypic traits. In this study, the effects of four AMF inoculation treatments on the growth and reproductive performance of cherry tomato (Solanum lycopersicum var. cerasiforme) were investigated under three nutrient levels by pot experiment. It was found that the growth-promoting effect of AMF on cherry tomato decreased with nutrient reduction, and the effects of the same AMF inoculation treatment on cherry tomato were different at different nutrient levels. Nutrient levels and AMF had interactive effects on flower characteristics, fruit yield, resource allocation, and seed germination of the cherry tomato. In addition, AMF could promote sexual reproductive investment. Nutrient levels and AMF also affected the accumulation of nitrogen and phosphorus in cherry tomato, and there were significant differences among different AMF inoculation treatments. The results indicated that nutrient differences could affect the symbiosis between AMF and plants, and confirmed that there were differences in the effects of the four AMF inoculation treatments on the growth and reproductive traits of plants. The differences in growth and reproduction characteristics of cherry tomato between different AMF inoculation treatments at different nutrient levels indicated that the effects of AMF mycorrhizal on the traits of cherry tomato were regulated by nutrients.

The Delay of Raphanus raphanistrum subsp. sativus (L.) Domin Seed Germination Induced by Coumarin Is Mediated by a Lower Ability to Sustain the Energetic Metabolism

In the present study, the mode of action of coumarin using the germination process as a target was investigated. A dose–response curve, built using a range of concentrations from 0 to 800 µM, allowed us to identify a key concentration (400 µM) inhibiting the germination process, reducing its speed without compromising seed development. Successively, short time-course (0–48 h) experiments were carried out to evaluate the biochemical and metabolic processes involved in coumarin-induced germination delay. The results pointed out that coumarin delayed K+, Ca2+, and Mg2+ reabsorption, suggesting a late membrane reorganisation. Similarly, seed respiration was inhibited during the first 24 h but recovered after 48 h. Those results agreed with ATP levels, which followed the same trend. In addition, the untargeted metabolomic analysis allowed to identify, among the pathways significantly impacted by the treatment, amino acids metabolism, the TCA cycle, and the glyoxylate pathway. The results highlighted that coumarin was able to interact with membranes reorganisation, delaying them and reducing the production of ATP, as also supported by pathway analysis and cell respiration. The in vivo 31P-NMR analysis supported the hypothesis that the concentration chosen was able to affect plant metabolism, maintaining, on the other hand, its viability, which is extremely important for studying natural compounds’ mode of action.

Seed Germination Mechanism of Carex rigescens Under Variable Temperature Determinded Using Integrated Single-Molecule Long-Read and Illumina Sequence Analysis

The turfgrass species Carex rigescens has broad development and utilization prospects in landscaping construction. However, seed dormancy and a low germination rate have inhibited its application. Furthermore, the molecular mechanisms of seed germination in C. rigescens have not been thoroughly studied. Therefore, in the present study, PacBio full-length transcriptome sequencing combined with Illumina sequencing was employed to elucidate the germination mechanism of C. rigescens seeds under variable temperatures. In general, 156,750 full-length non-chimeric sequences, including those for 62,086 high-quality transcripts, were obtained using single-molecule long read sequencing. In total, 40,810 high-quality non-redundant, 1,675 alternative splicing, 28,393 putative coding sequences, and 1,052 long non-coding RNAs were generated. Based on the newly constructed full-length reference transcriptome, 23,147 differentially expressed genes were identified. We screened four hub genes participating in seed germination using weighted gene co-expression network analysis. Combining these results with the physiological observations, the important roles of sucrose and starch metabolic pathways in germination are further discussed. In conclusion, we report the first full-length transcriptome of C. rigescens, and investigated the physiological and transcriptional mechanisms of seed germination under variable temperatures. Our results provide valuable information for future transcriptional analyses and gene function studies of C. rigescens.

Effect of an Environment Friendly Heat and Relative Humidity Approach on γ-Aminobutyric Acid Accumulation in Different Highland Barley Cultivars

In this study, heat and relative humidity (HRH) treatment was applied in highland barley for γ-aminobutyric acid (GABA) accumulation. Tibetan highland barley cultivars (25) were selected for comparison and analysis. HRH treatment could accumulate GABA in several hours with low moisture content and high temperature, and the grains were treated for 2.5 h at 65 °C in this study. The GABA content of processed grains under HRH optimal condition ranged from 26.91 to 76.28 mg·100 g−1, which was significantly higher than the initial content (12.78−43.00 mg·100 g−1). The highest GABA accumulation capacity was observed in two-row yellow cultivars (YT1), increasing from 36.52 to 76.28 mg·100 g−1. Correlation analysis showed that the accumulation of GABA after HRH treatment was positively and significantly (p < 0.05) correlated with the contents of protein (0.52), total free amino acids (0.68), threonine (0.53), serine (0.51), glutamate (0.69), glycine (0.49), alanine (0.46), cysteine (0.57), tyrosine (0.50), lysine (0.53), proline (0.40), and glutamate decarboxylase (GAD) activity (0.62), which were closely related to GABA-shunt pathway. The polyamines contents, diamine oxidase (DAO) and polyamine oxidase (PAO) activities, as the substrates and critical enzymes of polyamine degradation pathway, showed no significant correlation with GABA accumulation. The results suggested that the main pathway of GABA accumulation in highland barley under HRH treatment was GABA-shunt pathway.

Biosynthesis and the Roles of Plant Sterols in Development and Stress Responses

Plant sterols are important components of the cell membrane and lipid rafts, which play a crucial role in various physiological and biochemical processes during development and stress resistance in plants. In recent years, many studies in higher plants have been reported in the biosynthesis pathway of plant sterols, whereas the knowledge about the regulation and accumulation of sterols is not well understood. In this review, we summarize and discuss the recent findings in the field of plant sterols, including their biosynthesis, regulation, functions, as well as the mechanism involved in abiotic stress responses. These studies provide better knowledge on the synthesis and regulation of sterols, and the review also aimed to provide new insights for the global role of sterols, which is liable to benefit future research on the development and abiotic stress tolerance in plant.