Seed dormancy and germination

Map-based cloning of Zmccr3 and its network construction and validation for regulating maize seed germination

KEY MESSAGE

Map-based cloning of Zmccr3 for regulate SG and its molecular regulatory pathway was performed and validated. WGCNA, target genes/pathways during the process of seed dormancy formation were obtained. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect the grain yield and quality of grain in cereal and hybrid seed production. Although the benefits of studying SD and seed germination (SG) during seed development are well established, research into the genetic variation and molecular regulation of SD, particularly during the transition from SD to SG, remains very limited. In this study, bulked segregant analysis (BSA) and linkage analysis were used to map the QTL for the maize vp16 mutant of PHS. Using genetic and biological methods, the candidate gene was identified as Zmccr3, encoding cinnamoyl-CoA reductase 3 (ccr3), which is involved in the phenylalanine pathway of lignin metabolism and affects SG. Based on RNA-seq (RNA sequencing) at two stages of grain development with extreme PHS traits, a weighted gene coexpression network analysis (WGCNA) related to SD and SG formation was constructed, and ten target genes and three pathways during the transition from SD to SG were identified. Simultaneously, the Zmccr3 pathway was established and validated, involving upstream lipid metabolism, redox modification and degradation of cell wall oligosaccharides (as electrophilic compounds), regulation of GA signaling and intracellular ROS homeostasis, and downstream oxidation of cell wall lignin units and synthesis of phenolic compounds that affect endosperm weakening and cell wall loosening, ultimately regulating SG or SD. Therefore, we propose the Zmccr3 hypothesis to elucidate its possible functions. These findings have important theoretical and practical implications for understanding the genetic basis of PHS and SD in maize, increasing genetic resources and improving traits.

A space for time. Exploring temporal regulation of plant development across spatial scales

Plants continuously undergo change during their life cycle, experiencing dramatic phase transitions altering plant form, and regulating the assignment and progression of cell fates. The relative timing of developmental events is tightly controlled and involves integration of environmental, spatial, and relative age-related signals and actors. While plant phase transitions have been studied extensively and many of their regulators have been described, less is known about temporal regulation on a smaller, cell-level scale. Here, using examples from both plant and animal systems, we outline time-dependent changes. Looking at systemic scale changes, we discuss the timing of germination, juvenile-to-adult transition, flowering, and senescence, together with regeneration timing. Switching to temporal regulation on a cellular level, we discuss several instances from the animal field in which temporal control has been examined extensively at this scale. Then, we switch back to plants and summarize examples where plant cell-level changes are temporally regulated. As time cannot easily be separated from signaling derived from the environment and tissue context, we next discuss factors that have been implicated in controlling the timing of developmental events, reviewing temperature, photoperiod, nutrient availability, as well as tissue context and mechanical cues on the cellular scale. Afterwards, we provide an overview of mechanisms that have been shown or implicated in the temporal control of development, considering metabolism, division control, mobile signals, epigenetic regulation, and the action of transcription factors. Lastly, we look at remaining questions for the future study of developmental timing in plants and how recent technical advancement can enable these efforts.

Role of functional genes for seed vigor related traits through genome-wide association mapping in finger millet (Eleusine coracana L. Gaertn.)

Finger millet (Eleusine coracana (L.) Gaertn.) is a calcium-rich, nutritious and resilient crop that thrives even in harsh environmental conditions. In such ecologies, seed longevity and seedling vigor are crucial for sustainable crop production amid climate change. The current study explores the genetics of accelerated aging on seed longevity traits across 221 diverse accessions of finger millet through genome-wide association approach (GWAS). A significant variation was identified in germination percentage, germination rate indices, mean germination time, seedling vigor indices and dry weight upon aging treatment. GWAS model from 11,832 high-quality SNPs identified through Genotyping-by-Sequencing (GBS) approach produced 491 marker-trait associations (MTAs) for 27 traits, of which 54 were FDR-corrected. A pleiotropic SNP, FM_SNP_9478 identified on chromosome 7B was associated with the traits viz., germination after aging, germination index after aging and their relative measures. Functional annotation revealed DET1 and expansin-A2 influenced seed coat integrity, critical for germination and aging resilience. Probable protein phosphatase 2C3 and piezo-type ion channels contributed to mechanical sensing and stress adaptation in seeds. Beta-amylase and acetyl-CoA carboxylase 2 were identified for seed metabolism and stress response. These insights lay the framework for targeted breeding efforts to improve seed quality and resilience under diverse production conditions.

De novo root regeneration from leaf explant: a mechanistic review of key factors behind cell fate transition

MAIN CONCLUSION

De novo root regeneration (DNRR) involves activation of special cells after wounding, along with the converter cells, reactive oxygen species, ethylene, and jasmonic acid, also playing key roles. An updated DNRR model is presented here with gene regulatory networks. Root formation after tissue injury is a type of plant regeneration known as de novo root regeneration (DNRR). DNRR system has wide applications in agriculture and tissue culture biotechnology. This review summarizes the recent advancements in the DNRR model for the cellular and molecular framework, targeting leaf explant of Arabidopsis and highlighting differences among direct and indirect pathways. Key findings highlight the presence of special cells in leaf explants after wounding, under different time lapses, through single-cell sequencing of the transcriptional landscape. The possible roles of reactive oxygen species (ROS), ethylene, and jasmonic acid are explored in the early establishment of wounding signals (short/long) for auxin biosynthesis, ultimately leading to adventitious root formation. The synergistic manner of 3rd type of special cells along converter and regeneration-competent cells automatically leads towards cell fate transition for auxin flux in regeneration-competent cells. The signaling mechanisms of these suggested special cells need to be further investigated to understand the DNRR mechanistic story entirely, in addition to root-to-root regeneration and stem-to-root regeneration. Meta-analysis of DNRR is also presented for past and future reference.

Warm temperature perceived at the vegetative stage affects progeny seed germination in natural accessions of Arabidopsis thaliana

Temperatures perceived early in the life cycle of mother plants can affect the germination of the offspring seeds. In Arabidopsis thaliana, vernalisation-insensitive mutants showed altered germination response to elevated maternal temperature, hence revealing a strong genetic determinism. However, the genetic control of this maternal effect and its prevalence across natural populations remain unclear. Here, we exposed a collection of European accessions of A. thaliana to increased temperature during the vegetative phase and assessed germination in their progeny to identify the genetic basis of transgenerational germination response. We found that genotypes with rapidly germinating progeny after early maternal exposure to elevated temperature originated from regions with low-light radiation. Combining genome-wide association, expression analysis and functional assays across multiple genetic backgrounds, we show a central role for PHYB in mediating the response to maternally perceived temperature at the vegetative stage. Differential gene expression analysis in leaves identified a similar genetic network as previously found in seed endosperm under elevated temperature, supporting the pleiotropic involvement of PHYB signalling across different tissues and stages. This provides evidence that complex environmental responses modulated by the maternal genotype can rely on a consistent set of genes yet produce different effects at the different stages of exposure.

Arachis hypogaea monoacylglycerol lipase AhMAGL3b participates in lipid metabolism

BACKGROUND

Monoacylglycerol lipase (MAGL) belongs to the serine hydrolase family; it catalyzes MAG to produce glycerol and free fatty acids (FFAs), which is the final step in triacylglycerol (TAG) hydrolysis. The effects of MAGL on comprehensive lipid metabolism and plant growth and development have not been elucidated, especially in Arachis hypogaea, an important oil crop.

RESULTS

Herein, AhMAGL3b encoding a protein with both hydrolase and acyltransferase regions, a member of MAGL gene family, was cloned and overexpressed in Arabidopsis thaliana. A total of 9 homozygous T3 generation transgenic lines were obtained. Compared with wild type (WT), overexpression (OE) of AhMAGL3b had no obvious growth inhibition by investigation of agronomic traits, including growth and photosynthetic parameters. The leaf fatty acid (FA) content was increased by 12.1-27.4% in AhMAGL3b-OE lines, while seed oil content was decreased by 10.7-17.3%. Furthermore, the overexpression of AhMAGL3b resulted in higher soluble sugar and starch content, and lower total soluble protein content in both leaves and seeds. Additionally, during seed germination, AhMAGL3b-OE seeds were more dormant than that of WT and the sensitivity to abscisic acid (ABA) treatment was decreased.

CONCLUSIONS

Taken together, our results indicate that AhMAGL3b is involved in homeostasis among carbohydrates, lipids and protein in A. hypogaea.

The phosphatidylethanolamine-binding proteins OsMFT1 and OsMFT2 regulate seed dormancy in rice

Seed dormancy is crucial for optimal plant life-cycle timing. However, domestication has largely diminished seed dormancy in modern cereal cultivars, leading to challenges such as preharvest sprouting (PHS) and subsequent declines in yield and quality. Therefore, it is imperative to unravel the molecular mechanisms governing seed dormancy for the development of PHS-resistant varieties. In this study, we screened a mutant of BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR4 (OsbHLH004) with decreased seed dormancy and revealed that OsbHLH004 directly regulates the expression of 9-CIS-EPOXYCAROTENOID DIOXYGENASE3 (OsNCED3) and GIBBERELLIN 2-OXIDASE6 (OsGA2ox6) in rice (Oryza sativa). Additionally, we determined that two phosphatidylethanolamine-binding proteins, MOTHER OF FT AND TFL1 and 2 (OsMFT1 and OsMFT2; hereafter OsMFT1/2) interact with OsbHLH004 and Ideal Plant Architecture 1 (IPA1) to regulate their binding capacities on OsNCED3 and OsGA2ox6, thereby promoting seed dormancy. Intriguingly, FT-INTERACTING PROTEIN1 (OsFTIP1) interacts with OsMFT1/2 and affects their nucleocytoplasmic translocation into the nucleus, where OsMFT1/2-OsbHLH004 and OsMFT1/2-IPA1 antagonistically modulate the expression of OsNCED3 and OsGA2ox6. Our findings reveal that OsFTIP1-mediated inhibition of nuclear translocation of OsMFT1/2 and the dynamic transcriptional modulation of OsNCED3 and OsGA2ox6 by OsMFT1/2-OsbHLH004 and OsMFT1/2-IPA1 complexes in seed dormancy in rice.

Characterizing seed dormancy in Epimedium brevicornu Maxim.: Development of novel chill models and determination of dormancy release mechanisms by transcriptomics

PURPOSE

Epimedium brevicornu Maxim. is a perennial persistent C3 plant of the genus Epimedium Linn. in the family Berberaceae that exhibits severe physiological and morphological seed dormancy.We placed mature E. brevicornu seeds under nine stratification treatment conditions and explored the mechanisms of influence by combining seed embryo growth status assessment with related metabolic pathways and gene co-expression analysis.

RESULTS

We identified 3.9 °C as the optimum cold-stratification temperature of E. brevicornu seeds via a chilling unit (CU) model. The best treatment was variable-temperature stratification (10/20 °C, 12/12 h) for 4 months followed by low-temperature stratification (4 °C) for 3 months (4-3). A total of 63801 differentially expressed genes were annotated to 2587 transcription factors (TFs) in 17 clusters in nine treatments (0-0, 0-3, 1-3, 2-3, 3-3, 4-3, 4-2, 4-1, 4-0). Genes specifically highly expressed in the dormancy release treatment group were significantly enriched in embryo development ending in seed dormancy and fatty acid degradation, indicating the importance of these two processes. Coexpression analysis implied that the TF GRF had the most reciprocal relationships with genes, and multiple interactions centred on zf-HD and YABBY as well as on MYB, GRF, and TCP were observed.

CONCLUSION

In this study, analyses of plant hormone signal pathways and fatty acid degradation pathways revealed changes in key genes during the dormancy release of E. brevicornu seeds, providing evidence for the filtering of E. brevicornu seed dormancy-related genes.

Ectopic overexpression of ShCBF1 and SlCBF1 in tomato suggests an alternative view of fruit responses to chilling stress postharvest

Postharvest chilling injury (PCI) is a physiological disorder that often impairs tomato fruit ripening; this reduces fruit quality and shelf-life, and even accelerates spoilage at low temperatures. The CBF gene family confers cold tolerance in Arabidopsis thaliana, and constitutive overexpression of CBF in tomato increases vegetative chilling tolerance, in part by retarding growth, but, whether CBF increases PCI tolerance in fruit is unknown. We hypothesized that CBF1 overexpression (OE) would be induced in the cold and increase resistance to PCI. We induced high levels of CBF1 in fruit undergoing postharvest chilling by cloning it from S. lycopersicum and S. habrochaites, using the stress-inducible RD29A promoter. Harvested fruit were cold-stored (2.5°C) for up to three weeks, then rewarmed at 20°C for three days. Transgene upregulation was triggered during cold storage from 8.6- to 28.6-fold in SlCBF1-OE, and between 3.1- to 8.3-fold in ShCBF1-OE fruit, but developmental abnormalities in the absence of cold induction were visible. Remarkably, transgenic fruit displayed worsening of PCI symptoms, i.e., failure to ripen after rewarming, comparatively higher susceptibility to decay relative to wild-type (WT) fruit, lower total soluble solids, and the accumulation of volatile compounds responsible for off-odors. These symptoms correlated with CBF1 overexpression levels. Transcriptomic analysis revealed that the ripening and biotic and abiotic stress responses were altered in the cold-stored transgenic fruit. Seedlings grown from 'chilled' and 'non-chilled' WT fruit, in addition to 'non-chilled' transgenic fruit were also exposed to 0°C to test their photosynthetic response to chilling injury. Chilled WT seedlings adjusted their photosynthetic rates to reduce oxidative damage; 'non-chilled' WT seedlings did not. Photosynthetic parameters between transgenic seedlings were similar at 0°C, but SlCBF1-OE showed more severe photoinhibition than ShCBF1-OE, mirroring phenotypic observations. These results suggest that 1) CBF1 overexpression accelerated fruit deterioration in response to cold storage, and 2) Chilling acclimation in fructus can increase chilling tolerance in seedling progeny of WT tomato.

Mapping of flumioxazin tolerance in a snap bean diversity panel leads to the discovery of a master genomic region controlling multiple stress resistance genes

Introduction

Effective weed management tools are crucial for maintaining the profitable production of snap bean (Phaseolus vulgaris L.). Preemergence herbicides help the crop to gain a size advantage over the weeds, but the few preemergence herbicides registered in snap bean have poor waterhemp (Amaranthus tuberculatus) control, a major pest in snap bean production. Waterhemp and other difficult-to-control weeds can be managed by flumioxazin, an herbicide that inhibits protoporphyrinogen oxidase (PPO). However, there is limited knowledge about crop tolerance to this herbicide. We aimed to quantify the degree of snap bean tolerance to flumioxazin and explore the underlying mechanisms.

Methods

We investigated the genetic basis of herbicide tolerance using genome-wide association mapping approach utilizing field-collected data from a snap bean diversity panel, combined with gene expression data of cultivars with contrasting response. The response to a preemergence application of flumioxazin was measured by assessing plant population density and shoot biomass variables.

Results

Snap bean tolerance to flumioxazin is associated with a single genomic location in chromosome 02. Tolerance is influenced by several factors, including those that are indirectly affected by seed size/weight and those that directly impact the herbicide's metabolism and protect the cell from reactive oxygen species-induced damage. Transcriptional profiling and co-expression network analysis identified biological pathways likely involved in flumioxazin tolerance, including oxidoreductase processes and programmed cell death. Transcriptional regulation of genes involved in those processes is possibly orchestrated by a transcription factor located in the region identified in the GWAS analysis. Several entries belonging to the Romano class, including Bush Romano 350, Roma II, and Romano Purpiat presented high levels of tolerance in this study. The alleles identified in the diversity panel that condition snap bean tolerance to flumioxazin shed light on a novel mechanism of herbicide tolerance and can be used in crop improvement.

Effect of magnetic field pretreatment on germination characteristics, phenolic biosynthesis, and antioxidant capacity of quinoa

The development of quinoa-based functional foods with cost-effective methods has gained considerable attention. In this study, the effects of magnetic field pretreatment on the germination characteristics, phenolic synthesis, and antioxidant system of quinoa (Chenopodium quinoa Willd.) were investigated. The results showed that the parameters of magnetic field pretreatment had different effects on the germination properties of five quinoa varieties, in which Sanjiang-1 (SJ-1) was more sensitive to magnetic field pretreatment. The content of total phenolics and phenolic acids in 24-h germinated seeds increased by 20.48% and 26.54%, respectively, under the pretreatment of 10 mT magnetic fields for 10 min compared with the control. This was closely related to the activation of the phenylpropanoid pathway by increasing enzyme activities and gene expression. In addition, magnetic field improved 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-Azinobis-(3-ethylbenzthiazoline-6-sulphonate) (ABTS) free radicals scavenging capacities and increased peroxidase (POD), catalase (CAT), superoxide dismutase (SOD), ascorbate peroxidase (APX) and glutathione peroxidase (GSH-Px) activities. This study suggests that magnetic field pretreatment enhanced gene expression of phenylalanine ammonia lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS) and chalcone isomerase (CHI), increased antioxidant enzyme activity and phenolics content. Thereby lead to an increase in the antioxidative capacity of quinoa.

Spatial specificity of metabolism regulation of abscisic acid-imposed seed germination inhibition in Korean pine (Pinus koraiensis sieb et zucc)

Introduction

Abscisic acid (ABA) can negatively regulate seed germination, but the mechanisms of ABA-mediated metabolism modulation are not well understood. Moreover, it remains unclear whether metabolic pathways vary with the different tissue parts of the embryo, such as the radicle, hypocotyl and cotyledon.

Methods

In this report, we performed the first comprehensive metabolome analysis of the radicle and hypocotyl + cotyledon in Pinus koraiensis seeds in response to ABA treatment during germination.

Results and discussion

Metabolome profiling showed that following ABA treatment, 67 significantly differentially accumulated metabolites in the embryo were closely associated with pyrimidine metabolism, phenylalanine metabolism, cysteine and methionine metabolism, galactose metabolism, terpenoid backbone biosynthesis, and glutathione metabolism. Meanwhile, 62 metabolites in the hypocotyl + cotyledon were primarily involved in glycerophospholipid metabolism and glycolysis/gluconeogenesis. We can conclude that ABA may inhibit Korean pine seed germination primarily by disrupting the biosynthesis of certain plant hormones mediated by cysteine and methionine metabolism and terpenoid backbone biosynthesis, as well as reducing the reactive oxygen species scavenging ability regulated by glutathione metabolism and shikimate pathway in radicle. ABA may strongly disrupt the structure and function of cellular membranes due to alterations in glycerophospholipid metabolism, and weaken glycolysis/gluconeogenesis in the hypocotyl + cotyledon, both of which are major contributors to ABA-mediated inhibition of seed germination. These results highlight that the spatial modulation of metabolic pathways in Pinus koraiensis seeds underlies the germination response to ABA.

Identification of ARF Genes and Elucidation of the Regulatory Effects of PsARF16a on the Dormancy of Tree Peony Plantlets

The low survival rate of transplanted plantlets, which has limited the utility of tissue-culture-based methods for the rapid propagation of tree peonies, is due to plantlet dormancy after rooting. We previously determined that the auxin response factor PsARF may be a key regulator of tree peony dormancy. To clarify the mechanism mediating tree peony plantlet dormancy, PsARF genes were systematically identified and analyzed. Additionally, PsARF16a was transiently expressed in the leaves of tree peony plantlets to examine its regulatory effects on a downstream gene network. Nineteen PsARF genes were identified and divided into four classes. All PsARF genes encoded proteins with conserved B3 and ARF domains. The number of motifs, exons, and introns varied between PsARF genes in different classes. The overexpression of PsARF16a altered the expression of NCED, ZEP, PYL, GA2ox1, GID1, and other key genes in abscisic acid (ABA) and gibberellin (GA) signal transduction pathways, thereby promoting ABA synthesis and decreasing GA synthesis. Significant changes to the expression of some key genes contributing to starch and sugar metabolism (e.g., AMY2A, BAM3, BGLU, STP, and SUS2) may be associated with the gradual conversion of sugar into starch. This study provides important insights into PsARF functions in tree peonies.

Developmental pleiotropy of SDP1 from seedling to mature stages in B. napus

Rapeseed, an important oil crop, relies on robust seedling emergence for optimal yields. Seedling emergence in the field is vulnerable to various factors, among which inadequate self-supply of energy is crucial to limiting seedling growth in early stage. SUGAR-DEPENDENT1 (SDP1) initiates triacylglycerol (TAG) degradation, yet its detailed function has not been determined in B. napus. Here, we focused on the effects of plant growth during whole growth stages and energy mobilization during seedling establishment by mutation in BnSDP1. Protein sequence alignment and haplotypic analysis revealed the conservation of SDP1 among species, with a favorable haplotype enhancing oil content. Investigation of agronomic traits indicated bnsdp1 had a minor impact on vegetative growth and no obvious developmental defects when compared with wild type (WT) across growth stages. The seed oil content was improved by 2.0-2.37% in bnsdp1 lines, with slight reductions in silique length and seed number per silique. Furthermore, bnsdp1 resulted in lower seedling emergence, characterized by a shrunken hypocotyl and poor photosynthetic capacity in the early stages. Additionally, impaired seedling growth, especially in yellow seedlings, was not fully rescued in medium supplemented with exogenous sucrose. The limited lipid turnover in bnsdp1 was accompanied by induced amino acid degradation and PPDK-dependent gluconeogenesis pathway. Analysis of the metabolites in cotyledons revealed active amino acid metabolism and suppressed lipid degradation, consistent with the RNA-seq results. Finally, we proposed strategies for applying BnSDP1 in molecular breeding. Our study provides theoretical guidance for understanding trade-off between oil accumulation and seedling energy mobilization in B. napus.

S-nitrosylation of the transcription factor MYB30 facilitates nitric oxide-promoted seed germination in Arabidopsis

The gaseous signaling molecule nitric oxide (NO) plays an important role in breaking seed dormancy. NO induces a decrease in abscisic acid (ABA) content by transcriptionally activating its catabolic enzyme, the ABA 8'-hydroxylase CYP707A2. However, the underlying mechanism of this process remains unclear. Here, we report that the transcription factor MYB30 plays a critical role in NO-induced seed germination in Arabidopsis (Arabidopsis thaliana). MYB30 loss-of-function attenuates NO-mediated seed dormancy breaking. MYB30 triggers a NO-induced decrease in ABA content during germination by directly promoting CYP707A2 expression. NO induces S-nitrosylation at Cys-49 of MYB30 and enhances its transcriptional activity. Conversely, the ABA receptors PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS (RCAR) interact with MYB30 and repress its transcriptional activity. ABA promotes the interaction between PYL4 and MYB30, whereas S-nitrosylation releases the PYL4-mediated inhibition of MYB30 by interfering with the PYL4-MYB30 interaction. Genetic analysis showed that MYB30 functions downstream of PYLs during seed dormancy and germination in response to NO. Furthermore, MYB30 mutation significantly represses the reduced dormancy phenotype and the enhanced CYP707A2 expression of the pyr1 pyl1 pyl2 pyl4 quadruple mutant. Our findings reveal that S-nitrosylation of MYB30 precisely regulates the balance of seed dormancy and germination, providing insights into the underlying mechanism of NO-promoted seed germination.

Involvement of Abscisic Acid in Transition of Pea (Pisum sativum L.) Seeds from Germination to Post-Germination Stages

The transition from seed to seedling represents a critical developmental step in the life cycle of higher plants, dramatically affecting plant ontogenesis and stress tolerance. The release from dormancy to acquiring germination ability is defined by a balance of phytohormones, with the substantial contribution of abscisic acid (ABA), which inhibits germination. We studied the embryonic axis of Pisum sativum L. before and after radicle protrusion. Our previous work compared RNA sequencing-based transcriptomics in the embryonic axis isolated before and after radicle protrusion. The current study aims to analyze ABA-dependent gene regulation during the transition of the embryonic axis from the germination to post-germination stages. First, we determined the levels of abscisates (ABA, phaseic acid, dihydrophaseic acid, and neo-phaseic acid) using ultra-high-performance liquid chromatography-tandem mass spectrometry. Second, we made a detailed annotation of ABA-associated genes using RNA sequencing-based transcriptome profiling. Finally, we analyzed the DNA methylation patterns in the promoters of the PsABI3, PsABI4, and PsABI5 genes. We showed that changes in the abscisate profile are characterized by the accumulation of ABA catabolites, and the ABA-related gene profile is accompanied by the upregulation of genes controlling seedling development and the downregulation of genes controlling water deprivation. The expression of ABI3, ABI4, and ABI5, which encode crucial transcription factors during late maturation, was downregulated by more than 20-fold, and their promoters exhibited high levels of methylation already at the late germination stage. Thus, although ABA remains important, other regulators seems to be involved in the transition from seed to seedling.

Effect of Reactive Oxygen Scavenger N,N'-Dimethylthiourea (DMTU) on Seed Germination and Radicle Elongation of Maize

Reactive oxygen species (ROS) are an important part of adaptation to biotic and abiotic stresses and regulate seed germination through positive or negative signaling. Seed adaptation to abiotic stress may be mediated by hydrogen peroxide (H2O2). The effects of the ROS scavenger N,N'-dimethylthiourea (DMTU) on maize seed germination through endogenous H2O2 regulation is unclear. In this study, we investigated the effects of different doses of DMTU on seed endogenous H2O2 and radicle development parameters using two maize varieties (ZD958 and DMY1). The inhibitory effect of DMTU on the germination rate and radicle growth was dose-dependent. The inhibitory effect of DMTU on radicle growth ceased after transferring maize seeds from DMTU to a water medium. Histochemical analyses showed that DMTU eliminated stable H2O2 accumulation in the radicle sheaths and radicles. The activity of antioxidant enzyme and the expression of antioxidant enzyme-related genes (ZmAPX2 and ZmCAT2) were reduced in maize seeds cultured with DMTU compared with normal culture conditions (0 mmol·dm-3 DMTU). We suggest the use of 200 mmol·dm-3 DMTU as an H2O2 scavenger to study the ROS equilibrium mechanisms during the germination of maize seeds, assisting in the future with the efficient development of plant growth regulators to enhance the seed germination performance of test maize varieties under abiotic stress.

Autophagy in maternal tissues contributes to Arabidopsis seed development

Seeds are an essential food source, providing nutrients for germination and early seedling growth. Degradation events in the seed and the mother plant accompany seed development, including autophagy, which facilitates cellular component breakdown in the lytic organelle. Autophagy influences various aspects of plant physiology, specifically nutrient availability and remobilization, suggesting its involvement in source-sink interactions. During seed development, autophagy affects nutrient remobilization from mother plants and functions in the embryo. However, it is impossible to distinguish between the contribution of autophagy in the source (i.e. the mother plant) and the sink tissue (i.e. the embryo) when using autophagy knockout (atg mutant) plants. To address this, we employed an approach to differentiate between autophagy in source and sink tissues. We investigated how autophagy in the maternal tissue affects seed development by performing reciprocal crosses between wild type and atg mutant Arabidopsis (Arabidopsis thaliana) plants. Although F1 seedlings possessed a functional autophagy mechanism, etiolated F1 plants from maternal atg mutants displayed reduced growth. This was attributed to altered protein but not lipid accumulation in the seeds, suggesting autophagy differentially regulates carbon and nitrogen remobilization. Surprisingly, F1 seeds of maternal atg mutants exhibited faster germination, resulting from altered seed coat development. Our study emphasizes the importance of examining autophagy in a tissue-specific manner, revealing valuable insights into the interplay between different tissues during seed development. It also sheds light on the tissue-specific functions of autophagy, offering potential for research into the underlying mechanisms governing seed development and crop yield.

Plant Hormone Modularity and the Survival-Reproduction Trade-Off

Biological modularity refers to the organization of living systems into separate functional units that interact in different combinations to promote individual well-being and species survival. Modularity provides a framework for generating and selecting variations that can lead to adaptive evolution. While the exact mechanisms underlying the evolution of modularity are still being explored, it is believed that the pressure of conflicting demands on limited resources is a primary selection force. One prominent example of conflicting demands is the trade-off between survival and reproduction. In this review, we explore the available evidence regarding the modularity of plant hormones within the context of the survival-reproduction trade-off. Our findings reveal that the cytokinin module is dedicated to maximizing reproduction, while the remaining hormone modules function to ensure reproduction. The signaling mechanisms of these hormone modules reflect their roles in this survival-reproduction trade-off. While the cytokinin response pathway exhibits a sequence of activation events that aligns with the developmental robustness expected from a hormone focused on reproduction, the remaining hormone modules employ double-negative signaling mechanisms, which reflects the necessity to prevent the excessive allocation of resources to survival.

Effect of Abiotic Stresses from Drought, Temperature, and Density on Germination and Seedling Growth of Barley (Hordeum vulgare L.)

Seed germination and seedling growth are highly sensitive to deficit moisture and temperature stress. This study was designed to investigate barley (Hordeum vulgare L.) seeds' germination and seedling growth under conditions of abiotic stresses. Constant temperature levels of 5, 10, 15, 20, 25, 30, and 35 °C were used for the germination test. Drought and waterlogging stresses using 30 different water levels were examined using two methods: either based at 1 milliliter intervals or, on the other hand, as percentages of thousand kernel weight (TKW). Seedling density in a petri dish and antifungal application techniques were also investigated. Temperature significantly impacted germination time and seedling development with an ideal range of 15-20 °C, with a more comprehensive range to 10 °C. Higher temperatures reversely affected germination percentage, and the lower ones affected the germination and seedling growth rate. Germination commenced at 130% water of the TKW, and the ideal water range for seedling development was greater and more extensive than the range for germination, which means there is a difference between the starting point for germination and the seedling development. Seed size define germination water requirements and provides an objective and more precise basis suggesting an optimal range supply of 720% and 1080% of TKW for barley seedling development. A total of 10 seeds per 9 cm petri dish may be preferable over greater densities. The techniques of priming seeds with an antifungal solution (Bordóilé or Hypo) or antifungal application at even 5 ppm in the media significantly prevented fungal growth. This study is novel regarding the levels and types of abiotic stresses, the crop, the experimental and measurement techniques, and in comparison to the previous studies.

Characterization of Invasiveness, Thermotolerance and Light Requirement of Nine Invasive Species in China

Understanding responsible functional traits for promoting plant invasiveness could be important to aid in the development of adequate management strategies for invasive species. Seed traits play an important role in the plant life cycle by affecting dispersal ability, formation of the soil seed bank, type and level of dormancy, germination, survival and/or competitive ability. We assessed seed traits and germination strategies of nine invasive species under five temperature regimes and light/dark treatments. Our results showed a considerable level of interspecific variation in germination percentage among the tested species. Both cooler (5/10 °C) and warmer (35/40 °C) temperatures tended to inhibit germination. All study species were considered small-seeded, and seed size did not affect germination in the light. Yet, a slightly negative correlation was found between germination in the dark and seed dimensions. We classified the species into three categories according to their germination strategies: (i) risk-avoiders, mostly displaying dormant seeds with low G%; (ii) risk-takers, reaching a high G% in a broad range of temperatures; (iii) intermediate species, showing moderate G% values, which could be enhanced in specific temperature regimes. Variability in germination requirements could be important to explain species coexistence and invasion ability of plants to colonize different ecosystems.

Transcriptome and proteome analyses reveal the potential mechanism of seed dormancy release in Amomum tsaoko during warm stratification

BACKGROUND

In Amomum tsaoko breeding, the low germination rate is the major limitation for their large-scale reproduction. We found that warm stratification was an effective treatment to break the seed dormancy of A. tsaoko prior to sowing and could be an important component of improving breeding programs. The mechanism of seed dormancy release during warm stratification remains unclear. Therefore, we studied the differences between transcripts and proteomes at 0, 30, 60, and 90 days of warm stratification, to identify some regulatory genes and functional proteins that may cause seed dormancy release in A. tsaoko and reveal their regulatory mechanism.

RESULTS

RNA-seq was performed for the seed dormancy release process, and the number of differentially expressed genes (DEGs) was 3196 in three dormancy release periods. Using TMT-labelling quantitative proteome analysis, a total of 1414 proteins were defined as differentially expressed proteins (DEPs). Functional enrichment analyses revealed that the DEGs and DEPs were mainly involved in signal transduction pathways (MAPK signaling, hormone) and metabolism processes (cell wall, storage and energy reserves), suggesting that these differentially expressed genes and proteins are somehow involved in response to seed dormancy release process, including MAPK, PYR/PYL, PP2C, GID1, GH3, ARF, AUX/IAA, TPS, SPS, and SS. In addition, transcription factors ARF, bHLH, bZIP, MYB, SBP, and WRKY showed differential expression during the warm stratification stage, which may relate to dormancy release. Noteworthy, XTH, EXP, HSP and ASPG proteins may be involved in a complex network to regulate cell division and differentiation, chilling response and the seed germination status in A. tsaoko seed during warm stratification.

CONCLUSION

Our transcriptomic and proteomic analysis highlighted specific genes and proteins that warrant further study in fully grasping the precise molecular mechanisms that control the seed dormancy and germination of A. tsaoko. A hypothetical model of the genetic regulatory network provides a theoretical basis for overcoming the physiological dormancy in A. tsaoko in the future.

Systematic analysis of photo/sko-regulated germination and post-germination development of shallow photodormant seeds in Nicotiana tabacum L

INTRODUCTION

Light is a major environmental factor in regulating germination and post-germination development of shallow photo-dormant seeds in Nicotiana tabacum L. (tobacco). However, its molecular mechanism remains largely unclear.

METHODS AND RESULTS

In this study, we compared the phenotypes of the seeds germinated under light and dark, and systematically investigated their regulatory networks by integrating transcriptomic and proteomic data. Under light, the germination increased ~25%, the length of the hypocotyl shortened ~3 cm, and the apical hook disappeared. 9, 161, 342 differentially expressed genes (DEGs) and 128, 185, 81 differentially expressed proteins (DEPs) were regulated by light in the development stage of seed imbibition, radicle protrusion and cotyledon expansion respectively. 0, 19 and 1 co-up-regulated and 1, 30 and 64 co-down-regulated DEGs (DEP) were observed in the three stages, respectively. Of them, 2S albumin large chain, was down-regulated by light in imbibed seed. Oleosin 18.5 kDa (OLEO1) and Glyceraldehyde-3-phosphate dehydrogenase (GAPA1), Oxygen-evolving enhancer protein 1-1 and anchloroplastic (PSBO1), hub genes (proteins) in protein-protein interaction network (PPI), were downregulated and up-regulated in germinated seeds by light, respectively. OLEO1, a hub gene (proteins), was down-regulated by light in post-germination seedling.

CONCLUSION

These results systematically revealed the molecular networks regulated by light during germination and post-germination development of shallow photo-dormant tobacco seeds.

Protein phosphatases and their targets: Comprehending the interactions in plant signaling pathways

Protein phosphorylation is a vital reversible post-translational modification. This process is established by two classes of enzymes: protein kinases and protein phosphatases. Protein kinases phosphorylate proteins while protein phosphatases dephosphorylate phosphorylated proteins, thus, functioning as 'critical regulators' in signaling pathways. The eukaryotic protein phosphatases are classified as phosphoprotein phosphatases (PPP), metallo-dependent protein phosphatases (PPM), protein tyrosine (Tyr) phosphatases (PTP), and aspartate (Asp)-dependent phosphatases. The PPP and PPM families are serine (Ser)/threonine (Thr) specific phosphatases (STPs) that dephosphorylate Ser and Thr residues. The PTP family dephosphorylates Tyr residues while dual-specificity phosphatases (DsPTPs/DSPs) dephosphorylate Ser, Thr, and Tyr residues. The composition of these enzymes as well as their substrate specificity are important determinants of their functional significance in a number of cellular processes and stress responses. Their role in animal systems is well-understood and characterized. The functional characterization of protein phosphatases has been extensively covered in plants, although the comprehension of their mechanistic basis is an ongoing pursuit. The nature of their interactions with other key players in the signaling process is vital to our understanding. The substrates or targets determine their potential as well as magnitude of the impact they have on signaling pathways. In this article, we exclusively overview the various substrates of protein phosphatases in plant signaling pathways, which are a critical determinant of the outcome of various developmental and stress stimuli.

Seed priming to optimize germination in Arthrocnemum Moq

BACKGROUND

Seed germination and seedling growth constitute the first stage of a plant's life cycle for crop establishment. Arthrocnemum Moq. is a halophyte of the subfamily Salicornioideae (Amaranthaceae), which could be recognized in the foreseeable future as an emerging candidate in applied biosaline agricultural programs, mainly due to the large biomass it represents in coastal and inland saltmarshes, in addition to its interesting nutritional and pharmacological properties. However, to ensure their subsequent use as a crop, it is necessary to optimize their germination through appropriate seed priming treatments. The main goal of this work was to seek the optimization of Arthrocnemum germination process using different pretreatments: exposure to sodium chloride (100 to 1200 mM) in the dark and its subsequent transferred to distilled water separately and together with the combination of pH (5, 7, 9), salinity (0, 100, 200 mM NaCl), and iron conditions (0, 200, 400 µM FeSO₄). The experiments were tested on six samples of two different species: A. meridionale (from Tunisia) and A. macrostachyum (from Spain).

RESULTS

Salinity priming of seeds for 15 days in darkness improved germination percentages by almost 25% at 600 mM NaCl, in both Tunisian and Spanish species. However, keeping seeds at different salt concentrations for 30 days produced higher improvement percentages at lower concentrations in A. meridionale (100-200 mM NaCl), while in A. macrostachyum the highest improvement percentages were obtained at 600 mM NaCl (percentage improvement of 47%). When the dark time period is reduced to 5 days at higher salt concentrations, the greater germination percentages were reached in all the samples at the concentration of 800 mM NaCl, increasing the improvement of germination between 17 and 50%. Finally, the conditions of pH = 7, pretreatment in darkness at 800 mM NaCl and 400 µM or iron, turned out to be an effective medium for seed germination.

CONCLUSIONS

Therefore, before using Arthrocnemum seeds in applied biotechnological programs, a seed priming treatment based on prior exposure to high salt concentrations (600-1000 mM NaCl) is recommended in order to maximize germination percentages.

Transcriptome mining of hormonal and floral integrators in the leafless flowers of three cymbidium orchids

Flowering is the most studied ornamental trait in orchids where long vegetative phase may span up to three years. Cymbidium orchids produce beautiful flowers with astonishing shapes and pleasant scent. However, an unusually long vegetative phase is a major drawback to their ornamental value. We observed that under certain culture conditions, three cymbidium species (Cymbidium ensifolium, C. goeringii and C. sinense) skipped vegetative growth phase and directly flowered within six months, that could be a breakthrough for future orchids with limited vegetative growth. Hormonal and floral regulators could be the key factors arresting vegetative phase. Therefore, transcriptomic analyses were performed for leafless flowers and normal vegetative leaves to ascertain differentially expressed genes (DEGs) related to hormones (auxin, cytokinin, gibberellin, abscisic acid and ethylene), floral integrators and MADS-box genes. A significant difference of cytokinin and floral regulators was observed among three species as compared to other hormones. The MADS-box genes were significantly expressed in the leafless flowers of C. sinense as compared to other species. Among the key floral regulators, CONSTANS and AGAMOUS-like genes showed the most differential expression in the leafless flowers as compared to leaves where the expression was negligible. However, CONSTANS also showed downregulation. Auxin efflux carriers were mainly downregulated in the leafless flowers of C. ensifolium and C. sinense, while they were upregulated in C. goeringii. Moreover, gibberellin and cytokinin genes were also downregulated in C. ensifolium and C. sinense flowers, while they were upregulated in C. goeringii, suggesting that species may vary in their responses. The data mining thus, outsources the valuable information to direct future research on orchids at industrial levels.

A Role for Allantoate Amidohydrolase (AtAAH) in the Germination of Arabidopsis thaliana Seeds

Seed dormancy is a very complex trait controlled by interactions between genetic and environmental factors. Nitrate is inversely correlated with seed dormancy in Arabidopsis. This is explained by the fact that seed dry storage (after-ripening) reduces the need for nitrogen for germination. When nitrate is absorbed by plants, it is first reduced to nitrite and then to ammonium for incorporation into amino acids, nucleic acids and chlorophyll. Previously, we showed that ALLANTOATE AMIDOHYDROLASE (AtAAH) transcripts are up-regulated in imbibed dormant seeds compared with after-ripened seeds. AAH is an enzyme in the uric acid catabolic pathway which catalyzes the hydrolysis of allantoate to yield CO2, NH3 and S-ureidoglycine. This pathway is the final stage of purine catabolism, and functions in plants and some bacteria to provide nitrogen, particularly when other nitrogen sources are depleted. Ataah mutant seeds are more dormant and accumulate high levels of allantoate, allantoin and urea, whereas energy-related metabolites and several amino acids are lower upon seed imbibition in comparison with Columbia-0. AtAAH expression could be detected during the early stages of seed development, with a transient increase around 8 d after pollination. AtAAH expression is the highest in mature pollen. The application of exogenous potassium nitrate can partly complement the higher dormancy phenotype of the Ataah mutant seeds, whereas other nitrogen sources cannot. Our results indicate that potassium nitrate does not specifically overcome the alleviated dormancy levels in Ataah mutant seeds, but promotes germination in general. Possible pathways by which AtAAH affects seed germination are discussed.

LEAFY COTYLEDONs: Connecting different stages of plant development

The life of higher plants progresses successively through embryonic, juvenile, adult, and reproductive stages. LEAFY COTYLEDON (LEC) transcription factors, first discovered in Arabidopsis thaliana several decades ago, play a key role in regulating plant embryonic development, seed maturation, and subsequent growth. Existing studies have demonstrated that LECs together with other transcription factors form a huge and complex regulatory network to regulate many aspects of plant growth and development and respond to environmental stresses. Here, we focus on the role that has received little attention about the LECs linking different developmental stages and generational cycles in plants. We summarize the current fragmented research progress on the LECs role and molecular mechanism in connecting embryonic and vegetative growth periods and the reproductive stage. Furthermore, the possibility of LECs controlling the maintenance and transition of plant growth stages through epigenetic modifications is discussed.

The Modulatory Effects of Non-Thermal Plasma on Seed’s Morphology, Germination and Genetics—A Review

Non-thermal plasma (NTP) is a novel and promising technique in the agricultural field that has the potential to improve vegetal material by modulating the expression of various genes involved in seed germination, plant immune response to abiotic stress, resistance to pathogens, and growth. Seeds are most frequently treated, in order to improve their ability to growth and evolve, but the whole plant can also be treated for a fast adaptive response to stress factors (heat, cold, pathogens). This review focuses mainly on the application of NTP on seeds. Non-thermal plasma treated seeds present both external and internal changes. The external ones include the alterations of seed coat to improve hydrophilicity and the internal ones refer to interfere with cellular processes that are later visible in metabolic and plant biology modifications. The usage of plasma aims to decrease the usage of fertilizers and pesticides in order to reduce the negative impact on natural ecosystem and to reduce the costs of production.

Viability of Wildflower Seeds After Mesophilic Anaerobic Digestion in Lab-Scale Biogas Reactors

The use of wildflower species as biogas feedstock carries the risk that their seeds survive anaerobic digestion (AD) and cause weed problems if spread with the digestate. Risk factors for seed survival in AD include low temperature, short exposure and hardseededness (HS). However, it is not possible to predict how AD will affect seed viability of previously unstudied species. In laboratory-scale reactors, we exposed seeds of eight species from a mixture of flowering wild plants intended as biogas feedstock and three reference species to AD at two mesophilic temperatures. Half of the species were HS, the other was non-HS (NHS). Viability was determined using a combination of tetrazolium and germination tests. Viability and germinability were modeled as functions of exposure time using a dose-response approach. Responses to AD varied considerably among species, and none of the considered influencing factors (time, temperature, HS) had a consistent effect. Seed lots of a species differed in inactivation times and seed-killing efficacy. The HS species Melilotus officinalis, Melilotus albus, and Malva sylvestris were particularly AD-resistant. They were the only ones that exhibited biphasic viability curves and tended to survive and germinate more at 42°C than at 35°C. Viability of the remaining species declined in a sigmoidal curve. Most NHS species were inactivated within a few days (Cichorium intybus, Daucus carota, Echium vulgare, and Verbascum thapsus), while HS species survived longer (Malva alcea). AD stimulated germination in the HS species A. theophrasti and its AD-resistance overlapped with that of the most resistant NHS species, C. album and tomato. In all seed lots, germinability was lost faster than viability, implying that mainly dormant seeds survived. After the maximum exposure time of 36 days, seeds of HS species and Chenopodium album were still viable. We concluded that viability responses to mesophilic AD were determined by the interplay of AD-conditions and species- and seed-lot-specific traits, of which HS was an important but only one factor. For the use of wildflowers as biogas feedstock, we recommended long retention times and special care with regard to HS species.

Species-Specific Variation in Abscisic Acid Homeostasis and Responses Impacts Important Traits in Crassocephalum Orphan Crops

Crassocephalum rubens and Crassocephalum crepidioides are plant species native to Africa, but grow in most tropical and subtropical regions of the world. They are rich in vitamins, minerals, and essential oils and are traditional leafy vegetables and medicinal plants in Sub-Saharan Africa. The plants are still mainly collected from the wild but shall be taken into cultivation and an important aim in the domestication of these species is to improve traits that are relevant for crop production. Here, seed formation and germination capacities in C. crepidioides and C. rubens were investigated, and it was found that C. crepidioides exhibits a higher level of seed dormancy, which could be broken with light, and was correlated with higher amounts of abscisic acid (ABA), a plant hormone that promotes seed dormancy. ABA is also very well-known for its role in abiotic stress tolerance, and it is shown that tetraploid C. crepidioides exhibits a higher level of resistance against drought and heat stress than diploid C. rubens, traits that will benefit the cultivation of these plants, particularly in rain-fed cropping systems. The potential of Crassocephalum to improve nutrition and increase the resilience of marginal cropping systems in Africa is discussed.

Magnetopriming Actuates Nitric Oxide Synthesis to Regulate Phytohormones for Improving Germination of Soybean Seeds under Salt Stress

In this study, the role of the signalling molecule nitric oxide (NO) in magnetopriming-mediated induction of salinity tolerance in soybean seeds is established. The cross-talk of NO with germination-related hormones gibberellic acid (GA), abscisic acid (ABA) and auxin (IAA) for their ability to reduce the Na+/K+ ratio in the seeds germinating under salinity is highlighted. Salt tolerance index was significantly high for seedlings emerging from magnetoprimed seeds and sodium nitroprusside (SNP, NO-donor) treatment. The NO and superoxide (O2•−) levels were also increased in both of these treatments under non-saline and saline conditions. NO generation through nitrate reductase (NR) and nitric oxide synthase-like (NOS-like) pathways indicated the major contribution of NO from the NR-catalysed reaction. The relative expression of genes involved in the NO biosynthetic pathways reiterated the indulgence of NR in NO in magnetoprimed seeds, as a 3.86-fold increase in expression was observed over unprimed seeds under salinity. A 23.26-fold increase in relative expression of NR genes by the NO donor (SNP) was observed under salinity, while the NR inhibitor (sodium tungstate, ST) caused maximum reduction in expression of NR genes as compared to other inhibitors [L-NAME (N(G)-nitro-L-arginine methyl ester; inhibitor of nitric oxide synthase-like enzyme) and DPI (diphenylene iodonium; NADPH oxidase inhibitor)]. The ratio of ABA/GA and IAA/GA decreased in magnetoprimed and NO donor-treated seeds, suggesting homeostasis amongst hormones during germination under salinity. The magnetoprimed seeds showed low Na+/K+ ratio in all treatments irrespective of NO inhibitors. Altogether, our results indicate that a balance of ABA, GA and IAA is maintained by the signalling molecule NO in magnetoprimed seeds which lowers the Na+/K+ ratio to offset the adverse effects of salinity in soybean seeds.

Seed-to-Seedling Transition in Pisum sativum L.: A Transcriptomic Approach

The seed-to-seedling transition is a crucial step in the plant life cycle. The transition occurs at the end of seed germination and corresponds to the initiation of embryonic root growth. To improve our understanding of how a seed transforms into a seedling, we germinated the Pisum sativum L. seeds for 72 h and divided them into samples before and after radicle protrusion. Before radicle protrusion, seeds survived after drying and formed normally developed seedlings upon rehydration. Radicle protrusion increased the moisture content level in seed axes, and the accumulation of ROS first generated in the embryonic root and plumule. The water and oxidative status shift correlated with the desiccation tolerance loss. Then, we compared RNA sequencing-based transcriptomics in the embryonic axes isolated from pea seeds before and after radicle protrusion. We identified 24,184 differentially expressed genes during the transition to the post-germination stage. Among them, 2101 genes showed more prominent expression. They were related to primary and secondary metabolism, photosynthesis, biosynthesis of cell wall components, redox status, and responses to biotic stress. On the other hand, 415 genes showed significantly decreased expression, including the groups related to water deprivation (eight genes) and response to the ABA stimulus (fifteen genes). We assume that the water deprivation group, especially three genes also belonging to ABA stimulus (LTI65, LTP4, and HVA22E), may be crucial for the desiccation tolerance loss during a metabolic switch from seed to seedling. The latter is also accompanied by the suppression of ABA-related transcription factors ABI3, ABI4, and ABI5. Among them, HVA22E, ABI4, and ABI5 were highly conservative in functional domains and showed homologous sequences in different drought-tolerant species. These findings elaborate on the critical biochemical pathways and genes regulating seed-to-seedling transition.

ABI3- and PIF1-mediated regulation of GIG1 enhances seed germination by detoxification of methylglyoxal in Arabidopsis

Methylglyoxal (MG) is a toxic by-product of the glycolysis pathway in most living organisms and was previously shown to inhibit seed germination. MG is detoxified by glyoxalase I and II family proteins in plants. MG is abundantly produced during early embryogenesis in Arabidopsis seeds. However, the mechanism that alleviates the toxic effect of MG in maturing seeds is poorly understood. In this study, by T-DNA mutant population screening, we found that mutations in a glyoxalase I gene (named GERMINATION-IMPAIRED GLYOXALASE 1, GIG1) led to significantly impaired germination compared with wild-type seeds. Transformation of full-length GIG1 cDNA under the constitutively active cauliflower mosaic virus 35S promoter in the gig1 background completely recovered the seed germination phenotype. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses revealed that GIG1 is uniquely expressed in seeds and is upregulated by abscisic acid (ABA) and downregulated by gibberellic acid (GA) during seed germination. An ABA signaling component, ABI3, directly activated GIG1 in maturing seeds. In addition, PHYTOCHROME INTERACTING FACTOR 1 (PIF1) also plays cooperatively with ABI3 in the regulation of GIG1 expression in the early stage of imbibed seeds. Furthermore, GIG1 expression is stably silenced by epigenetic repressors such as polycomb repressor complexes. Altogether, our results indicate that light and ABA signaling cooperate to enhance seed germination by the upregulation of GIG1 to detoxify MG in maturing seeds.

Priming Seeds with Indole and (Z)-3-Hexenyl Acetate Enhances Resistance Against Herbivores and Stimulates Growth

A striking feature of plant ecology is the ability of plants to detect and respond to environmental cues such as herbivore-induced plant volatiles (HIPVs) by priming or directly activating defenses against future herbivores. However, whether seeds also respond to compounds that are common constituents of HIPV blends and initiate future plant resistance is unknown. Considering that seeds depend on other environmental cues to determine basic survival traits such as germination timing, we predicted that seeds exposed to synthetic constituents of HIPV blends would generate well-defended plants. We investigated the effect of seed exposure to common volatiles on growth, reproduction, and resistance characteristics in the model plants Arabidopsis thaliana and Medicago truncatula using herbivores from two feeding guilds. After seed scarification and vernalization, we treated seeds with one of seven different plant-derived volatile compounds for 24 h. Seeds were then germinated and the resulting plants were assayed for growth, herbivore resistance, and expression of inducible defense genes. Of all the synthetic volatiles tested, indole specifically reduced both beet armyworm growth on A. thaliana and pea aphid fecundity on M. truncatula. The induction of defense genes was not affected by seed exposure to indole in either plant species, indicating that activation of direct resistance rather than inducible resistance is the mechanism by which seed priming operates. Moreover, neither plant species showed any negative effect of seed exposure to any synthetic volatile on vegetative and reproductive growth. Rather, M. truncatula plants derived from seeds exposed to (Z)-3-hexanol and (Z)-3-hexenyl acetate grew larger compared to controls. Our results indicate that seeds are sensitive to specific volatiles in ways that enhance resistance profiles with no apparent costs in terms of growth. Seed priming by HIPVs may represent a novel ecological mechanism of plant-to-plant interactions, with broad potential applications in agriculture and seed conservation.

The Effect of Temperature and Water Stresses on Seed Germination and Seedling Growth of Wheat (Triticum aestivum L.)

Temperature and moisture are essential factors in germination and seedling growth. The purpose of this research was to assess the germination and growth of wheat (Triticum aestivum L.) seeds under various abiotic stressors. It was conducted in the Agronomy Institute of the Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary. Six distinct temperature levels were used: 5, 10, 15, 20, 25, and 30 °C. Stresses of drought and waterlogging were quantified using 25 water levels based on single-milliliter intervals and as a percentage based on thousand kernel weight (TKW). Seedling density was also tested. Temperature significantly influenced germination duration and seedling development. 20 °C was ideal with optimal range of 15 °C to less than 25 °C. Germination occurred at water amount of 75% of the TKW, and its ideal range was lower and narrower than the range for seedling development. Seed size provided an objective basis for defining germination water requirements. The current study established an optimal water supply range for wheat seedling growth of 525–825 percent of the TKW. Fifteen seeds within a 9 cm Petri dish may be preferred to denser populations.

Seed Dormancy Release and Germination Requirements of Cinnamomum migao, an Endangered and Rare Woody Plant in Southwest China

Seed dormancy is a complex adaptive trait of plants that are influenced by several physiological and environmental factors. The endangered plant Cinnamomum migao is also known to exhibit seed dormancy and low germination, which may influence its regeneration; however, these characteristics remain unexplored. To our knowledge, this study is the first to examine the type of dormancy and improve the germination percentage of C. migao seeds. We evaluated the structure and characteristics of the embryo and endocarp of C. migao seeds as well as the effects of endogenous inhibitors. Furthermore, we assessed the effects of light, stratification, alternating temperature, and gibberellic acid 3 (GA3) on the dormancy release of these seeds. The embryo was well developed the endocarp was water-permeable, and no obvious mechanical hindrance to germination was observed. However, the endocarp and embryo contained phenols and other germination inhibitors. The seed extracts of C. migao delayed the germination of cabbage and ryegrass seeds, which indicates the presence of endogenous inhibitors. These findings suggest that C. migao seeds exhibit physiological dormancy. Light and an alternating temperature (15/20°C) did not influence germination. However, GA3 pretreatment, alternating temperatures, and warm stratification relieved dormancy. GA3 pretreatment combined with the 15°C stratification treatment was most effective in rapidly releasing the C. migao seed dormancy. Our findings may facilitate the storage and conservation of this endangered plant, which is currently underrepresented in ex situ collections.

Transcriptional Proposition for Uniquely Developed Protocorm Flowering in Three Orchid Species: Resources for Innovative Breeding

During orchid seed culture, seeds germinate as protocorms, and protocorms normally develop into plant with leaves and roots. Orchids require many years of vegetative development for flowering. However, under a certain combination of growth cultures, we observed that protocorms can directly flower without leaves and roots. Therefore, we performed comparative transcriptome analysis to identify the different transcriptional regulators of two types of protocorms of Cymbidium ensifolium, Cymbidium sinense, and Cymbidium goeringii. Zinc finger, MYB, AP2, and bHLH were the most abundant transcription factor (TF) families in the transcriptome. Weighted gene coexpression network analysis (WGCNA) was performed to identify hub genes related to leaf and flower development. The key hubs included SPL6, SVP, SEP2, KNOX1, AP2, OFP1, COL12, MYB13, MYB36, MYB59, bHLH086, and ARF7. The hub genes were further validated through statistical tools to propose the roles of key TFs. Therefore, this study initiates to answer that why there is no leaf initiation and root development and how can protocorm bypass the vegetative phase to flower? The outcomes can direct future research on short-span flowering in orchids through protocorms.

ENAP1 retrains seed germination via H3K9 acetylation mediated positive feedback regulation of ABI5

Histone acetylation is involved in the regulation of seed germination. The transcription factor ABI5 plays an essential role in ABA- inhibited seed germination. However, the molecular mechanism of how ABI5 and histone acetylation coordinate to regulate gene expression during seed germination is still ambiguous. Here, we show that ENAP1 interacts with ABI5 and they co-bind to ABA responsive genes including ABI5 itself. The hypersensitivity to ABA of ENAP1ox seeds germination is recovered by the abi5 null mutation. ABA enhances H3K9Ac enrichment in the promoter regions as well as the transcription of target genes co-bound by ENAP1 and ABI5, which requires both ENAP1 and ABI5. ABI5 gene is directly regulated by ENAP1 and ABI5. In the enap1 deficient mutant, H3K9Ac enrichment and the binding activity of ABI5 in its own promoter region, along with ABI5 transcription and protein levels are all reduced; while in the abi5-1 mutant, the H3K9Ac enrichment and ENAP1 binding activity in ABI5 promoter are decreased, suggesting that ENAP1 and ABI5 function together to regulate ABI5- mediated positive feedback regulation. Overall, our research reveals a new molecular mechanism by which ENAP1 regulates H3K9 acetylation and mediates the positive feedback regulation of ABI5 to inhibit seed germination.

To optimize the fitness in natural environment, flowering plants initiate seed germination in the favorable environment and maintain seed dormancy under stressful conditions. Precise mechanisms have been evolved to regulate germination timing to ensure plant adaptation to unfavorable environment. ABA, a major stress hormone in plants, induces seed dormancy and represses seed germination. Epigenetic regulation has been known involved in ABA signaling in which the transcription factor ABI5 acts as a regulatory hub. However, the epigenetic regulation such as histone acetylation on ABI5 transcription remains elusive. In this study, we revealed a new molecular mechanism by which histone binding protein ENAP1 regulates H3K9 acetylation, which mediates the positive feedback regulation of ABI5 in an ABI5 dependent manner to inhibit seed germination.

Late-maturity α-amylase (LMA): exploring the underlying mechanisms and end-use quality effects in wheat

MAIN CONCLUSION

A comprehensive understanding of LMA from the underlying molecular aspects to the end-use quality effects will greatly benefit the global wheat industry and those whose livelihoods depend upon it. Late-maturity α-amylase (LMA) leads to the expression and protein accumulation of high pI α-amylases during late grain development. This α-amylase is maintained through harvest and leads to an unacceptable low falling number (FN), the wheat industry's standard measure for predicting end-use quality. Unfortunately, low FN leads to significant financial losses for growers. As a result, wheat researchers are working to understand and eliminate LMA from wheat breeding programs, with research aims that include unraveling the genetic, biochemical, and physiological mechanisms that lead to LMA expression. In addition, cereal chemists and quality scientists are working to determine if and how LMA-affected grain impacts end-use quality. This review is a comprehensive overview of studies focused on LMA and includes open questions and future directions.

Auxin Interactions with Other Hormones in Plant Development

Auxin is a crucial growth regulator that governs plant development and responses to environmental perturbations. It functions at the heart of many developmental processes, from embryogenesis to organ senescence, and is key to plant interactions with the environment, including responses to biotic and abiotic stimuli. As remarkable as auxin is, it does not act alone, but rather solicits the help of, or is solicited by, other endogenous signals, including the plant hormones abscisic acid, brassinosteroids, cytokinins, ethylene, gibberellic acid, jasmonates, salicylic acid, and strigolactones. The interactions between auxin and other hormones occur at multiple levels: hormones regulate one another's synthesis, transport, and/or response; hormone-specific transcriptional regulators for different pathways physically interact and/or converge on common target genes; etc. However, our understanding of this crosstalk is still fragmentary, with only a few pieces of the gigantic puzzle firmly established. In this review, we provide a glimpse into the complexity of hormone interactions that involve auxin, underscoring how patchy our current understanding is.

Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects

Transition from seed to seedling is one of the critical developmental steps, dramatically affecting plant growth and viability. Before plants enter the vegetative phase of their ontogenesis, massive rearrangements of signaling pathways and switching of gene expression programs are required. This results in suppression of the genes controlling seed maturation and activation of those involved in regulation of vegetative growth. At the level of hormonal regulation, these events are controlled by the balance of abscisic acid and gibberellins, although ethylene, auxins, brassinosteroids, cytokinins, and jasmonates are also involved. The key players include the members of the LAFL network-the transcription factors LEAFY COTYLEDON1 and 2 (LEC 1 and 2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (FUS3), as well as DELAY OF GERMINATION1 (DOG1). They are the negative regulators of seed germination and need to be suppressed before seedling development can be initiated. This repressive signal is mediated by chromatin remodeling complexes-POLYCOMB REPRESSIVE COMPLEX 1 and 2 (PRC1 and PRC2), as well as PICKLE (PKL) and PICKLE-RELATED2 (PKR2) proteins. Finally, epigenetic methylation of cytosine residues in DNA, histone post-translational modifications, and post-transcriptional downregulation of seed maturation genes with miRNA are discussed. Here, we summarize recent updates in the study of hormonal and epigenetic switches involved in regulation of the transition from seed germination to the post-germination stage.

FHY3 interacts with phytochrome B and regulates seed dormancy and germination

Seed dormancy and germination are fundamental processes for plant propagation, both of which are tightly regulated by internal and external cues. Phytochrome B (phyB) is a major red/far-red-absorbing photoreceptor that senses light signals that modulate seed dormancy and germination. However, the components that directly transduce that signal downstream of phyB are mostly unknown. Here, we show that the transposase-derived transcription factor FAR-RED ELONGATED HYPOCOTYL3 (FHY3) inhibits seed dormancy and promotes phyB-mediated seed germination in Arabidopsis thaliana. FHY3 physically interacts with phyB in vitro and in vivo. RNA-sequencing and reverse transcription-quantitative polymerase chain reaction analyses showed that FHY3 regulates multiple downstream genes, including REVEILLE2 (RVE2), RVE7, and SPATULA (SPT). Yeast one-hybrid, electrophoresis mobility shift, and chromatin immunoprecipitation assays demonstrated that FHY3 directly binds these genes via a conserved FBS cis-element in their promoters. Furthermore, RVE2, RVE7, and GIBBERELLIN 3-OXIDASE 2 (GA3ox2) genetically act downstream of FHY3. Strikingly, light and phyB promote FHY3 protein accumulation. Our study reveals a transcriptional cascade consisting of phyB-FHY3-RVE2/RVE7/SPT-GA3ox2 that relays environmental light signals and thereby controls seed dormancy and germination.

Seeding depth and seeding rate regulate apical hook formation by inducing GhHLS1 expression via ethylene during cotton emergence

Apical hook formation is essential for the emergence and stand establishment of cotton plants. Searching for agronomic measures to regulate apical hook formation and clarifying its mechanism are important for full stand establishment in cotton. In this study, cotton seeds were sown at varying seeding rates or depths in sand to determine if and how apical hook formation was regulated by seeding rates or depths. The results showed that deep seeding or low seeding rates increased mechanical pressure and then increased ethylene content by increasing GhACO1 and GhACS2 expression to improve apical hook formation. Silencing of the GhACO1 and GhACS2 genes or exogenous application of 1-methylcyclopropene (1-MCP) decreased the ethylene content and inhibited apical hook formation in the cotton seedlings. Deep seeding, a low seeding rate, or 1-amino cyclopropane-1-carboxylic acid (ACC) treatment increased the expression of GhHLS1 and GhPIF3 genes, but their expression was decreased in theVIGS-ACO1 and VIGS-ACS2 seedlings. Silencing of the GhHLS1 and GhPIF3 genes inhibited apical hook formation, although the expression of GhACO1 and GhACS2 was unchanged. GhPIF3 may act upstream of GhHLS1, as the expression of GhPIF3 in the VIGS-HLS1 seedlings was unchanged, while the expression of GhHLS1 in the VIGS-PIF3 seedlings decreased. These results suggested that raised mechanical pressure could increase ethylene content by inducing GhACO1 and GhACS2 gene expression, which promoted apical hook formation by increasing the expression of GhHLS1. Therefore, adjusting the mechanical pressure through changing the seeding depth or seeding rate is an important means to regulate apical hook formation and emergence.

Primary Root and Mesocotyl Elongation in Maize Seedlings: Two Organs with Antagonistic Growth below the Soil Surface

Maize illustrates one of the most complex cases of embryogenesis in higher plants that results in the development of early embryo with distinctive organs such as the mesocotyl, seminal and primary roots, coleoptile, and plumule. After seed germination, the elongation of root and mesocotyl follows opposite directions in response to specific tropisms (positive and negative gravitropism and hydrotropism). Tropisms represent the differential growth of an organ directed toward several stimuli. Although the life cycle of roots and mesocotyl takes place in darkness, their growth and functions are controlled by different mechanisms. Roots ramify through the soil following the direction of the gravity vector, spreading their tips into new territories looking for water; when water availability is low, the root hydrotropic response is triggered toward the zone with higher moisture. Nonetheless, there is a high range of hydrotropic curvatures (angles) in maize. The processes that control root hydrotropism and mesocotyl elongation remain unclear; however, they are influenced by genetic and environmental cues to guide their growth for optimizing early seedling vigor. Roots and mesocotyls are crucial for the establishment, growth, and development of the plant since both help to forage water in the soil. Mesocotyl elongation is associated with an ancient agriculture practice known as deep planting. This tradition takes advantage of residual soil humidity and continues to be used in semiarid regions of Mexico and USA. Due to the genetic diversity of maize, some lines have developed long mesocotyls capable of deep planting while others are unable to do it. Hence, the genetic and phenetic interaction of maize lines with a robust hydrotropic response and higher mesocotyl elongation in response to water scarcity in time of global heating might be used for developing more resilient maize plants.

A transcriptional hub integrating gibberellin-brassinosteroid signals to promote seed germination in Arabidopsis

Seed germination is regulated by multiple phytohormones, including gibberellins (GAs) and brassinosteroids (BRs); however, the molecular mechanism underlying GA and BR co-induced seed germination is not well elucidated. We demonstrated that BRs induce seed germination through promoting testa and endosperm rupture in Arabidopsis. BRs promote cell elongation, rather than cell division, at the hypocotyl-radicle transition region of the embryonic axis during endosperm rupture. Two key basic helix-loop-helix transcription factors in the BR signaling pathway, HBI1 and BEE2, are involved in the regulation of endosperm rupture. Expression of HBI1 and BEE2 was induced in response to BR and GA treatment. In addition, HBI1- or BEE2-overexpressing Arabidopsis plants are less sensitive to the BR biosynthesis inhibitor, brassinazole, and the GA biosynthesis inhibitor, paclobutrazol. HBI1 and BEE2 promote endosperm rupture and seed germination by directly regulating the GA-Stimulated Arabidopsis 6 (GASA6) gene. Expression of GASA6 was altered in Arabidopsis overexpressing HBI1, BEE2, or SRDX-repressor forms of the two transcription factors. In addition, HBI1 interacts with BEE2 to synergistically activate GASA6 expression. Our findings define a new role for GASA6 in GA and BR signaling and reveal a regulatory module that controls GA and BR co-induced seed germination in Arabidopsis.

Anatomy and Histochemistry of Seed Coat Development of Wild (Pisum sativum subsp. elatius (M. Bieb.) Asch. et Graebn. and Domesticated Pea (Pisum sativum subsp. sativum L.)

In angiosperms, the mature seed consists of embryo, endosperm, and a maternal plant-derived seed coat (SC). The SC plays a role in seed filling, protects the embryo, mediates dormancy and germination, and facilitates the dispersal of seeds. SC properties have been modified during the domestication process, resulting in the removal of dormancy, mediated by SC impermeability. This study compares the SC anatomy and histochemistry of two wild (JI64 and JI1794) and two domesticated (cv. Cameor and JI92) pea genotypes. Histochemical staining of five developmental stages: 13, 21, 27, 30 days after anthesis (DAA), and mature dry seeds revealed clear differences between both pea types. SC thickness is established early in the development (13 DAA) and is primarily governed by macrosclereid cells. Polyanionic staining by Ruthenium Red indicated non homogeneity of the SC, with a strong signal in the hilum, the micropyle, and the upper parts of the macrosclereids. High peroxidase activity was detected in both wild and cultivated genotypes and increased over the development peaking prior to desiccation. The detailed knowledge of SC anatomy is important for any molecular or biochemical studies, including gene expression and proteomic analysis, especially when comparing different genotypes and treatments. Analysis is useful for other crop-to-wild-progenitor comparisons of economically important legume crops.

Identification of a major-effect QTL associated with pre-harvest sprouting in cucumber (Cucumis sativus L.) using the QTL-seq method

Background

Cucumber (Cucumis sativus L.) is cultivated worldwide, and it is essential to produce enough high-quality seeds to meet demand. Pre-harvest sprouting (PHS) in cucumber is a critical problem and causes serious damage to seed production and quality. Nevertheless, the genetic basis and molecular mechanisms underlying cucumber PHS remain unclear. QTL-seq is an efficient approach for rapid quantitative trait loci (QTL) identification that simultaneously takes advantage of bulked-segregant analysis (BSA) and whole-genome resequencing. In the present research, QTL-seq analysis was performed to identify QTLs associated with PHS in cucumber using an F₂ segregating population.

Results

Two QTLs that spanned 7.3 Mb on Chromosome 4 and 0.15 Mb on Chromosome 5 were identified by QTL-seq and named qPHS4.1 and qPHS5.1, respectively. Subsequently, SNP and InDel markers selected from the candidate regions were used to refine the intervals using the extended F₂ populations grown in the 2016 and 2017 seasons. Finally, qPHS4.1 was narrowed to 0.53 Mb on chromosome 4 flanked by the markers SNP-16 and SNP-24 and was found to explain 19–22% of the phenotypic variation in cucumber PHS. These results reveal that qPHS4.1 is a major-effect QTL associated with PHS in cucumber. Based on gene annotations and qRT-PCR expression analyses, Csa4G622760 and Csa4G622800 were proposed as the candidate genes.

Conclusions

These results provide novel insights into the genetic mechanism controlling PHS in cucumber and highlight the potential for marker-assisted selection of PHS resistance breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07548-8.

Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research

Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA-seq libraries and 136 307 full-length PacBio Iso-seq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At-α polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS-box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full-length transcripts related to ABA-mediated seed dormancy discovered a conserved isoform of PIF6-β and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni-marburg.de/aetar_db).